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Jul 21

Structure and Redundancy in Large Language Models: A Spectral Study via Random Matrix Theory

This thesis addresses two persistent and closely related challenges in modern deep learning, reliability and efficiency, through a unified framework grounded in Spectral Geometry and Random Matrix Theory (RMT). As deep networks and large language models continue to scale, their internal behavior becomes increasingly opaque, leading to hallucinations, fragile generalization under distribution shift, and growing computational and energy demands. By analyzing the eigenvalue dynamics of hidden activations across layers and inputs, this work shows that spectral statistics provide a compact, stable, and interpretable lens on model behavior, capable of separating structured, causal representations from noise-dominated variability. Within this framework, the first contribution, EigenTrack, introduces a real-time method for detecting hallucinations and out-of-distribution behavior in large language and vision-language models. EigenTrack transforms streaming activations into spectral descriptors such as entropy, variance, and deviations from the Marchenko-Pastur baseline, and models their temporal evolution using lightweight recurrent classifiers, enabling early detection of reliability failures before they appear in model outputs while offering interpretable insight into representation dynamics. The second contribution, RMT-KD, presents a principled approach to compressing deep networks via random matrix theoretic knowledge distillation. By interpreting outlier eigenvalues in activation spectra as carriers of task-relevant information, RMT-KD progressively projects networks onto lower-dimensional subspaces through iterative self-distillation, yielding significantly more compact and energy-efficient models while preserving accuracy and dense, hardware-friendly structure.

  • 1 authors
·
Feb 25

CGM-JEPA: Learning Consistent Continuous Glucose Monitor Representations via Predictive Self-Supervised Pretraining

Continuous Glucose Monitoring (CGM) can detect early metabolic subphenotypes (insulin resistance, IR; β-cell dysfunction), but population-scale deployment faces two coupled problems. First, the same physiological state appears through multiple views (CGM time series, venous OGTT, Glucodensity summaries), so single-view representations fail to transfer when deployment shifts the modality or setting. Second, baselines perform inconsistently across these shifts. Both problems point to one remedy: representations that abstract away from any single view to capture higher-level temporal and distributional structure. We propose CGM-JEPA, a self-supervised pretraining framework which predicts masked latent representations rather than raw values, yielding abstraction that transfers across modalities. X-CGM-JEPA adds a masked Glucodensity cross-view objective for complementary distributional information. We pretrain on sim389k unlabeled CGM readings from 228 subjects and evaluate on two clinical cohorts (N=27 and N=17 public-release subsets) across three regimes (cohort generalization, venous-to-CGM transfer, home CGM) under 20-iteration times 2-fold cross-validation. X-CGM-JEPA ranks first or second on AUROC for both endpoints across all three regimes while no baseline does, exceeding the strongest baseline by up to +6.5 pp in cohort generalization and +3.6 pp in venous-to-CGM transfer (paired Wilcoxon, p<0.001). Under modality shift, it matches mean AUROC while redistributing toward weaker subgroups (ethnicity AUROC gap shrinks 25-54%); on sparse in-domain venous data, the distributional view lifts label-aware clustering (ARI +39%, NMI +40%). Code and weights: https://github.com/cruiseresearchgroup/CGM-JEPA

google Google
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Apr 30 2

SHOVIR: A Benchmark for Evaluating Vision Shortcut Learning in Radiology Report Generation

Current evaluation protocols for Vision-Language Models (VLMs) in Radiology Report Generation (RRG) rely on report-level metrics that measure lexical overlap or aggregate clinical correctness. However, such metrics do not test whether individual diagnostic statements stem from the actual pathological evidence visible in the image. This allows models to achieve competitive scores by exploiting learned priors or spurious correlations, a failure mode we refer to as vision shortcut. We introduce SHOVIR, a benchmark for evaluating vision shortcut behavior in RRG. SHOVIR extends two spatially annotated chest X-ray datasets, MIMIC-CXR and PadChest-GR, with per-box CheXpert labels, and defines image-level and disease-level occlusion experiments that contrast baseline performance on clean images against localized, region-specific perturbations. Comparing predictions across these conditions isolates two failure modes at the disease-class level: direct shortcuts, where a finding persists after its visual evidence is removed, and contextual shortcuts, where detection degrades once co-occurring pathologies are occluded despite the target region remaining intact. Benchmarking eight state-of-the-art VLMs, we find that shortcut behavior varies substantially across architectures and datasets. Models achieving the highest baseline report quality do not necessarily rank highest in spatial grounding, revealing that clinically fluent generation can coexist with shallow reliance on visual evidence. These findings expose a blind spot in current RRG evaluation and motivate region-aware assessment protocols.

