Daily Papers

As large language models (LLMs) are increasingly deployed worldwide, ensuring their fair and comprehensive cultural understanding is important. However, LLMs exhibit cultural bias and limited awareness of underrepresented cultures, while the mechanisms underlying their cultural understanding remain underexplored. To fill this gap, we conduct a neuron-level analysis to identify neurons that drive cultural behavior, introducing a gradient-based scoring method with additional filtering for precise refinement. We identify both culture-general neurons contributing to cultural understanding regardless of cultures, and culture-specific neurons tied to an individual culture. These neurons account for less than 1% of all neurons and are concentrated in shallow to middle MLP layers. We validate their role by showing that suppressing them substantially degrades performance on cultural benchmarks (by up to 30%), while performance on general natural language understanding (NLU) benchmarks remains largely unaffected. Moreover, we show that culture-specific neurons support knowledge of not only the target culture, but also related cultures. Finally, we demonstrate that training on NLU benchmarks can diminish models' cultural understanding when we update modules containing many culture-general neurons. These findings provide insights into the internal mechanisms of LLMs and offer practical guidance for model training and engineering. Our code is available at https://github.com/ynklab/CULNIG

In this work, we demonstrate that the contextualized word vectors derived from pretrained masked language model-based encoders share a common, perhaps undesirable pattern across layers. Namely, we find cases of persistent outlier neurons within BERT and RoBERTa's hidden state vectors that consistently bear the smallest or largest values in said vectors. In an attempt to investigate the source of this information, we introduce a neuron-level analysis method, which reveals that the outliers are closely related to information captured by positional embeddings. We also pre-train the RoBERTa-base models from scratch and find that the outliers disappear without using positional embeddings. These outliers, we find, are the major cause of anisotropy of encoders' raw vector spaces, and clipping them leads to increased similarity across vectors. We demonstrate this in practice by showing that clipped vectors can more accurately distinguish word senses, as well as lead to better sentence embeddings when mean pooling. In three supervised tasks, we find that clipping does not affect the performance.

Language confusion -- where large language models (LLMs) generate unintended languages against the user's need -- remains a critical challenge, especially for English-centric models. We present the first mechanistic interpretability (MI) study of language confusion, combining behavioral benchmarking with neuron-level analysis. Using the Language Confusion Benchmark (LCB), we show that confusion points (CPs) -- specific positions where language switches occur -- are central to this phenomenon. Through layer-wise analysis with TunedLens and targeted neuron attribution, we reveal that transition failures in the final layers drive confusion. We further demonstrate that editing a small set of critical neurons, identified via comparative analysis with multilingual-tuned models, substantially mitigates confusion without harming general competence or fluency. Our approach matches multilingual alignment in confusion reduction for most languages and yields cleaner, higher-quality outputs. These findings provide new insights into the internal dynamics of LLMs and highlight neuron-level interventions as a promising direction for robust, interpretable multilingual language modeling.

Safety alignment is critical for the ethical deployment of large language models (LLMs), guiding them to avoid generating harmful or unethical content. Current alignment techniques, such as supervised fine-tuning and reinforcement learning from human feedback, remain fragile and can be bypassed by carefully crafted adversarial prompts. Unfortunately, such attacks rely on trial and error, lack generalizability across models, and are constrained by scalability and reliability. This paper presents NeuroStrike, a novel and generalizable attack framework that exploits a fundamental vulnerability introduced by alignment techniques: the reliance on sparse, specialized safety neurons responsible for detecting and suppressing harmful inputs. We apply NeuroStrike to both white-box and black-box settings: In the white-box setting, NeuroStrike identifies safety neurons through feedforward activation analysis and prunes them during inference to disable safety mechanisms. In the black-box setting, we propose the first LLM profiling attack, which leverages safety neuron transferability by training adversarial prompt generators on open-weight surrogate models and then deploying them against black-box and proprietary targets. We evaluate NeuroStrike on over 20 open-weight LLMs from major LLM developers. By removing less than 0.6% of neurons in targeted layers, NeuroStrike achieves an average attack success rate (ASR) of 76.9% using only vanilla malicious prompts. Moreover, Neurostrike generalizes to four multimodal LLMs with 100% ASR on unsafe image inputs. Safety neurons transfer effectively across architectures, raising ASR to 78.5% on 11 fine-tuned models and 77.7% on five distilled models. The black-box LLM profiling attack achieves an average ASR of 63.7% across five black-box models, including the Google Gemini family.

Large Language Models (LLMs) are composed of neurons that exhibit various behaviors and roles, which become increasingly diversified as models scale. Recent studies have revealed that not all neurons are active across different datasets, and this sparsity correlates positively with the task-specific ability, leading to advancements in model pruning and training efficiency. Traditional fine-tuning methods engage all parameters of LLMs, which is computationally expensive and may not be necessary. In contrast, Parameter-Efficient Fine-Tuning (PEFT) approaches aim to minimize the number of trainable parameters, yet they still operate at a relatively macro scale (e.g., layer-level). We introduce Neuron-Level Fine-Tuning (NeFT), a novel approach that refines the granularity of parameter training down to the individual neuron, enabling more precise and computationally efficient model updates. The experimental results show that NeFT not only exceeded the performance of full-parameter fine-tuning and PEFT but also provided insights into the analysis of neurons.

Transformer-based language models excel at both recall (retrieving memorized facts) and reasoning (performing multi-step inference), but whether these abilities rely on distinct internal mechanisms remains unclear. Distinguishing recall from reasoning is crucial for predicting model generalization, designing targeted evaluations, and building safer interventions that affect one ability without disrupting the other.We approach this question through mechanistic interpretability, using controlled datasets of synthetic linguistic puzzles to probe transformer models at the layer, head, and neuron level. Our pipeline combines activation patching and structured ablations to causally measure component contributions to each task type. Across two model families (Qwen and LLaMA), we find that interventions on distinct layers and attention heads lead to selective impairments: disabling identified "recall circuits" reduces fact-retrieval accuracy by up to 15\% while leaving reasoning intact, whereas disabling "reasoning circuits" reduces multi-step inference by a comparable margin. At the neuron level, we observe task-specific firing patterns, though these effects are less robust, consistent with neuronal polysemanticity.Our results provide the first causal evidence that recall and reasoning rely on separable but interacting circuits in transformer models. These findings advance mechanistic interpretability by linking circuit-level structure to functional specialization and demonstrate how controlled datasets and causal interventions can yield mechanistic insights into model cognition, informing safer deployment of large language models.

Large language models (LLMs) have demonstrated impressive capabilities across a wide range of natural language processing tasks. However, their outputs often exhibit social biases, raising fairness concerns. Existing debiasing methods, such as fine-tuning on additional datasets or prompt engineering, face scalability issues or compromise user experience in multi-turn interactions. To address these challenges, we propose a framework for detecting stereotype-inducing words and attributing neuron-level bias in LLMs, without the need for fine-tuning or prompt modification. Our framework first identifies stereotype-inducing adjectives and nouns via comparative analysis across demographic groups. We then attribute biased behavior to specific neurons using two attribution strategies based on integrated gradients. Finally, we mitigate bias by directly intervening on their activations at the projection layer. Experiments on three widely used LLMs demonstrate that our method effectively reduces bias while preserving overall model performance. Code is available at the github link: https://github.com/XMUDeepLIT/Bi-directional-Bias-Attribution.

Prior studies on the emergence in large models have primarily focused on how the functional capabilities of large language models (LLMs) scale with model size. Our research, however, transcends this traditional paradigm, aiming to deepen our understanding of the emergence within LLMs by placing a special emphasis not just on the model size but more significantly on the complex behavior of neuron interactions during the training process. By introducing the concepts of "self-organization" and "multifractal analysis," we explore how neuron interactions dynamically evolve during training, leading to "emergence," mirroring the phenomenon in natural systems where simple micro-level interactions give rise to complex macro-level behaviors. To quantitatively analyze the continuously evolving interactions among neurons in large models during training, we propose the Neuron-based Multifractal Analysis (NeuroMFA). Utilizing NeuroMFA, we conduct a comprehensive examination of the emergent behavior in LLMs through the lens of both model size and training process, paving new avenues for research into the emergence in large models.

Vision Transformer models exhibit immense power yet remain opaque to human understanding, posing challenges and risks for practical applications. While prior research has attempted to demystify these models through input attribution and neuron role analysis, there's been a notable gap in considering layer-level information and the holistic path of information flow across layers. In this paper, we investigate the significance of influential neuron paths within vision Transformers, which is a path of neurons from the model input to output that impacts the model inference most significantly. We first propose a joint influence measure to assess the contribution of a set of neurons to the model outcome. And we further provide a layer-progressive neuron locating approach that efficiently selects the most influential neuron at each layer trying to discover the crucial neuron path from input to output within the target model. Our experiments demonstrate the superiority of our method finding the most influential neuron path along which the information flows, over the existing baseline solutions. Additionally, the neuron paths have illustrated that vision Transformers exhibit some specific inner working mechanism for processing the visual information within the same image category. We further analyze the key effects of these neurons on the image classification task, showcasing that the found neuron paths have already preserved the model capability on downstream tasks, which may also shed some lights on real-world applications like model pruning. The project website including implementation code is available at https://foundation-model-research.github.io/NeuronPath/.

Mixture-of-Experts (MoE) architectures have become the dominant choice for scaling Large Language Models (LLMs), activating only a subset of parameters per token. While MoE architectures are primarily adopted for computational efficiency, it remains an open question whether their sparsity makes them inherently easier to interpret than dense feed-forward networks (FFNs). We compare MoE experts and dense FFNs using k-sparse probing and find that expert neurons are consistently less polysemantic, with the gap widening as routing becomes sparser. This suggests that sparsity pressures both individual neurons and entire experts toward monosemanticity. Leveraging this finding, we zoom out from the neuron to the expert level as a more effective unit of analysis. We validate this approach by automatically interpreting hundreds of experts. This analysis allows us to resolve the debate on specialization: experts are neither broad domain specialists (e.g., biology) nor simple token-level processors. Instead, they function as fine-grained task experts, specializing in linguistic operations or semantic tasks (e.g., closing brackets in LaTeX). Our findings suggest that MoEs are inherently interpretable at the expert level, providing a clearer path toward large-scale model interpretability. Code is available at: https://github.com/jerryy33/MoE_analysis

Individual neurons participate in the representation of multiple high-level concepts. To what extent can different interpretability methods successfully disentangle these roles? To help address this question, we introduce RAVEL (Resolving Attribute-Value Entanglements in Language Models), a dataset that enables tightly controlled, quantitative comparisons between a variety of existing interpretability methods. We use the resulting conceptual framework to define the new method of Multi-task Distributed Alignment Search (MDAS), which allows us to find distributed representations satisfying multiple causal criteria. With Llama2-7B as the target language model, MDAS achieves state-of-the-art results on RAVEL, demonstrating the importance of going beyond neuron-level analyses to identify features distributed across activations. We release our benchmark at https://github.com/explanare/ravel.

Understanding the inner workings of neural networks is essential for enhancing model performance and interpretability. Current research predominantly focuses on examining the connection between individual neurons and the model's final predictions. Which suffers from challenges in interpreting the internal workings of the model, particularly when neurons encode multiple unrelated features. In this paper, we propose a novel framework that transitions the focus from analyzing individual neurons to investigating groups of neurons, shifting the emphasis from neuron-output relationships to functional interaction between neurons. Our automated framework, NeurFlow, first identifies core neurons and clusters them into groups based on shared functional relationships, enabling a more coherent and interpretable view of the network's internal processes. This approach facilitates the construction of a hierarchical circuit representing neuron interactions across layers, thus improving interpretability while reducing computational costs. Our extensive empirical studies validate the fidelity of our proposed NeurFlow. Additionally, we showcase its utility in practical applications such as image debugging and automatic concept labeling, thereby highlighting its potential to advance the field of neural network explainability.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Some neurons in deep networks specialize in recognizing highly specific perceptual, structural, or semantic features of inputs. In computer vision, techniques exist for identifying neurons that respond to individual concept categories like colors, textures, and object classes. But these techniques are limited in scope, labeling only a small subset of neurons and behaviors in any network. Is a richer characterization of neuron-level computation possible? We introduce a procedure (called MILAN, for mutual-information-guided linguistic annotation of neurons) that automatically labels neurons with open-ended, compositional, natural language descriptions. Given a neuron, MILAN generates a description by searching for a natural language string that maximizes pointwise mutual information with the image regions in which the neuron is active. MILAN produces fine-grained descriptions that capture categorical, relational, and logical structure in learned features. These descriptions obtain high agreement with human-generated feature descriptions across a diverse set of model architectures and tasks, and can aid in understanding and controlling learned models. We highlight three applications of natural language neuron descriptions. First, we use MILAN for analysis, characterizing the distribution and importance of neurons selective for attribute, category, and relational information in vision models. Second, we use MILAN for auditing, surfacing neurons sensitive to human faces in datasets designed to obscure them. Finally, we use MILAN for editing, improving robustness in an image classifier by deleting neurons sensitive to text features spuriously correlated with class labels.