  • 5 authors
·
Jun 28

A ResNet is All You Need? Modeling A Strong Baseline for Detecting Referable Diabetic Retinopathy in Fundus Images

Deep learning is currently the state-of-the-art for automated detection of referable diabetic retinopathy (DR) from color fundus photographs (CFP). While the general interest is put on improving results through methodological innovations, it is not clear how good these approaches perform compared to standard deep classification models trained with the appropriate settings. In this paper we propose to model a strong baseline for this task based on a simple and standard ResNet-18 architecture. To this end, we built on top of prior art by training the model with a standard preprocessing strategy but using images from several public sources and an empirically calibrated data augmentation setting. To evaluate its performance, we covered multiple clinically relevant perspectives, including image and patient level DR screening, discriminating responses by input quality and DR grade, assessing model uncertainties and analyzing its results in a qualitative manner. With no other methodological innovation than a carefully designed training, our ResNet model achieved an AUC = 0.955 (0.953 - 0.956) on a combined test set of 61007 test images from different public datasets, which is in line or even better than what other more complex deep learning models reported in the literature. Similar AUC values were obtained in 480 images from two separate in-house databases specially prepared for this study, which emphasize its generalization ability. This confirms that standard networks can still be strong baselines for this task if properly trained.

  • 5 authors
·
Oct 6, 2022

The Languini Kitchen: Enabling Language Modelling Research at Different Scales of Compute

The Languini Kitchen serves as both a research collective and codebase designed to empower researchers with limited computational resources to contribute meaningfully to the field of language modelling. We introduce an experimental protocol that enables model comparisons based on equivalent compute, measured in accelerator hours. The number of tokens on which a model is trained is defined by the model's throughput and the chosen compute class. Notably, this approach avoids constraints on critical hyperparameters which affect total parameters or floating-point operations. For evaluation, we pre-process an existing large, diverse, and high-quality dataset of books that surpasses existing academic benchmarks in quality, diversity, and document length. On it, we compare methods based on their empirical scaling trends which are estimated through experiments at various levels of compute. This work also provides two baseline models: a feed-forward model derived from the GPT-2 architecture and a recurrent model in the form of a novel LSTM with ten-fold throughput. While the GPT baseline achieves better perplexity throughout all our levels of compute, our LSTM baseline exhibits a predictable and more favourable scaling law. This is due to the improved throughput and the need for fewer training tokens to achieve the same decrease in test perplexity. Extrapolating the scaling laws leads of both models results in an intersection at roughly 50,000 accelerator hours. We hope this work can serve as the foundation for meaningful and reproducible language modelling research.

  • 8 authors
·
Sep 20, 2023 1

NOVA: A Benchmark for Anomaly Localization and Clinical Reasoning in Brain MRI

In many real-world applications, deployed models encounter inputs that differ from the data seen during training. Out-of-distribution detection identifies whether an input stems from an unseen distribution, while open-world recognition flags such inputs to ensure the system remains robust as ever-emerging, previously unknown categories appear and must be addressed without retraining. Foundation and vision-language models are pre-trained on large and diverse datasets with the expectation of broad generalization across domains, including medical imaging. However, benchmarking these models on test sets with only a few common outlier types silently collapses the evaluation back to a closed-set problem, masking failures on rare or truly novel conditions encountered in clinical use. We therefore present NOVA, a challenging, real-life evaluation-only benchmark of sim900 brain MRI scans that span 281 rare pathologies and heterogeneous acquisition protocols. Each case includes rich clinical narratives and double-blinded expert bounding-box annotations. Together, these enable joint assessment of anomaly localisation, visual captioning, and diagnostic reasoning. Because NOVA is never used for training, it serves as an extreme stress-test of out-of-distribution generalisation: models must bridge a distribution gap both in sample appearance and in semantic space. Baseline results with leading vision-language models (GPT-4o, Gemini 2.0 Flash, and Qwen2.5-VL-72B) reveal substantial performance drops across all tasks, establishing NOVA as a rigorous testbed for advancing models that can detect, localize, and reason about truly unknown anomalies.

  • 15 authors
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May 20, 2025 2

A Closer Look at AUROC and AUPRC under Class Imbalance

In machine learning (ML), a widespread adage is that the area under the precision-recall curve (AUPRC) is a superior metric for model comparison to the area under the receiver operating characteristic (AUROC) for binary classification tasks with class imbalance. This paper challenges this notion through novel mathematical analysis, illustrating that AUROC and AUPRC can be concisely related in probabilistic terms. We demonstrate that AUPRC, contrary to popular belief, is not superior in cases of class imbalance and might even be a harmful metric, given its inclination to unduly favor model improvements in subpopulations with more frequent positive labels. This bias can inadvertently heighten algorithmic disparities. Prompted by these insights, a thorough review of existing ML literature was conducted, utilizing large language models to analyze over 1.5 million papers from arXiv. Our investigation focused on the prevalence and substantiation of the purported AUPRC superiority. The results expose a significant deficit in empirical backing and a trend of misattributions that have fuelled the widespread acceptance of AUPRC's supposed advantages. Our findings represent a dual contribution: a significant technical advancement in understanding metric behaviors and a stark warning about unchecked assumptions in the ML community. All experiments are accessible at https://github.com/mmcdermott/AUC_is_all_you_need.

  • 5 authors
·
Jan 11, 2024

BrainAnytime: Anatomy-Aware Cross-Modal Pretraining for Brain Image Analysis with Arbitrary Modality Availability

Clinical diagnostic workups typically follow a modality escalation pathway: after initial clinical evaluation, clinicians begin with routine structural imaging (e.g., MRI), selectively add sequences such as FLAIR or T2 to refine the differential, and reserve molecular imaging (e.g., amyloid-PET) for cases that remain uncertain after standard evaluation. Consequently, patients are observed with heterogeneous and often incomplete modality subsets. However, most current AI models assume fixed data modalities as the model inputs. In this paper, we present BrainAnytime, a unified pretraining framework pretrained on 34,899 3D brain scans from five datasets that support brain image analysis under arbitrary modality availability spanning multi-sequence MRI and amyloid-PET. A single model accepts whatever imaging is available, from a lone T1 scan to a full multimodal workup. Pretraining learns structural-molecular correspondences between MRI and PET via cross-modal distillation (RCMD) and prioritizes disease-vulnerable anatomy via atlas-guided curriculum masking (PACM), all within a shared 3D masked autoencoder (Multi-MAE3D). Across four downstream tasks and five clinically motivated modality settings, BrainAnytime largely outperforms modality-specific models, missing-modality baselines, and large-scale brain MRI pretrained foundation models on most modality settings. Notably, it surpasses the strongest missing-modality baselines with relative improvements of 6.2% and 7.0% in average accuracy on CN vs. AD and CN vs. MCI classification, respectively. Code is available at https://github.com/SDH-Lab/BrainAnytime.

  • 7 authors
·
May 12

A Self-supervised Multimodal Deep Learning Approach to Differentiate Post-radiotherapy Progression from Pseudoprogression in Glioblastoma

Accurate differentiation of pseudoprogression (PsP) from True Progression (TP) following radiotherapy (RT) in glioblastoma (GBM) patients is crucial for optimal treatment planning. However, this task remains challenging due to the overlapping imaging characteristics of PsP and TP. This study therefore proposes a multimodal deep-learning approach utilizing complementary information from routine anatomical MR images, clinical parameters, and RT treatment planning information for improved predictive accuracy. The approach utilizes a self-supervised Vision Transformer (ViT) to encode multi-sequence MR brain volumes to effectively capture both global and local context from the high dimensional input. The encoder is trained in a self-supervised upstream task on unlabeled glioma MRI datasets from the open BraTS2021, UPenn-GBM, and UCSF-PDGM datasets to generate compact, clinically relevant representations from FLAIR and T1 post-contrast sequences. These encoded MR inputs are then integrated with clinical data and RT treatment planning information through guided cross-modal attention, improving progression classification accuracy. This work was developed using two datasets from different centers: the Burdenko Glioblastoma Progression Dataset (n = 59) for training and validation, and the GlioCMV progression dataset from the University Hospital Erlangen (UKER) (n = 20) for testing. The proposed method achieved an AUC of 75.3%, outperforming the current state-of-the-art data-driven approaches. Importantly, the proposed approach relies on readily available anatomical MRI sequences, clinical data, and RT treatment planning information, enhancing its clinical feasibility. The proposed approach addresses the challenge of limited data availability for PsP and TP differentiation and could allow for improved clinical decision-making and optimized treatment plans for GBM patients.