Large Language Models (LLMs) require efficient knowledge editing (KE) to update factual information, yet existing methods exhibit significant performance decay in multi-hop factual recall. This failure is particularly acute when edits involve intermediate implicit subjects within reasoning chains. Through causal analysis, we reveal that this limitation stems from an oversight of how chained knowledge is dynamically represented and utilized at the neuron level. We discover that during multi hop reasoning, implicit subjects function as query neurons, which sequentially activate corresponding value neurons across transformer layers to accumulate information toward the final answer, a dynamic prior KE work has overlooked. Guided by this insight, we propose ACE: Attribution-Controlled Knowledge Editing for Multi-hop Factual Recall, a framework that leverages neuron-level attribution to identify and edit these critical query-value (Q-V) pathways. ACE provides a mechanistically grounded solution for multi-hop KE, empirically outperforming state-of-the-art methods by 9.44% on GPT-J and 37.46% on Qwen3-8B. Our analysis further reveals more fine-grained activation patterns in Qwen3 and demonstrates that the semantic interpretability of value neurons is orchestrated by query-driven accumulation. These findings establish a new pathway for advancing KE capabilities based on the principled understanding of internal reasoning mechanisms.

The out-of-distribution (OOD) problem generally arises when neural networks encounter data that significantly deviates from the training data distribution, i.e., in-distribution (InD). In this paper, we study the OOD problem from a neuron activation view. We first formulate neuron activation states by considering both the neuron output and its influence on model decisions. Then, to characterize the relationship between neurons and OOD issues, we introduce the neuron activation coverage (NAC) -- a simple measure for neuron behaviors under InD data. Leveraging our NAC, we show that 1) InD and OOD inputs can be largely separated based on the neuron behavior, which significantly eases the OOD detection problem and beats the 21 previous methods over three benchmarks (CIFAR-10, CIFAR-100, and ImageNet-1K). 2) a positive correlation between NAC and model generalization ability consistently holds across architectures and datasets, which enables a NAC-based criterion for evaluating model robustness. Compared to prevalent InD validation criteria, we show that NAC not only can select more robust models, but also has a stronger correlation with OOD test performance.

Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recent advances in machine learning, it is shown that the hierarchically Deep Neural Networks (DNNs) perform optimally in decoding unique features out of complex datasets. In this study, we utilize the power of a DNN to explore the computational principles in the mammalian brain by exploiting the Neuropixel data from Allen Brain Institute. We decode the neural responses from mouse visual cortex to predict the presented stimuli to the animal for natural (bear, trees, cheetah, etc.) and artificial (drifted gratings, orientated bars, etc.) classes. Our results indicate that neurons in mouse visual cortex encode the features of natural and artificial objects in a distinct manner, and such neural code is consistent across animals. We investigate this by applying transfer learning to train a DNN on the neural responses of a single animal and test its generalized performance across multiple animals. Within a single animal, DNN is able to decode the neural responses with as much as 100% classification accuracy. Across animals, this accuracy is reduced to 91%. This study demonstrates the potential of utilizing the DNN models as a computational framework to understand the neural coding principles in the mammalian brain.

We propose a formal mathematical model for sparse representations and active dendrites in neocortex. Our model is inspired by recent experimental findings on active dendritic processing and NMDA spikes in pyramidal neurons. These experimental and modeling studies suggest that the basic unit of pattern memory in the neocortex is instantiated by small clusters of synapses operated on by localized non-linear dendritic processes. We derive a number of scaling laws that characterize the accuracy of such dendrites in detecting activation patterns in a neuronal population under adverse conditions. We introduce the union property which shows that synapses for multiple patterns can be randomly mixed together within a segment and still lead to highly accurate recognition. We describe simulation results that provide further insight into sparse representations as well as two primary results. First we show that pattern recognition by a neuron with active dendrites can be extremely accurate and robust with high dimensional sparse inputs even when using a tiny number of synapses to recognize large patterns. Second, equations representing recognition accuracy of a dendrite predict optimal NMDA spiking thresholds under a generous set of assumptions. The prediction tightly matches NMDA spiking thresholds measured in the literature. Our model matches many of the known properties of pyramidal neurons. As such the theory provides a mathematical framework for understanding the benefits and limits of sparse representations in cortical networks.

We find arithmetic ability resides within a limited number of attention heads, with each head specializing in distinct operations. To delve into the reason, we introduce the Comparative Neuron Analysis (CNA) method, which identifies an internal logic chain consisting of four distinct stages from input to prediction: feature enhancing with shallow FFN neurons, feature transferring by shallow attention layers, feature predicting by arithmetic heads, and prediction enhancing among deep FFN neurons. Moreover, we identify the human-interpretable FFN neurons within both feature-enhancing and feature-predicting stages. These findings lead us to investigate the mechanism of LoRA, revealing that it enhances prediction probabilities by amplifying the coefficient scores of FFN neurons related to predictions. Finally, we apply our method in model pruning for arithmetic tasks and model editing for reducing gender bias. Code is on https://github.com/zepingyu0512/arithmetic-mechanism.

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

Partially inspired by features of computation in visual cortex, deep neural networks compute hierarchical representations of their inputs. While these networks have been highly successful in machine learning, it remains unclear to what extent they can aid our understanding of cortical function. Several groups have developed metrics that provide a quantitative comparison between representations computed by networks and representations measured in cortex. At the same time, neuroscience is well into an unprecedented phase of large-scale data collection, as evidenced by projects such as the Allen Brain Observatory. Despite the magnitude of these efforts, in a given experiment only a fraction of units are recorded, limiting the information available about the cortical representation. Moreover, only a finite number of stimuli can be shown to an animal over the course of a realistic experiment. These limitations raise the question of how and whether metrics that compare representations of deep networks are meaningful on these datasets. Here, we empirically quantify the capabilities and limitations of these metrics due to limited image presentations and neuron samples. We find that the comparison procedure is robust to different choices of stimuli set and the level of subsampling that one might expect in a large-scale brain survey with thousands of neurons. Using these results, we compare the representations measured in the Allen Brain Observatory in response to natural image presentations to deep neural network. We show that the visual cortical areas are relatively high order representations (in that they map to deeper layers of convolutional neural networks). Furthermore, we see evidence of a broad, more parallel organization rather than a sequential hierarchy, with the primary area VISp(V1) being lower order relative to the other areas.

Large language models (LLMs) frequently generate hallucinations -- plausible but factually incorrect outputs -- undermining their reliability. While prior work has examined hallucinations from macroscopic perspectives such as training data and objectives, the underlying neuron-level mechanisms remain largely unexplored. In this paper, we conduct a systematic investigation into hallucination-associated neurons (H-Neurons) in LLMs from three perspectives: identification, behavioral impact, and origins. Regarding their identification, we demonstrate that a remarkably sparse subset of neurons (less than 0.1% of total neurons) can reliably predict hallucination occurrences, with strong generalization across diverse scenarios. In terms of behavioral impact, controlled interventions reveal that these neurons are causally linked to over-compliance behaviors. Concerning their origins, we trace these neurons back to the pre-trained base models and find that these neurons remain predictive for hallucination detection, indicating they emerge during pre-training. Our findings bridge macroscopic behavioral patterns with microscopic neural mechanisms, offering insights for developing more reliable LLMs.

Natural language is an appealing medium for explaining how large language models process and store information, but evaluating the faithfulness of such explanations is challenging. To help address this, we develop two modes of evaluation for natural language explanations that claim individual neurons represent a concept in a text input. In the observational mode, we evaluate claims that a neuron a activates on all and only input strings that refer to a concept picked out by the proposed explanation E. In the intervention mode, we construe E as a claim that the neuron a is a causal mediator of the concept denoted by E. We apply our framework to the GPT-4-generated explanations of GPT-2 XL neurons of Bills et al. (2023) and show that even the most confident explanations have high error rates and little to no causal efficacy. We close the paper by critically assessing whether natural language is a good choice for explanations and whether neurons are the best level of analysis.

We can better understand deep neural networks by identifying which features each of their neurons have learned to detect. To do so, researchers have created Deep Visualization techniques including activation maximization, which synthetically generates inputs (e.g. images) that maximally activate each neuron. A limitation of current techniques is that they assume each neuron detects only one type of feature, but we know that neurons can be multifaceted, in that they fire in response to many different types of features: for example, a grocery store class neuron must activate either for rows of produce or for a storefront. Previous activation maximization techniques constructed images without regard for the multiple different facets of a neuron, creating inappropriate mixes of colors, parts of objects, scales, orientations, etc. Here, we introduce an algorithm that explicitly uncovers the multiple facets of each neuron by producing a synthetic visualization of each of the types of images that activate a neuron. We also introduce regularization methods that produce state-of-the-art results in terms of the interpretability of images obtained by activation maximization. By separately synthesizing each type of image a neuron fires in response to, the visualizations have more appropriate colors and coherent global structure. Multifaceted feature visualization thus provides a clearer and more comprehensive description of the role of each neuron.

High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal physiology - specifically, the parameters (e.g., synaptic efficacies, local conductances) that govern neural dynamics. We propose to translate molecularly annotated ultrastructure into physiology, introducing the concept of an ultrastructure-to-dynamics compiler: a learned mapping from molecularly annotated ultrastructure to simulator-ready, uncertainty-aware physiological parameters. The requirement is paired training data, with jointly acquired ultrastructure from imaging, and dynamical responses to perturbations from physiological experiments. With this data we can train models that predict local physiology directly from structure. Such a compiler would support biophysical simulations by turning anatomical maps into models of circuit dynamics, shifting structure-to-function from a descriptive program to a predictive one and opening routes to understanding neural computation and forecasting intervention effects.

We characterise the dynamics of neuronal activity, in terms of field theory, using neural units placed on a 2D-lattice modelling the cortical surface. The electrical activity of neuronal units was analysed with the aim of deriving a neural field model with a simple functional form that still able to predict or reproduce empirical findings. Each neural unit was modelled using a neural mass and the accompanying field theory was derived in the continuum limit. The field theory comprised coupled (real) Klein-Gordon fields, where predictions of the model fall within the range of experimental findings. These predictions included the frequency spectrum of electric activity measured from the cortex, which was derived using an equipartition of energy over eigenfunctions of the neural fields. Moreover, the neural field model was invariant, within a set of parameters, to the dynamical system used to model each neuronal mass. Specifically, topologically equivalent dynamical systems resulted in the same neural field model when connected in a lattice; indicating that the fields derived could be read as a canonical cortical field theory. We specifically investigated non-dispersive fields that provide a structure for the coding (or representation) of afferent information. Further elaboration of the ensuing neural field theory, including the effect of dispersive forces, could be of importance in the understanding of the cortical processing of information.

In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep learning based classification is utilized in understanding neurodegeneration. The novelty of the proposed approach lies in utilizing two extreme scales of analysis. One branch considers the entire network within graph-analysis framework. Concurrently, the second branch scrutinizes each ROI within a network independently, focusing on evolution of dynamics. For each subject, graph-based approach employs partial correlation to profile the subject in a single graph where each ROI is a node, providing insights into differences in levels of participation. In contrast, non-linear analysis employs recurrence plots to profile a subject as a multichannel 2D image, revealing distinctions in underlying dynamics. The proposed approach is employed for classification of a cohort of 50 healthy control (HC) and 50 Mild Cognitive Impairment (MCI), sourced from ADNI dataset. Results point to: (1) reduced activity in ROIs such as PCC in MCI (2) greater activity in occipital in MCI, which is not seen in HC (3) when analysed for dynamics, all ROIs in MCI show greater predictability in time-series.

We propose a novel algorithm called Backpropagation Neural Tree (BNeuralT), which is a stochastic computational dendritic tree. BNeuralT takes random repeated inputs through its leaves and imposes dendritic nonlinearities through its internal connections like a biological dendritic tree would do. Considering the dendritic-tree like plausible biological properties, BNeuralT is a single neuron neural tree model with its internal sub-trees resembling dendritic nonlinearities. BNeuralT algorithm produces an ad hoc neural tree which is trained using a stochastic gradient descent optimizer like gradient descent (GD), momentum GD, Nesterov accelerated GD, Adagrad, RMSprop, or Adam. BNeuralT training has two phases, each computed in a depth-first search manner: the forward pass computes neural tree's output in a post-order traversal, while the error backpropagation during the backward pass is performed recursively in a pre-order traversal. A BNeuralT model can be considered a minimal subset of a neural network (NN), meaning it is a "thinned" NN whose complexity is lower than an ordinary NN. Our algorithm produces high-performing and parsimonious models balancing the complexity with descriptive ability on a wide variety of machine learning problems: classification, regression, and pattern recognition.