  • 22 authors
·
Feb 5, 2025

Compared to What? Baselines and Metrics for Counterfactual Prompting

Counterfactual prompting (i.e., perturbing a single factor and measuring output change) is widely used to evaluate things like LLM bias and CoT faithfulness. But in this work we argue that observed effects cannot be attributed to the targeted factor without accounting for baseline ``meaning-preserving'' modifications to text that establish general model sensitivity. This is because every counterfactual edit is a compound treatment that bundles the variable of interest with incidental surface-form variation; this violates treatment variation irrelevance. We observe prediction flip rates on MedQA of 14.9% when we surgically change patient gender. However, this is statistically indistinguishable from the flip rates induced by simply paraphrasing inputs (14.1%). In this case, it would therefore be unwarranted to conclude that the LLM is especially sensitive to patient gender. To account for this and robustly measure the effects of targeted interventions, we propose a framework in which we compare (via statistical testing) differences observed under target interventions to those induced by paraphrasing inputs. We then use this framework to revisit a analysis done on the MedPerturb dataset, which reported evidence of model sensitivity to patient demographics and stylistic cues. We find that these effects largely dissipate when we account for general model sensitivity, with only 5 of 120 tests reaching statistical significance. Applying the same framework to occupational biography classification, we detect clearly significant directional gender bias, showing that the framework identifies real directional effects even when they are small. We evaluate a range of metrics -- aggregate, per-sample distributional, and regression -- and find that per-sample metrics are dramatically more powerful than aggregate metrics and regression powerfully and uniquely characterizes effect direction and magnitude.

  • 4 authors
·
Apr 30

Benchmarking Neural Network Training Algorithms

Training algorithms, broadly construed, are an essential part of every deep learning pipeline. Training algorithm improvements that speed up training across a wide variety of workloads (e.g., better update rules, tuning protocols, learning rate schedules, or data selection schemes) could save time, save computational resources, and lead to better, more accurate, models. Unfortunately, as a community, we are currently unable to reliably identify training algorithm improvements, or even determine the state-of-the-art training algorithm. In this work, using concrete experiments, we argue that real progress in speeding up training requires new benchmarks that resolve three basic challenges faced by empirical comparisons of training algorithms: (1) how to decide when training is complete and precisely measure training time, (2) how to handle the sensitivity of measurements to exact workload details, and (3) how to fairly compare algorithms that require hyperparameter tuning. In order to address these challenges, we introduce a new, competitive, time-to-result benchmark using multiple workloads running on fixed hardware, the AlgoPerf: Training Algorithms benchmark. Our benchmark includes a set of workload variants that make it possible to detect benchmark submissions that are more robust to workload changes than current widely-used methods. Finally, we evaluate baseline submissions constructed using various optimizers that represent current practice, as well as other optimizers that have recently received attention in the literature. These baseline results collectively demonstrate the feasibility of our benchmark, show that non-trivial gaps between methods exist, and set a provisional state-of-the-art for future benchmark submissions to try and surpass.

  • 25 authors
·
Jun 12, 2023 1

Pressure-Testing Deception Probes in LLMs: Scaling, Robustness, and the Geometry of Deceptive Representations

Linear probes trained on LLM activations are increasingly proposed as deception-detection metrics, yet report AUROC exceeding 0.96 on clean benchmarks while collapsing under distributional shift. This paper systematically pressure-tests probe-based metrics across the Gemma 3 model family (1B-27B parameters), diagnosing why they fail rather than merely documenting that they fail. We test four hypotheses about deception encoding: (1) single linear direction, (2) multi-dimensional subspace, (3) convex conic hull, (4) entropy proxy. Our design includes cross-domain transfer matrices, multi-dimensional probe analysis with permutation null baselines, entropy-residualization tests, and distractor evaluations across 8 stylistic shifts. We find that: (a) probes achieve near-perfect AUROC (>=0.998) on clean data but collapse under stylistic shifts; style-augmented probes recover near-perfect detection (mean AUROC 0.979-0.983) on unseen styles; (b) the single-direction hypothesis is rejected (k=1 captures only 0.61-0.80 AUROC), with cross-domain transfer failure confirmed as geometric rather than layer-mismatch-driven; (c) the entropy-proxy hypothesis is rejected (max |rho|=0.454, max Delta-AUROC after residualization=0.004); and (d) deception does not form a significant linear subspace (per-domain k*=0), yet multi-dimensional probes (k>=5) recover the signal through distributed sub-threshold features. Probe fragility reflects distributional narrowness rather than an architectural limitation: style-augmented probes recover near-perfect detection at both 4B and 27B, establishing that the inverse scaling pattern is a training-distribution artifact rather than a genuine scale-dependent phenomenon.