The precise timing of spikes emitted by neurons plays a crucial role in shaping the response of efferent biological neurons. This temporal dimension of neural activity holds significant importance in understanding information processing in neurobiology, especially for the performance of neuromorphic hardware, such as event-based cameras. Nonetheless, many artificial neural models disregard this critical temporal dimension of neural activity. In this study, we present a model designed to efficiently detect temporal spiking motifs using a layer of spiking neurons equipped with heterogeneous synaptic delays. Our model capitalizes on the diverse synaptic delays present on the dendritic tree, enabling specific arrangements of temporally precise synaptic inputs to synchronize upon reaching the basal dendritic tree. We formalize this process as a time-invariant logistic regression, which can be trained using labeled data. To demonstrate its practical efficacy, we apply the model to naturalistic videos transformed into event streams, simulating the output of the biological retina or event-based cameras. To evaluate the robustness of the model in detecting visual motion, we conduct experiments by selectively pruning weights and demonstrate that the model remains efficient even under significantly reduced workloads. In conclusion, by providing a comprehensive, event-driven computational building block, the incorporation of heterogeneous delays has the potential to greatly improve the performance of future spiking neural network algorithms, particularly in the context of neuromorphic chips.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

In recent years, deep learning has been a revolution in the field of machine learning, for computer vision in particular. In this approach, a deep (multilayer) artificial neural network (ANN) is trained in a supervised manner using backpropagation. Huge amounts of labeled examples are required, but the resulting classification accuracy is truly impressive, sometimes outperforming humans. Neurons in an ANN are characterized by a single, static, continuous-valued activation. Yet biological neurons use discrete spikes to compute and transmit information, and the spike times, in addition to the spike rates, matter. Spiking neural networks (SNNs) are thus more biologically realistic than ANNs, and arguably the only viable option if one wants to understand how the brain computes. SNNs are also more hardware friendly and energy-efficient than ANNs, and are thus appealing for technology, especially for portable devices. However, training deep SNNs remains a challenge. Spiking neurons' transfer function is usually non-differentiable, which prevents using backpropagation. Here we review recent supervised and unsupervised methods to train deep SNNs, and compare them in terms of accuracy, but also computational cost and hardware friendliness. The emerging picture is that SNNs still lag behind ANNs in terms of accuracy, but the gap is decreasing, and can even vanish on some tasks, while the SNNs typically require much fewer operations.

Recent studies show that LLM hidden states encode reward-related information, such as answer correctness and model confidence. However, existing approaches typically fit black-box probes on the full hidden states, offering little insight into how this information is structured across neurons. In this paper, we show that reward-related information is concentrated in a sparse subset of neurons. Using simple probing, we identify two types of neurons: value neurons, whose activations predict state value, and dopamine neurons, whose activations encode step-level temporal difference (TD) errors. Together, these neurons form a sparse reward subsystem within LLM hidden states. These names are drawn by analogy with neuroscience, where value neurons and dopamine neurons in the biological reward subsystem also encode value and reward prediction errors, respectively. We demonstrate that value neurons are robust and transferable across diverse datasets and models, and provide causal evidence that they encode reward-related information. Finally, we show applications of the reward subsystem: value neurons serve as effective predictors of model confidence, and dopamine neurons can function as a process reward model (PRM) to guide inference-time search.

Large language models (LLMs) demonstrate remarkable performance across a spectrum of languages. In this work, we delve into the question: How do LLMs handle multilingualism? We introduce a framework that depicts LLMs' processing of multilingual inputs: In the first several layers, LLMs understand the question, converting multilingual inputs into English to facilitate the task-solving phase. In the intermediate layers, LLMs engage in problem-solving by thinking in English and incorporating multilingual knowledge to obtain factual content, leveraging the self-attention and feed-forward structures, respectively. In the last several layers, LLMs generate responses that align with the original language of the query. In addition, we investigate the existence of language-specific neurons when processing a certain language. To detect neurons activated by the input language, even without labels, we innovatively design a Parallel Language specific Neuron Detection (PLND) method that effectively measures the significance of neurons when handling multilingual inputs. By comprehensive ablation analysis through deactivating neurons of different layers and structures, we verify the framework that we propose. Additionally, we demonstrate that we can utilize such a framework to effectively enhance the multilingual ability with much less training effort.

Advances in neural recording present increasing opportunities to study neural activity in unprecedented detail. Latent variable models (LVMs) are promising tools for analyzing this rich activity across diverse neural systems and behaviors, as LVMs do not depend on known relationships between the activity and external experimental variables. However, progress with LVMs for neuronal population activity is currently impeded by a lack of standardization, resulting in methods being developed and compared in an ad hoc manner. To coordinate these modeling efforts, we introduce a benchmark suite for latent variable modeling of neural population activity. We curate four datasets of neural spiking activity from cognitive, sensory, and motor areas to promote models that apply to the wide variety of activity seen across these areas. We identify unsupervised evaluation as a common framework for evaluating models across datasets, and apply several baselines that demonstrate benchmark diversity. We release this benchmark through EvalAI. http://neurallatents.github.io

Artificial Neural Networks (ANN) have gained significant popularity thanks to their ability to learn using the well-known backpropagation algorithm. Conversely, Spiking Neural Networks (SNNs), despite having broader capabilities than ANNs, have always posed challenges in the training phase. This paper shows a new method to perform supervised learning on SNNs, using Spike Timing Dependent Plasticity (STDP) and homeostasis, aiming at training the network to identify spatial patterns. Spatial patterns refer to spike patterns without a time component, where all spike events occur simultaneously. The method is tested using the SpiNNaker digital architecture. A SNN is trained to recognise one or multiple patterns and performance metrics are extracted to measure the performance of the network. Some considerations are drawn from the results showing that, in the case of a single trained pattern, the network behaves as the ideal detector, with 100% accuracy in detecting the trained pattern. However, as the number of trained patterns on a single network increases, the accuracy of identification is linked to the similarities between these patterns. This method of training an SNN to detect spatial patterns may be applied to pattern recognition in static images or traffic analysis in computer networks, where each network packet represents a spatial pattern. It will be stipulated that the homeostatic factor may enable the network to detect patterns with some degree of similarity, rather than only perfectly matching patterns.The principles outlined in this article serve as the fundamental building blocks for more complex systems that utilise both spatial and temporal patterns by converting specific features of input signals into spikes.One example of such a system is a computer network packet classifier, tasked with real-time identification of packet streams based on features within the packet content

The neurons of artificial neural networks were originally invented when much less was known about biological neurons than is known today. Our work explores a modification to the core neuron unit to make it more parallel to a biological neuron. The modification is made with the knowledge that biological dendrites are not simply passive activation funnels, but also compute complex non-linear functions as they transmit activation to the cell body. The paper explores a novel system of "Perforated" backpropagation empowering the artificial neurons of deep neural networks to achieve better performance coding for the same features they coded for in the original architecture. After an initial network training phase, additional "Dendrite Nodes" are added to the network and separately trained with a different objective: to correlate their output with the remaining error of the original neurons. The trained Dendrite Nodes are then frozen, and the original neurons are further trained, now taking into account the additional error signals provided by the Dendrite Nodes. The cycle of training the original neurons and then adding and training Dendrite Nodes can be repeated several times until satisfactory performance is achieved. Our algorithm was successfully added to modern state-of-the-art PyTorch networks across multiple domains, improving upon original accuracies and allowing for significant model compression without a loss in accuracy.

This paper studies the problem of training a two-layer ReLU network for binary classification using gradient flow with small initialization. We consider a training dataset with well-separated input vectors: Any pair of input data with the same label are positively correlated, and any pair with different labels are negatively correlated. Our analysis shows that, during the early phase of training, neurons in the first layer try to align with either the positive data or the negative data, depending on its corresponding weight on the second layer. A careful analysis of the neurons' directional dynamics allows us to provide an O(log n{mu}) upper bound on the time it takes for all neurons to achieve good alignment with the input data, where n is the number of data points and mu measures how well the data are separated. After the early alignment phase, the loss converges to zero at a O(1{t}) rate, and the weight matrix on the first layer is approximately low-rank. Numerical experiments on the MNIST dataset illustrate our theoretical findings.

Attending to what is relevant is fundamental to both the mammalian brain and modern machine learning models such as Transformers. Yet, determining relevance remains a core challenge, traditionally offloaded to learning algorithms like backpropagation. Inspired by recent cellular neurobiological evidence linking neocortical pyramidal cells to distinct mental states, this work shows how models (e.g., Transformers) can emulate high-level perceptual processing and awake thought (imagination) states to pre-select relevant information before applying attention. Triadic neuronal-level modulation loops among questions (Q), clues (keys, K), and hypotheses (values, V) enable diverse, deep, parallel reasoning chains at the representation level and allow a rapid shift from initial biases to refined understanding. This leads to orders-of-magnitude faster learning with significantly reduced computational demand (e.g., fewer heads, layers, and tokens), at an approximate cost of O(N), where N is the number of input tokens. Results span reinforcement learning (e.g., CarRacing in a high-dimensional visual setup), computer vision, and natural language question answering.

Recently, interest has grown in exploring the hypothesis that neural activity conveys information through precise spiking motifs. To investigate this phenomenon, various algorithms have been proposed to detect such motifs in Single Unit Activity (SUA) recorded from populations of neurons. In this study, we present a novel detection model based on the inversion of a generative model of raster plot synthesis. Using this generative model, we derive an optimal detection procedure that takes the form of logistic regression combined with temporal convolution. A key advantage of this model is its differentiability, which allows us to formulate a supervised learning approach using a gradient descent on the binary cross-entropy loss. To assess the model's ability to detect spiking motifs in synthetic data, we first perform numerical evaluations. This analysis highlights the advantages of using spiking motifs over traditional firing rate based population codes. We then successfully demonstrate that our learning method can recover synthetically generated spiking motifs, indicating its potential for further applications. In the future, we aim to extend this method to real neurobiological data, where the ground truth is unknown, to explore and detect spiking motifs in a more natural and biologically relevant context.

Everyday tasks come with a target, and pretraining models around this target is what turns them into experts. In this paper, we study target-oriented language model (LM) pretraining by introducing Neuron-Activated Graph Ranking (NAG-based Ranking), a training-free and interpretable framework for target pretraining data selection. Rather than using black-box representations, our approach directly characterizes each target input by a sparse set of high-impact neurons in any off-the-shelf LLMs. Concretely, we quantify neuron impact and select the most influential neurons across layers into a compact Neuron-Activated Graph (NAG), and rank candidate data by NAG similarity to target examples. We conduct experiments across six benchmarks, where our NAG-based Ranking improves target-oriented pretraining by 4.9% on average over random sampling, and also outperforms state-of-the-art baselines by 5.3% accuracy on HellaSwag. It also remains effective under a more applicable multi-target setting, where our best setup surpasses two baselines by 1.1% and 4.1%, respectively. Furthermore, we provide a comprehensive analysis on why and how our NAG works, e.g., deactivating NAG-selected neurons (only 0.12% of all) causes a 23.5% performance collapse, and restricting NAG to the final layer incurs a 4.1% average drop, indicating that NAG captures a sparse "functional backbone" for learning target features. We release the code at https://github.com/asillycat/NAG.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

Large Language Models (LLMs) possess vast amounts of knowledge within their parameters, prompting research into methods for locating and editing this knowledge. Previous work has largely focused on locating entity-related (often single-token) facts in smaller models. However, several key questions remain unanswered: (1) How can we effectively locate query-relevant neurons in decoder-only LLMs, such as Llama and Mistral? (2) How can we address the challenge of long-form (or free-form) text generation? (3) Are there localized knowledge regions in LLMs? In this study, we introduce Query-Relevant Neuron Cluster Attribution (QRNCA), a novel architecture-agnostic framework capable of identifying query-relevant neurons in LLMs. QRNCA allows for the examination of long-form answers beyond triplet facts by employing the proxy task of multi-choice question answering. To evaluate the effectiveness of our detected neurons, we build two multi-choice QA datasets spanning diverse domains and languages. Empirical evaluations demonstrate that our method outperforms baseline methods significantly. Further, analysis of neuron distributions reveals the presence of visible localized regions, particularly within different domains. Finally, we show potential applications of our detected neurons in knowledge editing and neuron-based prediction.

Multilingual Alignment is an effective and representative paradigm to enhance LLMs' multilingual capabilities, which transfers the capabilities from the high-resource languages to the low-resource languages. Meanwhile, some researches on language-specific neurons reveal that there are language-specific neurons that are selectively activated in LLMs when processing different languages. This provides a new perspective to analyze and understand LLMs' mechanisms more specifically in multilingual scenarios. In this work, we propose a new finer-grained neuron identification algorithm, which detects language neurons~(including language-specific neurons and language-related neurons) and language-agnostic neurons. Furthermore, based on the distributional characteristics of different types of neurons, we divide the LLMs' internal process for multilingual inference into four parts: (1) multilingual understanding, (2) shared semantic space reasoning, (3) multilingual output space transformation, and (4) vocabulary space outputting. Additionally, we systematically analyze the models before and after alignment with a focus on different types of neurons. We also analyze the phenomenon of ''Spontaneous Multilingual Alignment''. Overall, our work conducts a comprehensive investigation based on different types of neurons, providing empirical results and valuable insights for better understanding multilingual alignment and multilingual capabilities of LLMs.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

Interpreting individual neurons or directions in activations space is an important component of mechanistic interpretability. As such, many algorithms have been proposed to automatically produce neuron explanations, but it is often not clear how reliable these explanations are, or which methods produce the best explanations. This can be measured via crowd-sourced evaluations, but they can often be noisy and expensive, leading to unreliable results. In this paper, we carefully analyze the evaluation pipeline and develop a cost-effective and highly accurate crowdsourced evaluation strategy. In contrast to previous human studies that only rate whether the explanation matches the most highly activating inputs, we estimate whether the explanation describes neuron activations across all inputs. To estimate this effectively, we introduce a novel application of importance sampling to determine which inputs are the most valuable to show to raters, leading to around 30x cost reduction compared to uniform sampling. We also analyze the label noise present in crowd-sourced evaluations and propose a Bayesian method to aggregate multiple ratings leading to a further ~5x reduction in number of ratings required for the same accuracy. Finally, we use these methods to conduct a large-scale study comparing the quality of neuron explanations produced by the most popular methods for two different vision models.

A neuroscience method to understanding the brain is to find and study the preferred stimuli that highly activate an individual cell or groups of cells. Recent advances in machine learning enable a family of methods to synthesize preferred stimuli that cause a neuron in an artificial or biological brain to fire strongly. Those methods are known as Activation Maximization (AM) or Feature Visualization via Optimization. In this chapter, we (1) review existing AM techniques in the literature; (2) discuss a probabilistic interpretation for AM; and (3) review the applications of AM in debugging and explaining networks.

We analyze a family of large language models in such a lightweight manner that can be done on a single GPU. Specifically, we focus on the OPT family of models ranging from 125m to 66b parameters and rely only on whether an FFN neuron is activated or not. First, we find that the early part of the network is sparse and represents many discrete features. Here, many neurons (more than 70% in some layers of the 66b model) are "dead", i.e. they never activate on a large collection of diverse data. At the same time, many of the alive neurons are reserved for discrete features and act as token and n-gram detectors. Interestingly, their corresponding FFN updates not only promote next token candidates as could be expected, but also explicitly focus on removing the information about triggering them tokens, i.e., current input. To the best of our knowledge, this is the first example of mechanisms specialized at removing (rather than adding) information from the residual stream. With scale, models become more sparse in a sense that they have more dead neurons and token detectors. Finally, some neurons are positional: them being activated or not depends largely (or solely) on position and less so (or not at all) on textual data. We find that smaller models have sets of neurons acting as position range indicators while larger models operate in a less explicit manner.

Several studies have explored the mechanisms of large language models (LLMs) in coding tasks, but most have focused on programming languages (PLs) in a monolingual setting. In this paper, we investigate the relationship between multiple PLs and English in the concept space of LLMs. We perform a few-shot translation task on 21 PL pairs using two Llama-based models. By decoding the embeddings of intermediate layers during this task, we observe that the concept space is closer to English (including PL keywords) and assigns high probabilities to English tokens in the second half of the intermediate layers. We analyze neuron activations for 11 PLs and English, finding that while language-specific neurons are primarily concentrated in the bottom layers, those exclusive to each PL tend to appear in the top layers. For PLs that are highly aligned with multiple other PLs, identifying language-specific neurons is not feasible. These PLs also tend to have a larger keyword set than other PLs and are closer to the model's concept space regardless of the input/output PL in the translation task. Our findings provide insights into how LLMs internally represent PLs, revealing structural patterns in the model's concept space. Code is available at https://github.com/cisnlp/code-specific-neurons.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

We create a reusable Transformer, BrainBERT, for intracranial recordings bringing modern representation learning approaches to neuroscience. Much like in NLP and speech recognition, this Transformer enables classifying complex concepts, i.e., decoding neural data, with higher accuracy and with much less data by being pretrained in an unsupervised manner on a large corpus of unannotated neural recordings. Our approach generalizes to new subjects with electrodes in new positions and to unrelated tasks showing that the representations robustly disentangle the neural signal. Just like in NLP where one can study language by investigating what a language model learns, this approach opens the door to investigating the brain by what a model of the brain learns. As a first step along this path, we demonstrate a new analysis of the intrinsic dimensionality of the computations in different areas of the brain. To construct these representations, we combine a technique for producing super-resolution spectrograms of neural data with an approach designed for generating contextual representations of audio by masking. In the future, far more concepts will be decodable from neural recordings by using representation learning, potentially unlocking the brain like language models unlocked language.

Multimodal large language models (MLLMs) have shown impressive capabilities, yet they often struggle to effectively capture the fine-grained textual information within images crucial for accurate image translation. This often leads to a modality gap between visual text inputs and textual inputs/outputs for image translation. Existing methods, primarily relying on instruction fine-tuning, risk parameter redundancy of pre-trained knowledge, hindering generalization performance. To address this, we introduce modality neuron-aware fine-tuning (MNAFT), a novel approach that takes advantage of the specialized roles of individual neurons within MLLMs for enhanced image translation. MNAFT identifies language-agnostic and language-specific neurons in both vision and language modules through an instruction-driven activation analysis, evaluating their importance in various translation tasks. We then perform selective fine-tuning, updating only the parameters of language-specific and language-agnostic neurons within the selected layers relevant to the target task, while preserving the knowledge encoded in other neurons and layers. Our extensive experiments on multiple benchmarks demonstrate that MNAFT significantly outperforms state-of-the-art image translation methods, including cascaded models, standard full fine-tuning, and parameter-efficient tuning techniques. Furthermore, we provide comprehensive analysis, including visualizations of neuron activations and clustering patterns, to offer insights into the roles of different neuron groups in mediating cross-modal understanding and facilitating accurate language-specific translation.

Despite rapid adoption and deployment of large language models (LLMs), the internal computations of these models remain opaque and poorly understood. In this work, we seek to understand how high-level human-interpretable features are represented within the internal neuron activations of LLMs. We train k-sparse linear classifiers (probes) on these internal activations to predict the presence of features in the input; by varying the value of k we study the sparsity of learned representations and how this varies with model scale. With k=1, we localize individual neurons which are highly relevant for a particular feature, and perform a number of case studies to illustrate general properties of LLMs. In particular, we show that early layers make use of sparse combinations of neurons to represent many features in superposition, that middle layers have seemingly dedicated neurons to represent higher-level contextual features, and that increasing scale causes representational sparsity to increase on average, but there are multiple types of scaling dynamics. In all, we probe for over 100 unique features comprising 10 different categories in 7 different models spanning 70 million to 6.9 billion parameters.

As one of the energy-efficient alternatives of conventional neural networks (CNNs), spiking neural networks (SNNs) have gained more and more interest recently. To train the deep models, some effective batch normalization (BN) techniques are proposed in SNNs. All these BNs are suggested to be used after the convolution layer as usually doing in CNNs. However, the spiking neuron is much more complex with the spatio-temporal dynamics. The regulated data flow after the BN layer will be disturbed again by the membrane potential updating operation before the firing function, i.e., the nonlinear activation. Therefore, we advocate adding another BN layer before the firing function to normalize the membrane potential again, called MPBN. To eliminate the induced time cost of MPBN, we also propose a training-inference-decoupled re-parameterization technique to fold the trained MPBN into the firing threshold. With the re-parameterization technique, the MPBN will not introduce any extra time burden in the inference. Furthermore, the MPBN can also adopt the element-wised form, while these BNs after the convolution layer can only use the channel-wised form. Experimental results show that the proposed MPBN performs well on both popular non-spiking static and neuromorphic datasets. Our code is open-sourced at https://github.com/yfguo91/MPBN{MPBN}.

As the prevalence of Alzheimer's disease (AD) rises, improving mechanistic insight from non-invasive biomarkers is increasingly critical. Recent work suggests that circuit-level brain alterations manifest as changes in electroencephalography (EEG) spectral features detectable by machine learning. However, conventional deep learning approaches for EEG-based AD detection are computationally intensive and mechanistically opaque. Spiking neural networks (SNNs) offer a biologically plausible and energy-efficient alternative, yet their application to AD diagnosis remains largely unexplored. We propose a neuro-bridge framework that links data-driven learning with minimal, biophysically grounded simulations, enabling bidirectional interpretation between machine learning signatures and circuit-level mechanisms in AD. Using resting-state clinical EEG, we train an SNN classifier that achieves competitive performance (AUC = 0.839) and identifies the aperiodic 1/f slope as a key discriminative marker. The 1/f slope reflects excitation-inhibition balance. To interpret this mechanistically, we construct spiking network simulations in which inhibitory-to-excitatory synaptic ratios are systematically varied to emulate healthy, mild cognitive impairment, and AD-like states. Using both membrane potential-based and synaptic current-based EEG proxies, we reproduce empirical spectral slowing and altered alpha organization. Incorporating empirical functional connectivity priors into multi-subnetwork simulations further enhances spectral differentiation, demonstrating that large-scale network topology constrains EEG signatures more strongly than excitation-inhibition balance alone. Overall, this neuro-bridge approach connects SNN-based classification with interpretable circuit simulations, advancing mechanistic understanding of EEG biomarkers while enabling scalable, explainable AD detection.

Artificial neural networks are being proposed as models of parts of the brain. The networks are compared to recordings of biological neurons, and good performance in reproducing neural responses is considered to support the model's validity. A key question is how much this system identification approach tells us about brain computation. Does it validate one model architecture over another? We evaluate the most commonly used comparison techniques, such as a linear encoding model and centered kernel alignment, to correctly identify a model by replacing brain recordings with known ground truth models. System identification performance is quite variable; it also depends significantly on factors independent of the ground truth architecture, such as stimuli images. In addition, we show the limitations of using functional similarity scores in identifying higher-level architectural motifs.

Regarded as the third generation of neural networks, Spiking Neural Networks (SNNs) have garnered significant traction due to their biological plausibility and energy efficiency. Recent advancements in large models necessitate spiking neurons capable of high performance, adaptability, and training efficiency. In this work, we first propose a novel functional perspective that provides general guidance for designing the new generation of spiking neurons. Following the insightful guidelines, we propose the Adaptive Spiking Neuron (ASN), which incorporates trainable parameters to learn membrane potential dynamics and enable adaptive firing. ASN adopts an integer training and spike inference paradigm, facilitating efficient SNN training. To further enhance robustness, we propose a specialized variant of ASN, the Normalized Adaptive Spiking Neuron (NASN), which integrates normalization to stabilize training. We evaluate our neuron model on 19 datasets spanning five distinct tasks in both vision and language modalities, demonstrating the effectiveness and versatility of the ASN family. Our ASN family is expected to become the new generation of general-purpose spiking neurons.

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.

Cortical neurons are complex, multi-timescale processors wired into recurrent circuits, shaped by long evolutionary pressure under stringent biological constraints. Mainstream machine learning, by contrast, predominantly builds models from extremely simple units, a default inherited from early neural-network theory. We treat this as a normative architectural question. How should one split a fixed parameter budget P between the number of units N, per-unit effective complexity k_e, and per-unit connectivity k_c? What controls the optimal allocation? This calls for a model in which per-unit complexity can be tuned independently of width and connectivity. Accordingly, we introduce the ELM Network, whose recurrent layer is built from Expressive Leaky Memory (ELM) neurons, chosen to mirror functional components of cortical neurons. The architecture allows for individually adjusting N, k_e, and k_c and trains stably across orders of magnitude in scale. We evaluate the model on two qualitatively different sequence benchmarks: the neuromorphic SHD-Adding task and Enwik8 character-level language modeling. Performance improves monotonically along each of the three axes individually. Under a fixed budget, a clear non-trivial optimum emerges in their tradeoff, and larger budgets favor both more and more complex neurons. A closed-form information-theoretic model captures these tradeoffs and attributes the diminishing returns at two ends to: per-neuron signal-to-noise saturation and across-neuron redundancy. A hyperparameter sweep spanning three orders of magnitude in trainable parameters traces a near-Pareto-frontier scaling law consistent with the framework. This suggests that the simple-unit default in ML is not obviously optimal once this tradeoff surface is probed, and offers a normative lens on cortex's reliance on complex spatio-temporal integrators.

Within the complex neuroarchitecture of the brain, astrocytes play crucial roles in development, structure, and metabolism. These cells regulate neural activity through tripartite synapses, directly impacting cognitive processes such as learning and memory. Despite the growing recognition of astrocytes' significance, traditional Spiking Neural Network (SNN) models remain predominantly neuron-centric, overlooking the profound influence of astrocytes on neural dynamics. Inspired by these biological insights, we have developed an Astrocyte-Modulated Spiking Unit (AM-SU), an innovative framework that integrates neuron-astrocyte interactions into the computational paradigm, demonstrating wide applicability across various hardware platforms. Our Astrocyte-Modulated Spiking Neural Network (AstroSNN) exhibits exceptional performance in tasks involving memory retention and natural language generation, particularly in handling long-term dependencies and complex linguistic structures. The design of AstroSNN not only enhances its biological authenticity but also introduces novel computational dynamics, enabling more effective processing of complex temporal dependencies. Furthermore, AstroSNN shows low latency, high throughput, and reduced memory usage in practical applications, making it highly suitable for resource-constrained environments. By successfully integrating astrocytic dynamics into intelligent neural networks, our work narrows the gap between biological plausibility and neural modeling, laying the groundwork for future biologically-inspired neural computing research that includes both neurons and astrocytes.

Biological cortical neurons are remarkably sophisticated computational devices, temporally integrating their vast synaptic input over an intricate dendritic tree, subject to complex, nonlinearly interacting internal biological processes. A recent study proposed to characterize this complexity by fitting accurate surrogate models to replicate the input-output relationship of a detailed biophysical cortical pyramidal neuron model and discovered it needed temporal convolutional networks (TCN) with millions of parameters. Requiring these many parameters, however, could stem from a misalignment between the inductive biases of the TCN and cortical neuron's computations. In light of this, and to explore the computational implications of leaky memory units and nonlinear dendritic processing, we introduce the Expressive Leaky Memory (ELM) neuron model, a biologically inspired phenomenological model of a cortical neuron. Remarkably, by exploiting such slowly decaying memory-like hidden states and two-layered nonlinear integration of synaptic input, our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. To further assess the computational ramifications of our neuron design, we evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets, as well as a novel neuromorphic dataset based on the Spiking Heidelberg Digits dataset (SHD-Adding). Leveraging a larger number of memory units with sufficiently long timescales, and correspondingly sophisticated synaptic integration, the ELM neuron displays substantial long-range processing capabilities, reliably outperforming the classic Transformer or Chrono-LSTM architectures on LRA, and even solving the Pathfinder-X task with over 70% accuracy (16k context length).