  • 1 authors
·
May 27 2

Measuring the Symmetry--Data Exchange Rate

Equivariance theory predicts that an architectural symmetry prior reduces sample complexity by a factor of |G|; this is widely cited but rarely measured as a scaling law with controls that separate the prior from its confounds. On a controlled C_n-symmetric task, we report three findings. First, a wrong-group control with identical orbit size and matched compute is worse than no constraint (joint pairwise CI [+0.79, +3.26] excludes zero, robust across estimators); misaligned constraint is actively harmful, not merely unhelpful. Second, an augmentation baseline equipped with test-time orbit averaging matches the equivariant model exactly -- bit-identical per-epoch validation curves across matched cells -- so the architecture-vs-augmentation gap is conditional on asymmetric test-time computation, not unconditional. Third, the relative exchange rate beta_diff = 1.28 is consistent in sign and order of magnitude with the theoretical 1.0 (single-level CI [+0.92, +2.05]); the more conservative two-level bootstrap (seeds x group sizes) widens this to [-0.63, +1.72], including zero, and a finer-N replication on a sqrt(2)-spaced grid is inconclusive (point estimate -0.82). The methodological contributions -- the relative-rate estimator that cancels the shared-difficulty confound, the wrong-group control, and a pre-specified failure taxonomy -- transfer to any inductive bias whose strength can be parameterised. Honest scoping: the primary estimator beta_diff was adopted post-hoc after the initial analysis revealed a positive-slope identifiability problem; the design was never externally pre-registered; and the headline number rests on an OLS slope over seven group sizes on a coarse N grid. This is an exploratory study, not a confirmatory measurement; the wrong-group result is the cleanest finding and the one we report with the most confidence. A registered replication on fresh seeds is future work.

  • 1 authors
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May 30 2

EpiCurveBench: Evaluating VLMs on Epidemic Curve Digitization

Chart-to-data extraction with vision-language models (VLMs) is increasingly evaluated on benchmarks that show diminishing headroom (frontier VLMs exceed 89% on ChartQA) and with metrics that treat extracted points as unordered key-value pairs, ignoring the temporal structure of time series and penalizing small alignment shifts as catastrophic failures. We address both gaps with EpiCurveBench, a benchmark of 1,000 real-world epidemic curve images curated from diverse public-health sources, and EpiCurveSimilarity (ECS), an evaluation metric that aligns predicted and ground-truth series via dynamic programming, tolerating local temporal shifts and gaps while penalizing them proportionally. Evaluating six methods--three frontier closed VLMs, one open VLM, and two specialized chart-extraction systems--we find the strongest model reaches only 52.3% ECS, and that ECS spreads the four general-purpose VLMs over a 25-point range where key-value metrics (RMS, SCRM) compress them into a 5-point band. We further validate ECS against four downstream epidemiological summary statistics, finding that higher ECS predicts smaller errors in total counts, peak timing, and peak magnitude, and higher growth-rate fidelity; across all four, ECS correlates 1.5--3.6 times more strongly than Dynamic Time Warping, which lacks a gap penalty and therefore cannot distinguish a truncated prediction from a temporally faithful one. EpiCurveBench targets a high-impact public-health application--unlocking decades of outbreak data trapped in published figures--but the benchmark and metric apply directly to any structured time-series chart-extraction setting.

  • 2 authors
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May 25

Disentanglement and Assessment of Shortcuts in Ophthalmological Retinal Imaging Exams

Diabetic retinopathy (DR) is a leading cause of vision loss in working-age adults. While screening reduces the risk of blindness, traditional imaging is often costly and inaccessible. Artificial intelligence (AI) algorithms present a scalable diagnostic solution, but concerns regarding fairness and generalization persist. This work evaluates the fairness and performance of image-trained models in DR prediction, as well as the impact of disentanglement as a bias mitigation technique, using the diverse mBRSET fundus dataset. Three models, ConvNeXt V2, DINOv2, and Swin V2, were trained on macula images to predict DR and sensitive attributes (SAs) (e.g., age and gender/sex). Fairness was assessed between subgroups of SAs, and disentanglement was applied to reduce bias. All models achieved high DR prediction performance in diagnosing (up to 94% AUROC) and could reasonably predict age and gender/sex (91% and 77% AUROC, respectively). Fairness assessment suggests disparities, such as a 10% AUROC gap between age groups in DINOv2. Disentangling SAs from DR prediction had varying results, depending on the model selected. Disentanglement improved DINOv2 performance (2% AUROC gain), but led to performance drops in ConvNeXt V2 and Swin V2 (7% and 3%, respectively). These findings highlight the complexity of disentangling fine-grained features in fundus imaging and emphasize the importance of fairness in medical imaging AI to ensure equitable and reliable healthcare solutions.