Large language models (LLMs) have demonstrated prowess in a wide range of tasks. However, many LLMs exhibit significant performance discrepancies between high- and low-resource languages. To mitigate this challenge, we present FuxiTranyu, an open-source multilingual LLM, which is designed to satisfy the need of the research community for balanced and high-performing multilingual capabilities. FuxiTranyu-8B, the base model with 8 billion parameters, is trained from scratch on a meticulously balanced multilingual data repository that contains 600 billion tokens covering 43 natural languages and 16 programming languages. In addition to the base model, we also develop two instruction-tuned models: FuxiTranyu-8B-SFT that is fine-tuned on a diverse multilingual instruction dataset, and FuxiTranyu-8B-DPO that is further refined with DPO on a preference dataset for enhanced alignment ability. Extensive experiments on a wide range of multilingual benchmarks demonstrate the competitive performance of FuxiTranyu against existing multilingual LLMs, e.g., BLOOM-7B, PolyLM-13B, Llama-2-Chat-7B and Mistral-7B-Instruct. Interpretability analyses at both the neuron and representation level suggest that FuxiTranyu is able to learn consistent multilingual representations across different languages. To promote further research into multilingual LLMs and their working mechanisms, we release both the base and instruction-tuned FuxiTranyu models together with 58 pretraining checkpoints at HuggingFace and Github.

Interpretability researchers have attempted to understand MLP neurons of language models based on both the contexts in which they activate and their output weight vectors. They have paid little attention to a complementary aspect: the interactions between input and output. For example, when neurons detect a direction in the input, they might add much the same direction to the residual stream ("enrichment neurons") or reduce its presence ("depletion neurons"). We address this aspect by examining the cosine similarity between input and output weights of a neuron. We apply our method to 12 models and find that enrichment neurons dominate in early-middle layers whereas later layers tend more towards depletion. To explain this finding, we argue that enrichment neurons are largely responsible for enriching concept representations, one of the first steps of factual recall. Our input-output perspective is a complement to activation-dependent analyses and to approaches that treat input and output separately.

This study introduces a novel approach by replacing the traditional perceptron neuron model with a biologically inspired probabilistic meta neuron, where the internal neuron parameters are jointly learned, leading to improved classification accuracy of spiking neural networks (SNNs). To validate this innovation, we implement and compare two SNN architectures: one based on standard leaky integrate-and-fire (LIF) neurons and another utilizing the proposed probabilistic meta neuron model. As a second key contribution, we present a new biologically inspired classification framework that uniquely integrates SNNs with Lempel-Ziv complexity (LZC) a measure closely related to entropy rate. By combining the temporal precision and biological plausibility of SNNs with the capacity of LZC to capture structural regularity, the proposed approach enables efficient and interpretable classification of spatiotemporal neural data, an aspect not addressed in existing works. We consider learning algorithms such as backpropagation, spike-timing-dependent plasticity (STDP), and the Tempotron learning rule. To explore neural dynamics, we use Poisson processes to model neuronal spike trains, a well-established method for simulating the stochastic firing behavior of biological neurons. Our results reveal that depending on the training method, the classifier's efficiency can improve by up to 11.00%, highlighting the advantage of learning additional neuron parameters beyond the traditional focus on weighted inputs alone.

Recurrent Neural Networks (RNNs) are popular models of brain function. The typical training strategy is to adjust their input-output behavior so that it matches that of the biological circuit of interest. Even though this strategy ensures that the biological and artificial networks perform the same computational task, it does not guarantee that their internal activity dynamics match. This suggests that the trained RNNs might end up performing the task employing a different internal computational mechanism, which would make them a suboptimal model of the biological circuit. In this work, we introduce a novel training strategy that allows learning not only the input-output behavior of an RNN but also its internal network dynamics, based on sparse neural recordings. We test the proposed method by training an RNN to simultaneously reproduce internal dynamics and output signals of a physiologically-inspired neural model. Specifically, this model generates the multiphasic muscle-like activity patterns typically observed during the execution of reaching movements, based on the oscillatory activation patterns concurrently observed in the motor cortex. Remarkably, we show that the reproduction of the internal dynamics is successful even when the training algorithm relies on the activities of a small subset of neurons sampled from the biological network. Furthermore, we show that training the RNNs with this method significantly improves their generalization performance. Overall, our results suggest that the proposed method is suitable for building powerful functional RNN models, which automatically capture important computational properties of the biological circuit of interest from sparse neural recordings.

Large Language Models have demonstrated impressive fluency across diverse tasks, yet their tendency to produce toxic content remains a critical challenge for AI safety and public trust. Existing toxicity mitigation approaches primarily manipulate individual neuron activations, but these methods suffer from instability, context dependence, and often compromise the model's core language abilities. To address these shortcomings, we investigate three key questions: the stability of neuron-level toxicity indicators, the advantages of structural (layer-wise) representations, and the interpretability of mechanisms driving toxic generation. Through extensive experiments on Jigsaw and ToxiCN datasets, we show that aggregated layer-wise features provide more robust signals than single neurons. Moreover, we observe conceptual limitations in prior works that conflate toxicity detection experts and generation experts within neuron-based interventions. To mitigate this, we propose a novel principled intervention technique, EigenShift, based on eigen-decomposition of the language model's final output layer. This method selectively targets generation-aligned components, enabling precise toxicity suppression without impairing linguistic competence. Our method requires no additional training or fine-tuning, incurs minimal computational cost, and is grounded in rigorous theoretical analysis.

Like any field of empirical science, AI may be approached axiomatically. We formulate requirements for a general-purpose, human-level AI system in terms of postulates. We review the methodology of deep learning, examining the explicit and tacit assumptions in deep learning research. Deep Learning methodology seeks to overcome limitations in traditional machine learning research as it combines facets of model richness, generality, and practical applicability. The methodology so far has produced outstanding results due to a productive synergy of function approximation, under plausible assumptions of irreducibility and the efficiency of back-propagation family of algorithms. We examine these winning traits of deep learning, and also observe the various known failure modes of deep learning. We conclude by giving recommendations on how to extend deep learning methodology to cover the postulates of general-purpose AI including modularity, and cognitive architecture. We also relate deep learning to advances in theoretical neuroscience research.

We interpret the function of individual neurons in CLIP by automatically describing them using text. Analyzing the direct effects (i.e. the flow from a neuron through the residual stream to the output) or the indirect effects (overall contribution) fails to capture the neurons' function in CLIP. Therefore, we present the "second-order lens", analyzing the effect flowing from a neuron through the later attention heads, directly to the output. We find that these effects are highly selective: for each neuron, the effect is significant for <2% of the images. Moreover, each effect can be approximated by a single direction in the text-image space of CLIP. We describe neurons by decomposing these directions into sparse sets of text representations. The sets reveal polysemantic behavior - each neuron corresponds to multiple, often unrelated, concepts (e.g. ships and cars). Exploiting this neuron polysemy, we mass-produce "semantic" adversarial examples by generating images with concepts spuriously correlated to the incorrect class. Additionally, we use the second-order effects for zero-shot segmentation and attribute discovery in images. Our results indicate that a scalable understanding of neurons can be used for model deception and for introducing new model capabilities.

Large language models (LLMs) exhibit strong multilingual abilities, yet the neural mechanisms behind language-specific processing remain unclear. We analyze language-specific neurons in Llama-3.1-8B, Mistral-Nemo-12B, and Aya-Expanse-8B & 32B across 21 typologically diverse languages, identifying neurons that control language behavior. Using the Language Activation Probability Entropy (LAPE) method, we show that these neurons cluster in deeper layers, with non-Latin scripts showing greater specialization. Related languages share overlapping neurons, reflecting internal representations of linguistic proximity. Through language arithmetics, i.e. systematic activation addition and multiplication, we steer models to deactivate unwanted languages and activate desired ones, outperforming simpler replacement approaches. These interventions effectively guide behavior across five multilingual tasks: language forcing, translation, QA, comprehension, and NLI. Manipulation is more successful for high-resource languages, while typological similarity improves effectiveness. We also demonstrate that cross-lingual neuron steering enhances downstream performance and reveal internal "fallback" mechanisms for language selection when neurons are progressively deactivated. Our code is made publicly available at https://github.com/d-gurgurov/Language-Neurons-Manipulation.

Large language models (LLMs) demonstrate remarkable multilingual capabilities without being pre-trained on specially curated multilingual parallel corpora. It remains a challenging problem to explain the underlying mechanisms by which LLMs process multilingual texts. In this paper, we delve into the composition of Transformer architectures in LLMs to pinpoint language-specific regions. Specially, we propose a novel detection method, language activation probability entropy (LAPE), to identify language-specific neurons within LLMs. Based on LAPE, we conduct comprehensive experiments on two representative LLMs, namely LLaMA-2 and BLOOM. Our findings indicate that LLMs' proficiency in processing a particular language is predominantly due to a small subset of neurons, primarily situated in the models' top and bottom layers. Furthermore, we showcase the feasibility to "steer" the output language of LLMs by selectively activating or deactivating language-specific neurons. Our research provides important evidence to the understanding and exploration of the multilingual capabilities of LLMs.

Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are only selective for a small number of linear projections of a potentially high-dimensional input. Here we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g. naturalistic) stimulus distribution, we review several inference methods, focussing in particular on two information-theory-based approaches (maximization of stimulus energy or of noise entropy) and a likelihood-based approach (Bayesian spike-triggered covariance, extensions of generalized linear models). We analyze the formal connection between the likelihood-based and information-based approaches to show how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.

Interpreting the information encoded in model weights remains a fundamental challenge in mechanistic interpretability. In this work, we introduce ROTATE (Rotation-Optimized Token Alignment in weighT spacE), a data-free method requiring no forward passes that disentangles MLP neurons directly in weight space. Our approach relies on a key statistical observation: neurons that encode coherent, monosemantic concepts exhibit high kurtosis when projected onto the model's vocabulary. By optimizing rotations of neuron weights to maximize their vocabulary-space kurtosis, our method recovers sparse, interpretable directions which we name vocabulary channels. Experiments on Llama-3.1-8B-Instruct and Gemma-2-2B-it demonstrate that ROTATE consistently recovers vocabulary channels that are faithful to the neuron's behavior. ablating individual channels selectively disables corresponding input activations or the promotion of specific concepts. Moreover, aggregating channel-level descriptions yields comprehensive neuron descriptions that outperform optimized activation-based baselines by 2-3x in head-to-head comparisons. By providing a data-free decomposition of neuron weights, ROTATE offers a scalable, fine-grained building block for interpreting LMs.

A basic question within the emerging field of mechanistic interpretability is the degree to which neural networks learn the same underlying mechanisms. In other words, are neural mechanisms universal across different models? In this work, we study the universality of individual neurons across GPT2 models trained from different initial random seeds, motivated by the hypothesis that universal neurons are likely to be interpretable. In particular, we compute pairwise correlations of neuron activations over 100 million tokens for every neuron pair across five different seeds and find that 1-5\% of neurons are universal, that is, pairs of neurons which consistently activate on the same inputs. We then study these universal neurons in detail, finding that they usually have clear interpretations and taxonomize them into a small number of neuron families. We conclude by studying patterns in neuron weights to establish several universal functional roles of neurons in simple circuits: deactivating attention heads, changing the entropy of the next token distribution, and predicting the next token to (not) be within a particular set.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.

The brain is the perfect place to look for inspiration to develop more efficient neural networks. The inner workings of our synapses and neurons provide a glimpse at what the future of deep learning might look like. This paper serves as a tutorial and perspective showing how to apply the lessons learnt from several decades of research in deep learning, gradient descent, backpropagation and neuroscience to biologically plausible spiking neural neural networks. We also explore the delicate interplay between encoding data as spikes and the learning process; the challenges and solutions of applying gradient-based learning to spiking neural networks (SNNs); the subtle link between temporal backpropagation and spike timing dependent plasticity, and how deep learning might move towards biologically plausible online learning. Some ideas are well accepted and commonly used amongst the neuromorphic engineering community, while others are presented or justified for the first time here. The fields of deep learning and spiking neural networks evolve very rapidly. We endeavour to treat this document as a 'dynamic' manuscript that will continue to be updated as the common practices in training SNNs also change. A series of companion interactive tutorials complementary to this paper using our Python package, snnTorch, are also made available. See https://snntorch.readthedocs.io/en/latest/tutorials/index.html .

Vision-language models (VLMs) achieve strong multimodal performance, yet how computation is organized across populations of neurons remains poorly understood. In this work, we study VLMs through the lens of neural topology, representing each layer as a within-layer correlation graph derived from neuron-neuron co-activations. This view allows us to ask whether population-level structure is behaviorally meaningful, how it changes across modalities and depth, and whether it identifies causally influential internal components under intervention. We show that correlation topology carries recoverable behavioral signal; moreover, cross-modal structure progressively consolidates with depth around a compact set of recurrent hub neurons, whose targeted perturbation substantially alters model output. Neural topology thus emerges as a meaningful intermediate scale for VLM interpretability: richer than local attribution, more tractable than full circuit recovery, and empirically tied to multimodal behavior. Code is publicly available at https://github.com/he-h/vlm-graph-probing.