  • 5 authors
·
Jul 13, 2025

Queries, Representation & Detection: The Next 100 Model Fingerprinting Schemes

The deployment of machine learning models in operational contexts represents a significant investment for any organisation. Consequently, the risk of these models being misappropriated by competitors needs to be addressed. In recent years, numerous proposals have been put forth to detect instances of model stealing. However, these proposals operate under implicit and disparate data and model access assumptions; as a consequence, it remains unclear how they can be effectively compared to one another. Our evaluation shows that a simple baseline that we introduce performs on par with existing state-of-the-art fingerprints, which, on the other hand, are much more complex. To uncover the reasons behind this intriguing result, this paper introduces a systematic approach to both the creation of model fingerprinting schemes and their evaluation benchmarks. By dividing model fingerprinting into three core components -- Query, Representation and Detection (QuRD) -- we are able to identify sim100 previously unexplored QuRD combinations and gain insights into their performance. Finally, we introduce a set of metrics to compare and guide the creation of more representative model stealing detection benchmarks. Our approach reveals the need for more challenging benchmarks and a sound comparison with baselines. To foster the creation of new fingerprinting schemes and benchmarks, we open-source our fingerprinting toolbox.

  • 5 authors
·
Dec 17, 2024

Calibrated Confidence Estimation for Tabular Question Answering

Large language models (LLMs) are increasingly deployed for tabular question answering, yet calibration on structured data is largely unstudied. This paper presents the first systematic comparison of five confidence estimation methods across five frontier LLMs and two tabular QA benchmarks. All models are severely overconfident (smooth ECE 0.35-0.64 versus 0.10-0.15 reported for textual QA). A consistent self-evaluation versus perturbation dichotomy replicates across both benchmarks and all four fully-covered models: self-evaluation methods (verbalized, P(True)) achieve AUROC 0.42-0.76, while perturbation methods (semantic entropy, self-consistency, and our Multi-Format Agreement) achieve AUROC 0.78-0.86. Per-model paired bootstrap tests reject the null at p<0.001 after Holm-Bonferroni correction, and a 3-seed check on GPT-4o-mini gives a per-seed standard deviation of only 0.006. The paper proposes Multi-Format Agreement (MFA), which exploits the lossless and deterministic serialization variation unique to structured data (Markdown, HTML, JSON, CSV) to estimate confidence at 20% lower API cost than sampling baselines. MFA reduces ECE by 44-63%, generalizes across all four models on TableBench (mean AUROC 0.80), and combines complementarily with sampling: an MFA + self-consistency ensemble lifts AUROC from 0.74 to 0.82. A secondary contribution, structure-aware recalibration, improves AUROC by +10 percentage points over standard post-hoc methods.

  • 1 authors
·
Apr 13

Hallucination Score: Towards Mitigating Hallucinations in Generative Image Super-Resolution

Generative super-resolution (GSR) currently sets the state-of-the-art in terms of perceptual image quality, overcoming the "regression-to-the-mean" blur of prior non-generative models. However, from a human perspective, such models do not fully conform to the optimal balance between quality and fidelity. Instead, a different class of artifacts, in which generated details fail to perceptually match the low resolution image (LRI) or ground-truth image (GTI), is a critical but under studied issue in GSR, limiting its practical deployments. In this work, we focus on measuring, analyzing, and mitigating these artifacts (i.e., "hallucinations"). We observe that hallucinations are not well-characterized with existing image metrics or quality models, as they are orthogonal to both exact fidelity and no-reference quality. Instead, we take advantage of a multimodal large language model (MLLM) by constructing a prompt that assesses hallucinatory visual elements and generates a "Hallucination Score" (HS). We find that our HS is closely aligned with human evaluations, and also provides complementary insights to prior image metrics used for super-resolution (SR) models. In addition, we find certain deep feature distances have strong correlations with HS. We therefore propose to align the GSR models by using such features as differentiable reward functions to mitigate hallucinations.

  • 6 authors
·
Jul 18, 2025

Counting Hallucinations in Diffusion Models

Diffusion probabilistic models (DPMs) have demonstrated remarkable progress in generative tasks, such as image and video synthesis. However, they still often produce hallucinated samples (hallucinations) that conflict with real-world knowledge, such as generating an implausible duplicate cup floating beside another cup. Despite their prevalence, the lack of feasible methodologies for systematically quantifying such hallucinations hinders progress in addressing this challenge and obscures potential pathways for designing next-generation generative models under factual constraints. In this work, we bridge this gap by focusing on a specific form of hallucination, which we term counting hallucination, referring to the generation of an incorrect number of instances or structured objects, such as a hand image with six fingers, despite such patterns being absent from the training data. To this end, we construct a dataset suite CountHalluSet, with well-defined counting criteria, comprising ToyShape, SimObject, and RealHand. Using these datasets, we develop a standardized evaluation protocol for quantifying counting hallucinations, and systematically examine how different sampling conditions in DPMs, including solver type, ODE solver order, sampling steps, and initial noise, affect counting hallucination levels. Furthermore, we analyze their correlation with common evaluation metrics such as FID, revealing that this widely used image quality metric fails to capture counting hallucinations consistently. This work aims to take the first step toward systematically quantifying hallucinations in diffusion models and offer new insights into the investigation of hallucination phenomena in image generation.

  • 10 authors
·
Dec 12, 2025

OCTolyzer: Fully automatic toolkit for segmentation and feature extracting in optical coherence tomography and scanning laser ophthalmoscopy data

Optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) of the eye has become essential to ophthalmology and the emerging field of oculomics, thus requiring a need for transparent, reproducible, and rapid analysis of this data for clinical research and the wider research community. Here, we introduce OCTolyzer, the first open-source toolkit for retinochoroidal analysis in OCT/SLO data. It features two analysis suites for OCT and SLO data, facilitating deep learning-based anatomical segmentation and feature extraction of the cross-sectional retinal and choroidal layers and en face retinal vessels. We describe OCTolyzer and evaluate the reproducibility of its OCT choroid analysis. At the population level, metrics for choroid region thickness were highly reproducible, with a mean absolute error (MAE)/Pearson correlation for macular volume choroid thickness (CT) of 6.7mum/0.99, macular B-scan CT of 11.6mum/0.99, and peripapillary CT of 5.0mum/0.99. Macular choroid vascular index (CVI) also showed strong reproducibility, with MAE/Pearson for volume CVI yielding 0.0271/0.97 and B-scan CVI 0.0130/0.91. At the eye level, measurement noise for regional and vessel metrics was below 5% and 20% of the population's variability, respectively. Outliers were caused by poor-quality B-scans with thick choroids and invisible choroid-sclera boundary. Processing times on a laptop CPU were under three seconds for macular/peripapillary B-scans and 85 seconds for volume scans. OCTolyzer can convert OCT/SLO data into reproducible and clinically meaningful retinochoroidal features and will improve the standardisation of ocular measurements in OCT/SLO image analysis, requiring no specialised training or proprietary software to be used. OCTolyzer is freely available here: https://github.com/jaburke166/OCTolyzer.

  • 12 authors
·
Jul 19, 2024

AUTOHALLUSION: Automatic Generation of Hallucination Benchmarks for Vision-Language Models

Large vision-language models (LVLMs) hallucinate: certain context cues in an image may trigger the language module's overconfident and incorrect reasoning on abnormal or hypothetical objects. Though a few benchmarks have been developed to investigate LVLM hallucinations, they mainly rely on hand-crafted corner cases whose fail patterns may hardly generalize, and finetuning on them could undermine their validity. These motivate us to develop the first automatic benchmark generation approach, AUTOHALLUSION, that harnesses a few principal strategies to create diverse hallucination examples. It probes the language modules in LVLMs for context cues and uses them to synthesize images by: (1) adding objects abnormal to the context cues; (2) for two co-occurring objects, keeping one and excluding the other; or (3) removing objects closely tied to the context cues. It then generates image-based questions whose ground-truth answers contradict the language module's prior. A model has to overcome contextual biases and distractions to reach correct answers, while incorrect or inconsistent answers indicate hallucinations. AUTOHALLUSION enables us to create new benchmarks at the minimum cost and thus overcomes the fragility of hand-crafted benchmarks. It also reveals common failure patterns and reasons, providing key insights to detect, avoid, or control hallucinations. Comprehensive evaluations of top-tier LVLMs, e.g., GPT-4V(ision), Gemini Pro Vision, Claude 3, and LLaVA-1.5, show a 97.7% and 98.7% success rate of hallucination induction on synthetic and real-world datasets of AUTOHALLUSION, paving the way for a long battle against hallucinations.

  • 12 authors
·
Jun 16, 2024 4

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.

  • 427 authors
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Apr 22, 2019

Accelerometry-Derived Digital Biomarkers for Cardiometabolic Risk: A Population-Representative Tabular Benchmark with Uncertainty Quantification

Structured tabular data dominates clinical medicine, yet existing benchmarks fail to reflect real-world properties like complex survey sampling, demographic oversampling, and subgroup fairness. We introduce the NHANES Accelerometry Cardiometabolic Benchmark, derived from NHANES 2003-2006, comprising 1,381 adults with hip-worn accelerometry, fasting laboratory biomarkers, dietary intake, and anthropometrics. We evaluate three tabular learning methods -- ridge regression, XGBoost, and the foundation model TabPFN v2 -- to predict glycated haemoglobin (HbA1c), fasting triglycerides, and C-reactive protein (CRP) from activity phenotypes and lifestyle covariates. TabPFN v2 achieves the best overall performance (HbA1c R^2=0.156, CRP R^2=0.383), while triglycerides remain largely unpredictable (R^2 < 0.05), consistent with known genetic dominance. We apply split conformal prediction to generate distribution-free 90% prediction intervals and evaluate demographic coverage equity across sex and race/ethnicity subgroups. Marginal coverage aligns with the 90% target for CRP and HbA1c but falls below for triglycerides. At the subgroup level, we observe localized undercoverage (e.g., HbA1c for Mexican American participants), illustrating the gap between marginal guarantees and the conditional coverage required for clinical fairness. Code and data are at https://github.com/felizzi/nhanes-accel-cardiometabolic-benchmark.

  • 1 authors
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Jun 28

BioDCASE 2026 Challenge Baseline for Cross-Domain Mosquito Species Classification

Mosquito-borne diseases affect more than one billion people each year and cause close to one million deaths. Traditional surveillance methods rely on traps and manual identification that are slow, labor-intensive, and difficult to scale. Audio-based mosquito monitoring offers a non-destructive, lower-cost, and more scalable complement to trap-based surveillance, but reliable species classification remains difficult under real-world recording conditions. Mosquito flight tones are narrow-band, often low in signal-to-noise ratio, and easily masked by background noise, and recordings for several epidemiologically relevant species remain limited, creating pronounced class imbalance. Variation across devices, environments, and collection protocols further increases the difficulty of robust classification. Such variation can cause models to rely on domain-specific recording artefacts rather than species-relevant acoustic cues, which makes transfer to new acquisition settings difficult. The BioDCASE 2026 Cross-Domain Mosquito Species Classification (CD-MSC) challenge is designed around this deployment problem by evaluating performance on both seen and unseen domains. This paper presents the official baseline system and evaluation pipeline as a simple, fully reproducible reference for the CD-MSC challenge task. The baseline uses log-mel features and a multitemporal resolution convolutional neural network (MTRCNN) with species and auxiliary domain outputs, together with complete training and test scripts. The baseline system performs strongly on seen domains but degrades markedly on unseen domains, showing that cross-domain generalisation, rather than within-domain recognition, is the central challenge for practical mosquito species classification from multi-source bioacoustic recordings.

  • 8 authors
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Mar 19

AdverX-Ray: Ensuring X-Ray Integrity Through Frequency-Sensitive Adversarial VAEs

Ensuring the quality and integrity of medical images is crucial for maintaining diagnostic accuracy in deep learning-based Computer-Aided Diagnosis and Computer-Aided Detection (CAD) systems. Covariate shifts are subtle variations in the data distribution caused by different imaging devices or settings and can severely degrade model performance, similar to the effects of adversarial attacks. Therefore, it is vital to have a lightweight and fast method to assess the quality of these images prior to using CAD models. AdverX-Ray addresses this need by serving as an image-quality assessment layer, designed to detect covariate shifts effectively. This Adversarial Variational Autoencoder prioritizes the discriminator's role, using the suboptimal outputs of the generator as negative samples to fine-tune the discriminator's ability to identify high-frequency artifacts. Images generated by adversarial networks often exhibit severe high-frequency artifacts, guiding the discriminator to focus excessively on these components. This makes the discriminator ideal for this approach. Trained on patches from X-ray images of specific machine models, AdverX-Ray can evaluate whether a scan matches the training distribution, or if a scan from the same machine is captured under different settings. Extensive comparisons with various OOD detection methods show that AdverX-Ray significantly outperforms existing techniques, achieving a 96.2% average AUROC using only 64 random patches from an X-ray. Its lightweight and fast architecture makes it suitable for real-time applications, enhancing the reliability of medical imaging systems. The code and pretrained models are publicly available.

  • 5 authors
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Feb 23, 2025