Nowadays, neural networks act as a synonym for artificial intelligence. Present neural network models, although remarkably powerful, are inefficient both in terms of data and energy. Several alternative forms of neural networks have been proposed to address some of these problems. Specifically, spiking neural networks are suitable for efficient hardware implementations. However, effective learning algorithms for spiking networks remain elusive, although it is suspected that effective plasticity mechanisms could alleviate the problem of data efficiency. Here, we present a new framework for spiking neural networks - Spark - built upon the idea of modular design, from simple components to entire models. The aim of this framework is to provide an efficient and streamlined pipeline for spiking neural networks. We showcase this framework by solving the sparse-reward cartpole problem with simple plasticity mechanisms. We hope that a framework compatible with traditional ML pipelines may accelerate research in the area, specifically for continuous and unbatched learning, akin to the one animals exhibit.

A key requirement for the development of effective learning representations is their evaluation and comparison to representations we know to be effective. In natural sensory domains, the community has viewed the brain as a source of inspiration and as an implicit benchmark for success. However, it has not been possible to directly test representational learning algorithms directly against the representations contained in neural systems. Here, we propose a new benchmark for visual representations on which we have directly tested the neural representation in multiple visual cortical areas in macaque (utilizing data from [Majaj et al., 2012]), and on which any computer vision algorithm that produces a feature space can be tested. The benchmark measures the effectiveness of the neural or machine representation by computing the classification loss on the ordered eigendecomposition of a kernel matrix [Montavon et al., 2011]. In our analysis we find that the neural representation in visual area IT is superior to visual area V4. In our analysis of representational learning algorithms, we find that three-layer models approach the representational performance of V4 and the algorithm in [Le et al., 2012] surpasses the performance of V4. Impressively, we find that a recent supervised algorithm [Krizhevsky et al., 2012] achieves performance comparable to that of IT for an intermediate level of image variation difficulty, and surpasses IT at a higher difficulty level. We believe this result represents a major milestone: it is the first learning algorithm we have found that exceeds our current estimate of IT representation performance. We hope that this benchmark will assist the community in matching the representational performance of visual cortex and will serve as an initial rallying point for further correspondence between representations derived in brains and machines.

Recent advancements have scaled neural networks to unprecedented sizes, achieving remarkable performance across a wide range of tasks. However, deploying these large-scale models on resource-constrained devices poses significant challenges due to substantial storage and computational requirements. Neural network pruning has emerged as an effective technique to mitigate these limitations by reducing model size and complexity. In this paper, we introduce an intuitive and interpretable pruning method based on activation statistics, rooted in information theory and statistical analysis. Our approach leverages the statistical properties of neuron activations to identify and remove weights with minimal contributions to neuron outputs. Specifically, we build a distribution of weight contributions across the dataset and utilize its parameters to guide the pruning process. Furthermore, we propose a Pruning-aware Training strategy that incorporates an additional regularization term to enhance the effectiveness of our pruning method. Extensive experiments on multiple datasets and network architectures demonstrate that our method consistently outperforms several baseline and state-of-the-art pruning techniques.

Modern neural recording techniques allow neuroscientists to obtain spiking activity of multiple neurons from different brain regions over long time periods, which requires new statistical methods to be developed for understanding structure of the large-scale data. In this paper, we develop a bi-clustering method to cluster the neural spiking activity spatially and temporally, according to their low-dimensional latent structures. The spatial (neuron) clusters are defined by the latent trajectories within each neural population, while the temporal (state) clusters are defined by (populationally) synchronous local linear dynamics shared with different periods. To flexibly extract the bi-clustering structure, we build the model non-parametrically, and develop an efficient Markov chain Monte Carlo (MCMC) algorithm to sample the posterior distributions of model parameters. Validating our proposed MCMC algorithm through simulations, we find the method can recover unknown parameters and true bi-clustering structures successfully. We then apply the proposed bi-clustering method to multi-regional neural recordings under different experiment settings, where we find that simultaneously considering latent trajectories and spatial-temporal clustering structures can provide us with a more accurate and interpretable result. Overall, the proposed method provides scientific insights for large-scale (counting) time series with elongated recording periods, and it can potentially have application beyond neuroscience.

The informational synthesis of neural structures, processes, parameters and characteristics that allow a unified description and modeling as neural machines of natural and artificial neural systems is presented. The general informational parameters as the global quantitative measure of the neural systems computing potential as absolute and relative neural power were proposed. Neural information organizing and processing follows the way in which nature manages neural information by developing functions, functionalities and circuits related to different internal or peripheral components and also to the whole system through a non-deterministic memorization, fragmentation and aggregation of afferent and efferent information, deep neural information processing representing multiple alternations of fragmentation and aggregation stages. The relevant neural characteristics were integrated into a neural machine type model that incorporates unitary also peripheral or interface components as the central ones. The proposed approach allows overcoming the technical constraints in artificial computational implementations of neural information processes and also provides a more relevant description of natural ones.

A central goal for mechanistic interpretability has been to identify the right units of analysis in large language models (LLMs) that causally explain their outputs. While early work focused on individual neurons, evidence that neurons often encode multiple concepts has motivated a shift toward analyzing directions in activation space. A key question is how to find directions that capture interpretable features in an unsupervised manner. Current methods rely on dictionary learning with sparse autoencoders (SAEs), commonly trained over residual stream activations to learn directions from scratch. However, SAEs often struggle in causal evaluations and lack intrinsic interpretability, as their learning is not explicitly tied to the computations of the model. Here, we tackle these limitations by directly decomposing MLP activations with semi-nonnegative matrix factorization (SNMF), such that the learned features are (a) sparse linear combinations of co-activated neurons, and (b) mapped to their activating inputs, making them directly interpretable. Experiments on Llama 3.1, Gemma 2 and GPT-2 show that SNMF derived features outperform SAEs and a strong supervised baseline (difference-in-means) on causal steering, while aligning with human-interpretable concepts. Further analysis reveals that specific neuron combinations are reused across semantically-related features, exposing a hierarchical structure in the MLP's activation space. Together, these results position SNMF as a simple and effective tool for identifying interpretable features and dissecting concept representations in LLMs.

Invasive brain-computer interfaces have garnered significant attention due to their high performance. The current intracranial stereoElectroEncephaloGraphy (sEEG) foundation models typically build univariate representations based on a single channel. Some of them further use Transformer to model the relationship among channels. However, due to the locality and specificity of brain computation, their performance on more difficult tasks, e.g., speech decoding, which demands intricate processing in specific brain regions, is yet to be fully investigated. We hypothesize that building multi-variate representations within certain brain regions can better capture the specific neural processing. To explore this hypothesis, we collect a well-annotated Chinese word-reading sEEG dataset, targeting language-related brain networks, over 12 subjects. Leveraging this benchmark dataset, we developed the Du-IN model that can extract contextual embeddings from specific brain regions through discrete codebook-guided mask modeling. Our model achieves SOTA performance on the downstream 61-word classification task, surpassing all baseline models. Model comparison and ablation analysis reveal that our design choices, including (i) multi-variate representation by fusing channels in vSMC and STG regions and (ii) self-supervision by discrete codebook-guided mask modeling, significantly contribute to these performances. Collectively, our approach, inspired by neuroscience findings, capitalizing on multi-variate neural representation from specific brain regions, is suitable for invasive brain modeling. It marks a promising neuro-inspired AI approach in BCI.

Networks capture our intuition about relationships in the world. They describe the friendships between Facebook users, interactions in financial markets, and synapses connecting neurons in the brain. These networks are richly structured with cliques of friends, sectors of stocks, and a smorgasbord of cell types that govern how neurons connect. Some networks, like social network friendships, can be directly observed, but in many cases we only have an indirect view of the network through the actions of its constituents and an understanding of how the network mediates that activity. In this work, we focus on the problem of latent network discovery in the case where the observable activity takes the form of a mutually-excitatory point process known as a Hawkes process. We build on previous work that has taken a Bayesian approach to this problem, specifying prior distributions over the latent network structure and a likelihood of observed activity given this network. We extend this work by proposing a discrete-time formulation and developing a computationally efficient stochastic variational inference (SVI) algorithm that allows us to scale the approach to long sequences of observations. We demonstrate our algorithm on the calcium imaging data used in the Chalearn neural connectomics challenge.

Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these complementary views through CLIP-style contrastive learning. Our vision branch processes a novel three-channel persistence image encoding unweighted, persistence-weighted, and radius-weighted topological densities via DINOv2-ViT-S. In parallel, a TreeLSTM encoder captures geometric and radial attributes from skeleton graphs. Both project to a shared embedding space trained with symmetric InfoNCE loss, augmented by persistence-space transformations that preserve topological semantics. Evaluated on six benchmarks (BIL-6, ACT-4, JML-4, N7, M1-Cell, M1-REG) spanning self-supervised and supervised settings, GraPHFormer achieves state-of-the-art performance on five benchmarks, significantly outperforming topology-only, graph-only, and morphometrics baselines. We demonstrate practical utility by discriminating glial morphologies across cortical regions and species, and detecting signatures of developmental and degenerative processes. Code: https://github.com/Uzshah/GraPHFormer

Measuring the quality of responses generated by LLMs is a challenging task, particularly when it comes to evaluating whether the response is aligned with human preference. A novel approach involves using the LLM itself to make evaluation and stabilizing the results through multiple independent evaluations, similar to a single-layer narrow LLM network. This network consists of a fixed number of neurons, with each neuron being the same LLM. In this paper, we draw upon the extensive research on deep neural networks to explore whether deeper and wider networks can lead to fairer evaluations. Specifically, inspired by the observation that different neurons in a neural network are responsible for detecting different concepts, we first adaptively generate as many neuron roles as possible for each evaluation sample. Each perspective corresponds to the role of a specific LLM neuron in the first layer. In subsequent layers, we follow the idea that higher layers in deep networks are responsible for more comprehensive features, each layer receives representations from all neurons in the previous layer, integrating the locally learned evaluation information to obtain a more comprehensive evaluation result. Interestingly, this network design resembles the process of academic paper reviewing. To validate the effectiveness of our method, we construct the largest and most diverse English evaluation benchmark LLMEval^2 for LLM evaluators, comprising 15 tasks, 8 abilities, and 2,553 samples. Experimental results demonstrate that a wider network (involving many reviewers) with 2 layers (one round of discussion) performs the best, improving kappa correlation coefficient from 0.28 to 0.34. We also leverage WideDeep to aid in the assessment of Chinese LLMs, which has accelerated the evaluation time by 4.6 times, resulting in a 60% cost saving. WideDeep achieves a remarkable 93% agreement level among humans.

Understanding what individual neurons encode is a core question in neuroscience. In primary visual cortex (V1), mathematical models (e.g., Gabor functions) capture neural selectivity, but no comparable framework exists for higher areas. We show that natural language can fill this role: across macaque V1 and V4, the selectivity of most neurons is captured by concise, verifiable semantic descriptions. Using digital twins of V1 and V4, we develop a closed-loop framework that translates each neuron's high- and low-activating images into dense captions, generates a semantic hypothesis and synthesized images, and verifies the hypothesis in silico. Descriptions range from oriented edges and spatial frequency in V1 to conjunctions of form, color, and texture in V4. In V4, images generated from activating and suppressing hypotheses drove 96.1% of neurons above the 95th and 97.6% below the 5th percentile of natural-image responses, respectively (vs. ~10% for random images); V1 activation results matched V4, while V1 suppression was less describable in language. Representational similarity analysis reveals partial alignment between neural activity, vision embeddings, and language embeddings, with vision most aligned to neural activity; alignment lost in the text bottleneck is recovered when hypotheses are rendered back into images, showing that linguistic compression is lossy yet semantically faithful. Together, these results show that combining generative models with neural digital twins enables interpretable, testable descriptions of neural function at scale, toward agentic scientific discovery.

The truthfulness of existing explanation methods in authentically elucidating the underlying model's decision-making process has been questioned. Existing methods have deviated from faithfully representing the model, thus susceptible to adversarial attacks. To address this, we propose a novel eXplainable AI (XAI) method called SRD (Sharing Ratio Decomposition), which sincerely reflects the model's inference process, resulting in significantly enhanced robustness in our explanations. Different from the conventional emphasis on the neuronal level, we adopt a vector perspective to consider the intricate nonlinear interactions between filters. We also introduce an interesting observation termed Activation-Pattern-Only Prediction (APOP), letting us emphasize the importance of inactive neurons and redefine relevance encapsulating all relevant information including both active and inactive neurons. Our method, SRD, allows for the recursive decomposition of a Pointwise Feature Vector (PFV), providing a high-resolution Effective Receptive Field (ERF) at any layer.

Mechanistic Interpretability (MI) promises a path toward fully understanding how neural networks make their predictions. Prior work demonstrates that even when trained to perform simple arithmetic, models can implement a variety of algorithms (sometimes concurrently) depending on initialization and hyperparameters. Does this mean neuron-level interpretability techniques have limited applicability? We argue that high-dimensional neural networks can learn low-dimensional representations of their training data that are useful beyond simply making good predictions. Such representations can be understood through the mechanistic interpretability lens and provide insights that are surprisingly faithful to human-derived domain knowledge. This indicates that such approaches to interpretability can be useful for deriving a new understanding of a problem from models trained to solve it. As a case study, we extract nuclear physics concepts by studying models trained to reproduce nuclear data.

Characterizing the relationship between neural population activity and behavioral data is a central goal of neuroscience. While latent variable models (LVMs) are successful in describing high-dimensional time-series data, they are typically only designed for a single type of data, making it difficult to identify structure shared across different experimental data modalities. Here, we address this shortcoming by proposing an unsupervised LVM which extracts temporally evolving shared and independent latents for distinct, simultaneously recorded experimental modalities. We do this by combining Gaussian Process Factor Analysis (GPFA), an interpretable LVM for neural spiking data with temporally smooth latent space, with Gaussian Process Variational Autoencoders (GP-VAEs), which similarly use a GP prior to characterize correlations in a latent space, but admit rich expressivity due to a deep neural network mapping to observations. We achieve interpretability in our model by partitioning latent variability into components that are either shared between or independent to each modality. We parameterize the latents of our model in the Fourier domain, and show improved latent identification using this approach over standard GP-VAE methods. We validate our model on simulated multi-modal data consisting of Poisson spike counts and MNIST images that scale and rotate smoothly over time. We show that the multi-modal GP-VAE (MM-GPVAE) is able to not only identify the shared and independent latent structure across modalities accurately, but provides good reconstructions of both images and neural rates on held-out trials. Finally, we demonstrate our framework on two real world multi-modal experimental settings: Drosophila whole-brain calcium imaging alongside tracked limb positions, and Manduca sexta spike train measurements from ten wing muscles as the animal tracks a visual stimulus.

The human brain is autonomously active, being characterized by a self-sustained neural activity which would be present even in the absence of external sensory stimuli. Here we study the interrelation between the self-sustained activity in autonomously active recurrent neural nets and external sensory stimuli. There is no a priori semantical relation between the influx of external stimuli and the patterns generated internally by the autonomous and ongoing brain dynamics. The question then arises when and how are semantic correlations between internal and external dynamical processes learned and built up? We study this problem within the paradigm of transient state dynamics for the neural activity in recurrent neural nets, i.e. for an autonomous neural activity characterized by an infinite time-series of transiently stable attractor states. We propose that external stimuli will be relevant during the sensitive periods, {\it viz} the transition period between one transient state and the subsequent semi-stable attractor. A diffusive learning signal is generated unsupervised whenever the stimulus influences the internal dynamics qualitatively. For testing we have presented to the model system stimuli corresponding to the bars and stripes problem. We found that the system performs a non-linear independent component analysis on its own, being continuously and autonomously active. This emergent cognitive capability results here from a general principle for the neural dynamics, the competition between neural ensembles.

Learning synaptic weights of spiking neural network (SNN) models that can reproduce target spike trains from provided neural firing data is a central problem in computational neuroscience and spike-based computing. The discovery of the optimal weight values can be posed as a supervised learning task wherein the weights of the model network are chosen to maximize the similarity between the target spike trains and the model outputs. It is still largely unknown whether optimizing spike train similarity of highly recurrent SNNs produces weight matrices similar to those of the ground truth model. To this end, we propose flexible heuristic supervised learning rules, termed Pre-Synaptic Pool Modification (PSPM), that rely on stochastic weight updates in order to produce spikes within a short window of the desired times and eliminate spikes outside of this window. PSPM improves spike train similarity for all-to-all SNNs and makes no assumption about the post-synaptic potential of the neurons or the structure of the network since no gradients are required. We test whether optimizing for spike train similarity entails the discovery of accurate weights and explore the relative contributions of local and homeostatic weight updates. Although PSPM improves similarity between spike trains, the learned weights often differ from the weights of the ground truth model, implying that connectome inference from spike data may require additional constraints on connectivity statistics. We also find that spike train similarity is sensitive to local updates, but other measures of network activity such as avalanche distributions, can be learned through synaptic homeostasis.

It has long been known in both neuroscience and AI that ``binding'' between neurons leads to a form of competitive learning where representations are compressed in order to represent more abstract concepts in deeper layers of the network. More recently, it was also hypothesized that dynamic (spatiotemporal) representations play an important role in both neuroscience and AI. Building on these ideas, we introduce Artificial Kuramoto Oscillatory Neurons (AKOrN) as a dynamical alternative to threshold units, which can be combined with arbitrary connectivity designs such as fully connected, convolutional, or attentive mechanisms. Our generalized Kuramoto updates bind neurons together through their synchronization dynamics. We show that this idea provides performance improvements across a wide spectrum of tasks such as unsupervised object discovery, adversarial robustness, calibrated uncertainty quantification, and reasoning. We believe that these empirical results show the importance of rethinking our assumptions at the most basic neuronal level of neural representation, and in particular show the importance of dynamical representations.

Our ability to use deep learning approaches to decipher neural activity would likely benefit from greater scale, in terms of both model size and datasets. However, the integration of many neural recordings into one unified model is challenging, as each recording contains the activity of different neurons from different individual animals. In this paper, we introduce a training framework and architecture designed to model the population dynamics of neural activity across diverse, large-scale neural recordings. Our method first tokenizes individual spikes within the dataset to build an efficient representation of neural events that captures the fine temporal structure of neural activity. We then employ cross-attention and a PerceiverIO backbone to further construct a latent tokenization of neural population activities. Utilizing this architecture and training framework, we construct a large-scale multi-session model trained on large datasets from seven nonhuman primates, spanning over 158 different sessions of recording from over 27,373 neural units and over 100 hours of recordings. In a number of different tasks, we demonstrate that our pretrained model can be rapidly adapted to new, unseen sessions with unspecified neuron correspondence, enabling few-shot performance with minimal labels. This work presents a powerful new approach for building deep learning tools to analyze neural data and stakes out a clear path to training at scale.

Large Language Models (LLMs) demonstrate human-level or even superior language abilities, effectively modeling syntactic structures, yet the specific computational modules responsible remain unclear. A key question is whether LLM behavioral capabilities stem from mechanisms akin to those in the human brain. To address these questions, we introduce the Hierarchical Frequency Tagging Probe (HFTP), a tool that utilizes frequency-domain analysis to identify neuron-wise components of LLMs (e.g., individual Multilayer Perceptron (MLP) neurons) and cortical regions (via intracranial recordings) encoding syntactic structures. Our results show that models such as GPT-2, Gemma, Gemma 2, Llama 2, Llama 3.1, and GLM-4 process syntax in analogous layers, while the human brain relies on distinct cortical regions for different syntactic levels. Representational similarity analysis reveals a stronger alignment between LLM representations and the left hemisphere of the brain (dominant in language processing). Notably, upgraded models exhibit divergent trends: Gemma 2 shows greater brain similarity than Gemma, while Llama 3.1 shows less alignment with the brain compared to Llama 2. These findings offer new insights into the interpretability of LLM behavioral improvements, raising questions about whether these advancements are driven by human-like or non-human-like mechanisms, and establish HFTP as a valuable tool bridging computational linguistics and cognitive neuroscience. This project is available at https://github.com/LilTiger/HFTP.

Compared with rate-based artificial neural networks, Spiking Neural Networks (SNN) provide a more biological plausible model for the brain. But how they perform supervised learning remains elusive. Inspired by recent works of Bengio et al., we propose a supervised learning algorithm based on Spike-Timing Dependent Plasticity (STDP) for a hierarchical SNN consisting of Leaky Integrate-and-fire (LIF) neurons. A time window is designed for the presynaptic neuron and only the spikes in this window take part in the STDP updating process. The model is trained on the MNIST dataset. The classification accuracy approach that of a Multilayer Perceptron (MLP) with similar architecture trained by the standard back-propagation algorithm.

Brain-computer interfaces (BCIs), transform neural signals in the brain into in-structions to control external devices. However, obtaining sufficient training data is difficult as well as limited. With the advent of advanced machine learning methods, the capability of brain-computer interfaces has been enhanced like never before, however, these methods require a large amount of data for training and thus require data augmentation of the limited data available. Here, we use spiking neural networks (SNN) as data generators. It is touted as the next-generation neu-ral network and is considered as one of the algorithms oriented to general artifi-cial intelligence because it borrows the neural information processing from bio-logical neurons. We use the SNN to generate neural spike information that is bio-interpretable and conforms to the intrinsic patterns in the original neural data. Ex-periments show that the model can directly synthesize new spike trains, which in turn improves the generalization ability of the BCI decoder. Both the input and output of the spiking neural model are spike information, which is a brain-inspired intelligence approach that can be better integrated with BCI in the future.

In theoretical neuroscience, recent work leverages deep learning tools to explore how some network attributes critically influence its learning dynamics. Notably, initial weight distributions with small (resp. large) variance may yield a rich (resp. lazy) regime, where significant (resp. minor) changes to network states and representation are observed over the course of learning. However, in biology, neural circuit connectivity could exhibit a low-rank structure and therefore differs markedly from the random initializations generally used for these studies. As such, here we investigate how the structure of the initial weights -- in particular their effective rank -- influences the network learning regime. Through both empirical and theoretical analyses, we discover that high-rank initializations typically yield smaller network changes indicative of lazier learning, a finding we also confirm with experimentally-driven initial connectivity in recurrent neural networks. Conversely, low-rank initialization biases learning towards richer learning. Importantly, however, as an exception to this rule, we find lazier learning can still occur with a low-rank initialization that aligns with task and data statistics. Our research highlights the pivotal role of initial weight structures in shaping learning regimes, with implications for metabolic costs of plasticity and risks of catastrophic forgetting.

Emergence of deep neural networks (DNNs) has raised enormous attention towards artificial neural networks (ANNs) once again. They have become the state-of-the-art models and have won different machine learning challenges. Although these networks are inspired by the brain, they lack biological plausibility, and they have structural differences compared to the brain. Spiking neural networks (SNNs) have been around for a long time, and they have been investigated to understand the dynamics of the brain. However, their application in real-world and complicated machine learning tasks were limited. Recently, they have shown great potential in solving such tasks. Due to their energy efficiency and temporal dynamics there are many promises in their future development. In this work, we reviewed the structures and performances of SNNs on image classification tasks. The comparisons illustrate that these networks show great capabilities for more complicated problems. Furthermore, the simple learning rules developed for SNNs, such as STDP and R-STDP, can be a potential alternative to replace the backpropagation algorithm used in DNNs.

Spiking neural networks (SNNs) possess energy-efficient potential due to event-based computation. However, supervised training of SNNs remains a challenge as spike activities are non-differentiable. Previous SNNs training methods can be generally categorized into two basic classes, i.e., backpropagation-like training methods and plasticity-based learning methods. The former methods are dependent on energy-inefficient real-valued computation and non-local transmission, as also required in artificial neural networks (ANNs), whereas the latter are either considered to be biologically implausible or exhibit poor performance. Hence, biologically plausible (bio-plausible) high-performance supervised learning (SL) methods for SNNs remain deficient. In this paper, we proposed a novel bio-plausible SNN model for SL based on the symmetric spike-timing dependent plasticity (sym-STDP) rule found in neuroscience. By combining the sym-STDP rule with bio-plausible synaptic scaling and intrinsic plasticity of the dynamic threshold, our SNN model implemented SL well and achieved good performance in the benchmark recognition task (MNIST dataset). To reveal the underlying mechanism of our SL model, we visualized both layer-based activities and synaptic weights using the t-distributed stochastic neighbor embedding (t-SNE) method after training and found that they were well clustered, thereby demonstrating excellent classification ability. Furthermore, to verify the robustness of our model, we trained it on another more realistic dataset (Fashion-MNIST), which also showed good performance. As the learning rules were bio-plausible and based purely on local spike events, our model could be easily applied to neuromorphic hardware for online training and may be helpful for understanding SL information processing at the synaptic level in biological neural systems.

Do large language models (LLMs) solve reasoning tasks by learning robust generalizable algorithms, or do they memorize training data? To investigate this question, we use arithmetic reasoning as a representative task. Using causal analysis, we identify a subset of the model (a circuit) that explains most of the model's behavior for basic arithmetic logic and examine its functionality. By zooming in on the level of individual circuit neurons, we discover a sparse set of important neurons that implement simple heuristics. Each heuristic identifies a numerical input pattern and outputs corresponding answers. We hypothesize that the combination of these heuristic neurons is the mechanism used to produce correct arithmetic answers. To test this, we categorize each neuron into several heuristic types-such as neurons that activate when an operand falls within a certain range-and find that the unordered combination of these heuristic types is the mechanism that explains most of the model's accuracy on arithmetic prompts. Finally, we demonstrate that this mechanism appears as the main source of arithmetic accuracy early in training. Overall, our experimental results across several LLMs show that LLMs perform arithmetic using neither robust algorithms nor memorization; rather, they rely on a "bag of heuristics".

Few algorithms for supervised training of spiking neural networks exist that can deal with patterns of multiple spikes, and their computational properties are largely unexplored. We demonstrate in a set of simulations that the ReSuMe learning algorithm can be successfully applied to layered neural networks. Input and output patterns are encoded as spike trains of multiple precisely timed spikes, and the network learns to transform the input trains into target output trains. This is done by combining the ReSuMe learning algorithm with multiplicative scaling of the connections of downstream neurons. We show in particular that layered networks with one hidden layer can learn the basic logical operations, including Exclusive-Or, while networks without hidden layer cannot, mirroring an analogous result for layered networks of rate neurons. While supervised learning in spiking neural networks is not yet fit for technical purposes, exploring computational properties of spiking neural networks advances our understanding of how computations can be done with spike trains.

Sparse computation offers a compelling solution for the inference of Large Language Models (LLMs) in low-resource scenarios by dynamically skipping the computation of inactive neurons. While traditional approaches focus on ReLU-based LLMs, leveraging zeros in activation values, we broaden the scope of sparse LLMs beyond zero activation values. We introduce a general method that defines neuron activation through neuron output magnitudes and a tailored magnitude threshold, demonstrating that non-ReLU LLMs also exhibit sparse activation. To find the most efficient activation function for sparse computation, we propose a systematic framework to examine the sparsity of LLMs from three aspects: the trade-off between sparsity and performance, the predictivity of sparsity, and the hardware affinity. We conduct thorough experiments on LLMs utilizing different activation functions, including ReLU, SwiGLU, ReGLU, and ReLU^2. The results indicate that models employing ReLU^2 excel across all three evaluation aspects, highlighting its potential as an efficient activation function for sparse LLMs. We will release the code to facilitate future research.

Human brains respond to semantic features of presented stimuli with different neurons. It is then curious whether modern deep neural networks admit a similar behavior pattern. Specifically, this paper finds a small cluster of neurons in a diffusion model corresponding to a particular subject. We call those neurons the concept neurons. They can be identified by statistics of network gradients to a stimulation connected with the given subject. The concept neurons demonstrate magnetic properties in interpreting and manipulating generation results. Shutting them can directly yield the related subject contextualized in different scenes. Concatenating multiple clusters of concept neurons can vividly generate all related concepts in a single image. A few steps of further fine-tuning can enhance the multi-concept capability, which may be the first to manage to generate up to four different subjects in a single image. For large-scale applications, the concept neurons are environmentally friendly as we only need to store a sparse cluster of int index instead of dense float32 values of the parameters, which reduces storage consumption by 90\% compared with previous subject-driven generation methods. Extensive qualitative and quantitative studies on diverse scenarios show the superiority of our method in interpreting and manipulating diffusion models.

The deep neural nets of modern artificial intelligence (AI) have not achieved defining features of biological intelligence, including abstraction, causal learning, and energy-efficiency. While scaling to larger models has delivered performance improvements for current applications, more brain-like capacities may demand new theories, models, and methods for designing artificial learning systems. Here, we argue that this opportunity to reassess insights from the brain should stimulate cooperation between AI research and theory-driven computational neuroscience (CN). To motivate a brain basis of neural computation, we present a dynamical view of intelligence from which we elaborate concepts of sparsity in network structure, temporal dynamics, and interactive learning. In particular, we suggest that temporal dynamics, as expressed through neural synchrony, nested oscillations, and flexible sequences, provide a rich computational layer for reading and updating hierarchical models distributed in long-term memory networks. Moreover, embracing agent-centered paradigms in AI and CN will accelerate our understanding of the complex dynamics and behaviors that build useful world models. A convergence of AI/CN theories and objectives will reveal dynamical principles of intelligence for brains and engineered learning systems. This article was inspired by our symposium on dynamical neuroscience and machine learning at the 6th Annual US/NIH BRAIN Initiative Investigators Meeting.

Deep neural networks (DNNs) have demonstrated state-of-the-art results on many pattern recognition tasks, especially vision classification problems. Understanding the inner workings of such computational brains is both fascinating basic science that is interesting in its own right - similar to why we study the human brain - and will enable researchers to further improve DNNs. One path to understanding how a neural network functions internally is to study what each of its neurons has learned to detect. One such method is called activation maximization (AM), which synthesizes an input (e.g. an image) that highly activates a neuron. Here we dramatically improve the qualitative state of the art of activation maximization by harnessing a powerful, learned prior: a deep generator network (DGN). The algorithm (1) generates qualitatively state-of-the-art synthetic images that look almost real, (2) reveals the features learned by each neuron in an interpretable way, (3) generalizes well to new datasets and somewhat well to different network architectures without requiring the prior to be relearned, and (4) can be considered as a high-quality generative method (in this case, by generating novel, creative, interesting, recognizable images).

Deep Learning has revolutionized various fields, including Computer Vision, Natural Language Processing, as well as Biomedical research. Within the field of neuroscience, specifically in electrophysiological neuroimaging, researchers are starting to explore leveraging deep learning to make predictions on their data without extensive feature engineering. The availability of large-scale datasets is a crucial aspect of allowing the experimentation of Deep Learning models. We are publishing the first large-scale clinical EEG dataset that simplifies data access and management for Deep Learning. This dataset contains eyes-closed EEG data prepared from a collection of 1,574 juvenile participants from the Healthy Brain Network. We demonstrate a use case integrating this framework, and discuss why providing such neuroinformatics infrastructure to the community is critical for future scientific discoveries.

The Spiking Neural Network (SNN) has attracted more and more attention recently. It adopts binary spike signals to transmit information. Benefitting from the information passing paradigm of SNNs, the multiplications of activations and weights can be replaced by additions, which are more energy-efficient. However, its ``Hard Reset" mechanism for the firing activity would ignore the difference among membrane potentials when the membrane potential is above the firing threshold, causing information loss. Meanwhile, quantifying the membrane potential to 0/1 spikes at the firing instants will inevitably introduce the quantization error thus bringing about information loss too. To address these problems, we propose to use the ``Soft Reset" mechanism for the supervised training-based SNNs, which will drive the membrane potential to a dynamic reset potential according to its magnitude, and Membrane Potential Rectifier (MPR) to reduce the quantization error via redistributing the membrane potential to a range close to the spikes. Results show that the SNNs with the ``Soft Reset" mechanism and MPR outperform their vanilla counterparts on both static and dynamic datasets.

Neuroscience employs diverse neuroimaging techniques, each offering distinct insights into brain activity, from electrophysiological recordings such as EEG, which have high temporal resolution, to hemodynamic modalities such as fMRI, which have increased spatial precision. However, integrating these heterogeneous data sources remains a challenge, which limits a comprehensive understanding of brain function. We present the Spatiotemporal Alignment of Multimodal Brain Activity (SAMBA) framework, which bridges the spatial and temporal resolution gaps across modalities by learning a unified latent space free of modality-specific biases. SAMBA introduces a novel attention-based wavelet decomposition for spectral filtering of electrophysiological recordings, graph attention networks to model functional connectivity between functional brain units, and recurrent layers to capture temporal autocorrelations in brain signal. We show that the training of SAMBA, aside from achieving translation, also learns a rich representation of brain information processing. We showcase this classify external stimuli driving brain activity from the representation learned in hidden layers of SAMBA, paving the way for broad downstream applications in neuroscience research and clinical contexts.

Spiking Neural Networks (SNNs) as one of the biology-inspired models have received much attention recently. It can significantly reduce energy consumption since they quantize the real-valued membrane potentials to 0/1 spikes to transmit information thus the multiplications of activations and weights can be replaced by additions when implemented on hardware. However, this quantization mechanism will inevitably introduce quantization error, thus causing catastrophic information loss. To address the quantization error problem, we propose a regularizing membrane potential loss (RMP-Loss) to adjust the distribution which is directly related to quantization error to a range close to the spikes. Our method is extremely simple to implement and straightforward to train an SNN. Furthermore, it is shown to consistently outperform previous state-of-the-art methods over different network architectures and datasets.

We present a simple mathematical model for the mammalian low visual pathway, taking into account its key elements: retina, lateral geniculate nucleus (LGN), primary visual cortex (V1). The analogies between the cortical level of the visual system and the structure of popular CNNs, used in image classification tasks, suggests the introduction of an additional preliminary convolutional module inspired to precortical neuronal circuits to improve robustness with respect to global light intensity and contrast variations in the input images. We validate our hypothesis on the popular databases MNIST, FashionMNIST and SVHN, obtaining significantly more robust CNNs with respect to these variations, once such extra module is added.

Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function. Overall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

Spiking Neural Networks (SNNs) offer a promising, biologically inspired approach for processing spatiotemporal data, particularly for time series forecasting. However, conventional neuron models like the Leaky Integrate-and-Fire (LIF) struggle to capture long-term dependencies and effectively process multi-scale temporal dynamics. To overcome these limitations, we introduce the Temporal Segment Leaky Integrate-and-Fire (TS-LIF) model, featuring a novel dual-compartment architecture. The dendritic and somatic compartments specialize in capturing distinct frequency components, providing functional heterogeneity that enhances the neuron's ability to process both low- and high-frequency information. Furthermore, the newly introduced direct somatic current injection reduces information loss during intra-neuronal transmission, while dendritic spike generation improves multi-scale information extraction. We provide a theoretical stability analysis of the TS-LIF model and explain how each compartment contributes to distinct frequency response characteristics. Experimental results show that TS-LIF outperforms traditional SNNs in time series forecasting, demonstrating better accuracy and robustness, even with missing data. TS-LIF advances the application of SNNs in time-series forecasting, providing a biologically inspired approach that captures complex temporal dynamics and offers potential for practical implementation in diverse forecasting scenarios. The source code is available at https://github.com/kkking-kk/TS-LIF.

In the mid-twentieth century, mathematician and polymath John von Neumann created a computational system on an array of cells as a simple model of the human brain, where each cell had one of a finite set of roles or states that he predicted would be modelled by a diffusion process. In this work, we show that such a system, when developed in a modern deep learning setting, enables the construction of an artificial neuron having specialized roles that can be learnt. We refer to this neuron as the Von Neumann neuron, and the resulting neural network from such neurons result in a self-engineered design whose architecture is only dependent on the structure and locations of its inputs and outputs on this cellular array. The mathematical framework for these Von Neumann Networks (VNNs) is also constructed and shows that they are based on the extension of neural operators and the learning of Green's functions with convolutions on a cellular topology having a diffusion signature. We also prove that these VNNs are part of a more general computational system called Cellular Machines that are computationally universal. Initial experiments show that VNN based multi-layered perceptrons outperform their equivalent deep learning variant on basic tasks, while being more parameter efficient and are capable of learning new types of tasks. This includes the ability to solve for and construct an extension of the Von Neumann (hardware) architecture common to all modern computers to cells and suggests new opportunities that could be explored.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Despite their remarkable success and deployment across diverse workflows, language models sometimes produce untruthful responses. Our limited understanding of how truthfulness is mechanistically encoded within these models jeopardizes their reliability and safety. In this paper, we propose a method for identifying representations of truthfulness at the neuron level. We show that language models contain truth neurons, which encode truthfulness in a subject-agnostic manner. Experiments conducted across models of varying scales validate the existence of truth neurons, confirming that the encoding of truthfulness at the neuron level is a property shared by many language models. The distribution patterns of truth neurons over layers align with prior findings on the geometry of truthfulness. Selectively suppressing the activations of truth neurons found through the TruthfulQA dataset degrades performance both on TruthfulQA and on other benchmarks, showing that the truthfulness mechanisms are not tied to a specific dataset. Our results offer novel insights into the mechanisms underlying truthfulness in language models and highlight potential directions toward improving their trustworthiness and reliability.

This study introduces BrainTransformers, an innovative Large Language Model (LLM) implemented using Spiking Neural Networks (SNN). Our key contributions include: (1) designing SNN-compatible Transformer components such as SNNMatmul, SNNSoftmax, and SNNSiLU; (2) implementing an SNN approximation of the SiLU activation function; and (3) developing a Synapsis module to simulate synaptic plasticity. Our 3-billion parameter model, BrainTransformers-3B-Chat, demonstrates competitive performance across various benchmarks, including MMLU (63.2), BBH (54.1), ARC-C (54.3), and GSM8K (76.3), while potentially offering improved energy efficiency and biological plausibility. The model employs a three-stage training approach, including SNN-specific neuronal synaptic plasticity training. This research opens new avenues for brain-like AI systems in natural language processing and neuromorphic computing. Future work will focus on hardware optimization, developing specialized SNN fine-tuning tools, and exploring practical applications in energy-efficient computing environments.

We propose NEURONA, a neuro-symbolic framework for fMRI decoding and concept grounding in neural activity. Leveraging image- and video-based fMRI question-answering datasets, NEURONA learns to decode interacting concepts from visual stimuli based on patterns of fMRI responses, integrating symbolic reasoning and compositional execution with fMRI grounding across brain regions. We demonstrate that incorporating structural priors (e.g., compositional predicate-argument dependencies between concepts) into the decoding process significantly improves both decoding accuracy over precise queries, and notably, generalization to unseen queries at test time. With NEURONA, we highlight neuro-symbolic frameworks as promising tools for understanding neural activity.

Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good gray-white matter contrast for 3D reconstruction. This precludes the analysis of most brain MRI scans acquired for clinical purposes. Analyzing such scans would enable neuroimaging studies with sample sizes that cannot be achieved with current research datasets, particularly for underrepresented populations and rare diseases. Here we present the first method for cortical reconstruction, registration, parcellation, and thickness estimation for clinical brain MRI scans of any resolution and pulse sequence. The methods has a learning component and a classical optimization module. The former uses domain randomization to train a CNN that predicts an implicit representation of the white matter and pial surfaces (a signed distance function) at 1mm isotropic resolution, independently of the pulse sequence and resolution of the input. The latter uses geometry processing to place the surfaces while accurately satisfying topological and geometric constraints, thus enabling subsequent parcellation and thickness estimation with existing methods. We present results on 5mm axial FLAIR scans from ADNI and on a highly heterogeneous clinical dataset with 5,000 scans. Code and data are publicly available at https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical