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Jul 6

Towards generalizable single-cell perturbation modeling via the Conditional Monge Gap

Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodological framework because it inherently accommodates the challenges of unpaired data induced by cell destruction during data acquisition. However, most existing OT approaches are incapable of conditioning on different treatment contexts (e.g., time, drug treatment, drug dosage, or cell type) and we still lack methods that unanimously show promising generalization performance to unseen treatments. Here, we propose the Conditional Monge Gap which learns OT maps conditionally on arbitrary covariates. We demonstrate its value in predicting single-cell perturbation responses conditional to one or multiple drugs, a drug dosage, or combinations thereof. We find that our conditional models achieve results comparable and sometimes even superior to the condition-specific state-of-the-art on scRNA-seq as well as multiplexed protein imaging data. Notably, by aggregating data across conditions we perform cross-task learning which unlocks remarkable generalization abilities to unseen drugs or drug dosages, widely outperforming other conditional models in capturing heterogeneity (i.e., higher moments) in the perturbed population. Finally, by scaling to hundreds of conditions and testing on unseen drugs, we narrow the gap between structure-based and effect-based drug representations, suggesting a promising path to the successful prediction of perturbation effects for unseen treatments.

  • 4 authors
·
Apr 11, 2025

The Monge Gap: A Regularizer to Learn All Transport Maps

Optimal transport (OT) theory has been been used in machine learning to study and characterize maps that can push-forward efficiently a probability measure onto another. Recent works have drawn inspiration from Brenier's theorem, which states that when the ground cost is the squared-Euclidean distance, the ``best'' map to morph a continuous measure in P(Rd) into another must be the gradient of a convex function. To exploit that result, [Makkuva+ 2020, Korotin+2020] consider maps T=nabla f_theta, where f_theta is an input convex neural network (ICNN), as defined by Amos+2017, and fit theta with SGD using samples. Despite their mathematical elegance, fitting OT maps with ICNNs raises many challenges, due notably to the many constraints imposed on theta; the need to approximate the conjugate of f_theta; or the limitation that they only work for the squared-Euclidean cost. More generally, we question the relevance of using Brenier's result, which only applies to densities, to constrain the architecture of candidate maps fitted on samples. Motivated by these limitations, we propose a radically different approach to estimating OT maps: Given a cost c and a reference measure rho, we introduce a regularizer, the Monge gap M^c_{rho}(T) of a map T. That gap quantifies how far a map T deviates from the ideal properties we expect from a c-OT map. In practice, we drop all architecture requirements for T and simply minimize a distance (e.g., the Sinkhorn divergence) between Tsharpmu and nu, regularized by M^c_rho(T). We study M^c_{rho}, and show how our simple pipeline outperforms significantly other baselines in practice.

  • 2 authors
·
Feb 9, 2023

Train longer, generalize better: closing the generalization gap in large batch training of neural networks

Background: Deep learning models are typically trained using stochastic gradient descent or one of its variants. These methods update the weights using their gradient, estimated from a small fraction of the training data. It has been observed that when using large batch sizes there is a persistent degradation in generalization performance - known as the "generalization gap" phenomena. Identifying the origin of this gap and closing it had remained an open problem. Contributions: We examine the initial high learning rate training phase. We find that the weight distance from its initialization grows logarithmically with the number of weight updates. We therefore propose a "random walk on random landscape" statistical model which is known to exhibit similar "ultra-slow" diffusion behavior. Following this hypothesis we conducted experiments to show empirically that the "generalization gap" stems from the relatively small number of updates rather than the batch size, and can be completely eliminated by adapting the training regime used. We further investigate different techniques to train models in the large-batch regime and present a novel algorithm named "Ghost Batch Normalization" which enables significant decrease in the generalization gap without increasing the number of updates. To validate our findings we conduct several additional experiments on MNIST, CIFAR-10, CIFAR-100 and ImageNet. Finally, we reassess common practices and beliefs concerning training of deep models and suggest they may not be optimal to achieve good generalization.

  • 3 authors
·
May 24, 2017

The Price of Differential Privacy under Continual Observation

We study the accuracy of differentially private mechanisms in the continual release model. A continual release mechanism receives a sensitive dataset as a stream of T inputs and produces, after receiving each input, an accurate output on the obtained inputs. In contrast, a batch algorithm receives the data as one batch and produces a single output. We provide the first strong lower bounds on the error of continual release mechanisms. In particular, for two fundamental problems that are widely studied and used in the batch model, we show that the worst case error of every continual release algorithm is tilde Omega(T^{1/3}) times larger than that of the best batch algorithm. Previous work shows only a polylogarithimic (in T) gap between the worst case error achievable in these two models; further, for many problems, including the summation of binary attributes, the polylogarithmic gap is tight (Dwork et al., 2010; Chan et al., 2010). Our results show that problems closely related to summation -- specifically, those that require selecting the largest of a set of sums -- are fundamentally harder in the continual release model than in the batch model. Our lower bounds assume only that privacy holds for streams fixed in advance (the "nonadaptive" setting). However, we provide matching upper bounds that hold in a model where privacy is required even for adaptively selected streams. This model may be of independent interest.

  • 4 authors
·
Dec 1, 2021

Domain-Specific Risk Minimization for Out-of-Distribution Generalization

Recent domain generalization (DG) approaches typically use the hypothesis learned on source domains for inference on the unseen target domain. However, such a hypothesis can be arbitrarily far from the optimal one for the target domain, induced by a gap termed ``adaptivity gap''. Without exploiting the domain information from the unseen test samples, adaptivity gap estimation and minimization are intractable, which hinders us to robustify a model to any unknown distribution. In this paper, we first establish a generalization bound that explicitly considers the adaptivity gap. Our bound motivates two strategies to reduce the gap: the first one is ensembling multiple classifiers to enrich the hypothesis space, then we propose effective gap estimation methods for guiding the selection of a better hypothesis for the target. The other method is minimizing the gap directly by adapting model parameters using online target samples. We thus propose Domain-specific Risk Minimization (DRM). During training, DRM models the distributions of different source domains separately; for inference, DRM performs online model steering using the source hypothesis for each arriving target sample. Extensive experiments demonstrate the effectiveness of the proposed DRM for domain generalization with the following advantages: 1) it significantly outperforms competitive baselines on different distributional shift settings; 2) it achieves either comparable or superior accuracies on all source domains compared to vanilla empirical risk minimization; 3) it remains simple and efficient during training, and 4) it is complementary to invariant learning approaches.

  • 8 authors
·
Aug 18, 2022

Unravelling the Probabilistic Forest: Arbitrage in Prediction Markets

Polymarket is a prediction market platform where users can speculate on future events by trading shares tied to specific outcomes, known as conditions. Each market is associated with a set of one or more such conditions. To ensure proper market resolution, the condition set must be exhaustive -- collectively accounting for all possible outcomes -- and mutually exclusive -- only one condition may resolve as true. Thus, the collective prices of all related outcomes should be \1, representing a combined probability of 1 of any outcome. Despite this design, Polymarket exhibits cases where dependent assets are mispriced, allowing for purchasing (or selling) a certain outcome for less than (or more than) 1, guaranteeing profit. This phenomenon, known as arbitrage, could enable sophisticated participants to exploit such inconsistencies. In this paper, we conduct an empirical arbitrage analysis on Polymarket data to answer three key questions: (Q1) What conditions give rise to arbitrage (Q2) Does arbitrage actually occur on Polymarket and (Q3) Has anyone exploited these opportunities. A major challenge in analyzing arbitrage between related markets lies in the scalability of comparisons across a large number of markets and conditions, with a naive analysis requiring O(2^{n+m}) comparisons. To overcome this, we employ a heuristic-driven reduction strategy based on timeliness, topical similarity, and combinatorial relationships, further validated by expert input. Our study reveals two distinct forms of arbitrage on Polymarket: Market Rebalancing Arbitrage, which occurs within a single market or condition, and Combinatorial Arbitrage, which spans across multiple markets. We use on-chain historical order book data to analyze when these types of arbitrage opportunities have existed, and when they have been executed by users. We find a realized estimate of 40 million USD of profit extracted.

  • 4 authors
·
Aug 4, 2025

Structured Proper Loss Geometries for Multiclass Classification: Theory and Controlled Empirical Evaluation

Strictly proper scoring rules identify the true conditional class distribution at population level, but their curvature can alter optimization and finite-sample behavior. We study three multiclass objectives: a class-aware quadratic Bregman score (CAPM), a strongly convex generator with constrained log-cosh ridges (HPG), and an HPG objective with an annealed probability-margin penalty (APMS). CAPM is treated as a structured instance of established quadratic scoring-rule theory. We derive conditional-regret, curvature, range, and logit-gradient bounds for CAPM and HPG, and prove exact penalty-range and conditional-target displacement bounds for APMS. Controlled five-seed experiments use Digits, Wisconsin breast cancer, and synthetic confusion and long-tail problems under clean labels, symmetric and pair-flip corruption, class imbalance, calibration evaluation, input corruption, and first-order adversarial perturbations. The candidates are close to cross-entropy on clean data and show descriptive gains in some noisy-label cells, but the five-seed comparisons are interpreted descriptively rather than as significance evidence. The selected noisy-label baselines perform better on Digits with 40% symmetric label noise, and explicit prior-adjustment methods perform better in the 30:1 synthetic long-tail experiment. Ablations do not show a consistent benefit from the candidate-specific graph, ridge, or margin components. The mathematical analysis establishes the stated properties, and the experiments delimit the empirical evidence; together they do not support a claim of general superiority.

  • 1 authors
·
Jun 27

Learning with Boolean threshold functions

We develop a method for training neural networks on Boolean data in which the values at all nodes are strictly pm 1, and the resulting models are typically equivalent to networks whose nonzero weights are also pm 1. The method replaces loss minimization with a nonconvex constraint formulation. Each node implements a Boolean threshold function (BTF), and training is expressed through a divide-and-concur decomposition into two complementary constraints: one enforces local BTF consistency between inputs, weights, and output; the other imposes architectural concurrence, equating neuron outputs with downstream inputs and enforcing weight equality across training-data instantiations of the network. The reflect-reflect-relax (RRR) projection algorithm is used to reconcile these constraints. Each BTF constraint includes a lower bound on the margin. When this bound is sufficiently large, the learned representations are provably sparse and equivalent to networks composed of simple logical gates with pm 1 weights. Across a range of tasks -- including multiplier-circuit discovery, binary autoencoding, logic-network inference, and cellular automata learning -- the method achieves exact solutions or strong generalization in regimes where standard gradient-based methods struggle. These results demonstrate that projection-based constraint satisfaction provides a viable and conceptually distinct foundation for learning in discrete neural systems, with implications for interpretability and efficient inference.

  • 2 authors
·
Feb 19

A Taxonomy of Event-Linked Perpetual Futures: Variant Designs Beyond the Single-Market Binary Case

Paper 1 of this research programme develops a resolution-aware risk-design framework for the simplest event-linked perpetual: a contract whose underlying tracks a single binary prediction-market probability through resolution. The instrument class is broader. Variants span conditional probabilities P(A|B), spreads p^A - p^B, weighted baskets sum w_i p^(i), derivatives on variance or entropy of the probability process, contracts on liquidity itself, perpetual-on-expiring-event roll structures, and funding-only derivatives with no settlement. Each variant inherits some framework components from the single-market binary case and requires its own design adaptations. This paper develops a formal taxonomy of seven pure-form canonical variants beyond the probability-index perpetual of Paper 1, organised along four orthogonal design axes: underlying geometry, temporal structure, settlement structure, and venue composition. The list is not exhaustive; combinations are not treated separately. For each variant we provide a precise payoff definition; an inheritance map identifying which Paper 1 components carry over, are modified, or fail; variant-specific design constraints; microstructure properties; empirical evaluability on the PMXT v2 archive; and limitations. Notable findings: the conditional variant admits a candidate non-portability proposition (denominator instability as the conditioning event becomes improbable); the spread variant requires a three-channel decomposition of resolution risk; the volatility/entropy variant avoids random binary terminal-collapse but introduces estimator-convention and entropy-decay issues; the basket variant requires multi-period jump-aware margin whose aggregation is correlation-dependent. The paper is theoretical primarily; it specifies how demonstrative time series can be constructed and provides evaluability criteria to guide future work.

  • 1 authors
·
May 10

The Ghosts of Polymarket: When Off-Chain Matches Meet On-Chain Reverts

Polymarket has emerged as a prominent prediction market platform and one of the fastest-growing applications in DeFi. To achieve low-latency trading, it adopts a hybrid architecture that matches orders off-chain but settles them on-chain for final execution. This design creates a consistency gap we call Ghost Fills: an order that is successfully matched off-chain may later fail during on-chain settlement. To understand the security implications of this gap, we investigate such failed settlements by building GHOSTHUNTER, which reconstructs them from on-chain traces and attributes to concrete attack patterns. Across 1,952,440 reverted match-order transactions, we find that attackers exploit the time gap between matching and settlement to invalidate already matched orders before they are finalized on-chain. We then identify four attack vectors from these incidents: nonce bump, balance drain, allowance revoke, and proxy trap, realized via 35 evolving variants. These vectors allow attackers to selectively revert 980,133 filled orders, enabling risk-free prediction, arbitrage-bot hunting, and liquidity reward manipulation, realizing at least \1.49M in profit, which places 1.78 B USD at risk and 2.17 M POL (about \212 K) paid by operator. During peak hours, more than 24.3% of all filled orders reverted, causing de facto DoS attacks. We also find that code derived from the flawed contract still appears in 167 independent contracts across 10 chains holding at least 23 M in user funds, extending the impact beyond Polymarket. We have disclosed our evidence to affected parties, and the issue has been partially mitigated.

  • 5 authors
·
Jun 14 1

Cross-Entropy Loss Functions: Theoretical Analysis and Applications

Cross-entropy is a widely used loss function in applications. It coincides with the logistic loss applied to the outputs of a neural network, when the softmax is used. But, what guarantees can we rely on when using cross-entropy as a surrogate loss? We present a theoretical analysis of a broad family of loss functions, comp-sum losses, that includes cross-entropy (or logistic loss), generalized cross-entropy, the mean absolute error and other cross-entropy-like loss functions. We give the first H-consistency bounds for these loss functions. These are non-asymptotic guarantees that upper bound the zero-one loss estimation error in terms of the estimation error of a surrogate loss, for the specific hypothesis set H used. We further show that our bounds are tight. These bounds depend on quantities called minimizability gaps. To make them more explicit, we give a specific analysis of these gaps for comp-sum losses. We also introduce a new family of loss functions, smooth adversarial comp-sum losses, that are derived from their comp-sum counterparts by adding in a related smooth term. We show that these loss functions are beneficial in the adversarial setting by proving that they admit H-consistency bounds. This leads to new adversarial robustness algorithms that consist of minimizing a regularized smooth adversarial comp-sum loss. While our main purpose is a theoretical analysis, we also present an extensive empirical analysis comparing comp-sum losses. We further report the results of a series of experiments demonstrating that our adversarial robustness algorithms outperform the current state-of-the-art, while also achieving a superior non-adversarial accuracy.

  • 3 authors
·
Apr 14, 2023

Perfect Detection, Failed Control: The Geometry of Knowing vs. Steering in Language Models

A central aspiration of mechanistic interpretability is controllability: if we know where a behavior is represented in a model's activations, we should be able to modify it. This rests on a hidden premise -- that the direction which detects a behavior and the direction which controls it are the same, or close. We test this geometrically: what is the angle between the direction that best detects a behavior and the one that best causes it? If detection implies control the cosine is near 1; otherwise it quantifies a detection-intervention gap. On Gemma 2-2B-it, output format (clean JSON vs markdown fencing) collapses both roles onto one axis. Hallucination does not: the model detects fake entities with perfect linear separability (AUC = 1.000 from layer 5), yet that direction sits at cos = 0.12 (about 83 degrees) from the direction producing a refusal -- a small, reproducible alignment, far from the cos = 1 that "detection is control" would require. A detector built from activations, with no chosen tokens, likewise fails to align (cos = -0.06). The gap generalizes: across four models from three families and two scales (1B-9B), cos stays in [0.12, 0.20], identical before and after instruction tuning (0.1197 vs 0.1200), placing its origin in pretraining. A 15-degree rotation toward the refusal direction partially bridges it -- 73% and 60% refusal on two held-out fake-entity categories at 1.8% false positives. We then ask whether this cosine predicts steerability, and it does not: detection is a high-dimensional class, not a single direction, and what separates the steerable case is functional, not readable from a static angle. The cosine is a weight-computable signature of the dissociation between knowing and steering, not a predictor of it.

  • 5 authors
·
Jun 22

DiffIER: Optimizing Diffusion Models with Iterative Error Reduction

Diffusion models have demonstrated remarkable capabilities in generating high-quality samples and enhancing performance across diverse domains through Classifier-Free Guidance (CFG). However, the quality of generated samples is highly sensitive to the selection of the guidance weight. In this work, we identify a critical ``training-inference gap'' and we argue that it is the presence of this gap that undermines the performance of conditional generation and renders outputs highly sensitive to the guidance weight. We quantify this gap by measuring the accumulated error during the inference stage and establish a correlation between the selection of guidance weight and minimizing this gap. Furthermore, to mitigate this gap, we propose DiffIER, an optimization-based method for high-quality generation. We demonstrate that the accumulated error can be effectively reduced by an iterative error minimization at each step during inference. By introducing this novel plug-and-play optimization framework, we enable the optimization of errors at every single inference step and enhance generation quality. Empirical results demonstrate that our proposed method outperforms baseline approaches in conditional generation tasks. Furthermore, the method achieves consistent success in text-to-image generation, image super-resolution, and text-to-speech generation, underscoring its versatility and potential for broad applications in future research.

  • 3 authors
·
Aug 19, 2025

CondAmbigQA: A Benchmark and Dataset for Conditional Ambiguous Question Answering

Large language models (LLMs) are prone to hallucinations in question-answering (QA) tasks when faced with ambiguous questions. Users often assume that LLMs share their cognitive alignment, a mutual understanding of context, intent, and implicit details, leading them to omit critical information in the queries. However, LLMs generate responses based on assumptions that can misalign with user intent, which may be perceived as hallucinations if they misalign with the user's intent. Therefore, identifying those implicit assumptions is crucial to resolve ambiguities in QA. Prior work, such as AmbigQA, reduces ambiguity in queries via human-annotated clarifications, which is not feasible in real application. Meanwhile, ASQA compiles AmbigQA's short answers into long-form responses but inherits human biases and fails capture explicit logical distinctions that differentiates the answers. We introduce Conditional Ambiguous Question-Answering (CondAmbigQA), a benchmark with 200 ambiguous queries and condition-aware evaluation metrics. Our study pioneers the concept of ``conditions'' in ambiguous QA tasks, where conditions stand for contextual constraints or assumptions that resolve ambiguities. The retrieval-based annotation strategy uses retrieved Wikipedia fragments to identify possible interpretations for a given query as its conditions and annotate the answers through those conditions. Such a strategy minimizes human bias introduced by different knowledge levels among annotators. By fixing retrieval results, CondAmbigQA evaluates how RAG systems leverage conditions to resolve ambiguities. Experiments show that models considering conditions before answering improve performance by 20%, with an additional 5% gain when conditions are explicitly provided. These results underscore the value of conditional reasoning in QA, offering researchers tools to rigorously evaluate ambiguity resolution.

  • 4 authors
·
Feb 3, 2025

Approximating the Top Eigenvector in Random Order Streams

When rows of an n times d matrix A are given in a stream, we study algorithms for approximating the top eigenvector of the matrix {A}^TA (equivalently, the top right singular vector of A). We consider worst case inputs A but assume that the rows are presented to the streaming algorithm in a uniformly random order. We show that when the gap parameter R = σ_1(A)^2/σ_2(A)^2 = Ω(1), then there is a randomized algorithm that uses O(h cdot d cdot polylog(d)) bits of space and outputs a unit vector v that has a correlation 1 - O(1/R) with the top eigenvector v_1. Here h denotes the number of heavy rows in the matrix, defined as the rows with Euclidean norm at least |{A}|_F/d cdot operatorname{polylog(d)}. We also provide a lower bound showing that any algorithm using O(hd/R) bits of space can obtain at most 1 - Ω(1/R^2) correlation with the top eigenvector. Thus, parameterizing the space complexity in terms of the number of heavy rows is necessary for high accuracy solutions. Our results improve upon the R = Ω(log n cdot log d) requirement in a recent work of Price and Xun (FOCS 2024). We note that the algorithm of Price and Xun works for arbitrary order streams whereas our algorithm requires a stronger assumption that the rows are presented in a uniformly random order. We additionally show that the gap requirements in their analysis can be brought down to R = Ω(log^2 d) for arbitrary order streams and R = Ω(log d) for random order streams. The requirement of R = Ω(log d) for random order streams is nearly tight for their analysis as we obtain a simple instance with R = Ω(log d/loglog d) for which their algorithm, with any fixed learning rate, cannot output a vector approximating the top eigenvector v_1.

  • 2 authors
·
Dec 16, 2024

The Data Manifold under the Microscope

A significant gap exists between theory and practice in deep learning. Generalization and approximation error bounds are often derived for simplified models or are too loose to be informative. Many rely on the manifold hypothesis and on geometric regularity such as intrinsic dimension, curvature, and reach. Progress requires insight into data-manifold geometry and suitable benchmarks, yet existing options are polarized: analytic manifolds with known geometry but limited applicability, or real-world datasets where geometry is only coarsely estimable. We introduce a benchmarking framework for studying data geometry. We repurpose and extend dSprites and COIL-20 with additional transformation dimensions and dense, axis-aligned sampling, and pair them with finite-difference estimators that recover curvature, reach, and volume at near-ground-truth accuracy in a regime where general-purpose estimators are unreliable or difficult to deploy. The framework is intended as a controlled testbed, useful as a calibration environment for geometric estimators and a sandbox for probing theoretical assumptions. To illustrate its use, we present two application studies, namely assessing the scaling behavior of the bounds of Genovese et al. and Fefferman et al., and tracking the layer-wise geometry of a β-VAE, highlighting the behavior of current bounds and the value of controlled benchmarks for guiding and validating future theory. A reference implementation is available at https://github.com/koulakis/manifold-microscope.

  • 2 authors
·
Jun 13 8

Resolution-Aware Perpetual Futures on Binary Prediction Markets: An Empirical Risk-Design Framework Using Polymarket Data

We develop and counterfactually evaluate a resolution-aware risk-design framework (PIRAP) for perpetual futures whose underlying tracks a single binary prediction-market probability through resolution. The framework specifies six components: an index estimator combining mid-price, depth-weighted mid, and time-decayed VWAP; jump-aware tiered margin sized against bounded-event terminal-collapse magnitude; leverage compression schedule contracting toward resolution; resolution-aware funding rule with boundary-aware correction; a multi-stage halt protocol; and an eligibility framework. Two formal non-portability propositions establish that standard basis-only funding paired with continuous-vol static margin fails on bounded-event underlyings. Empirical evaluation uses Polymarket's PMXT v2 archive for 2026-04-21 to 2026-04-27 (13,298-market analysis sample passing adequacy gates from 61,087 ingested; 13,115 resolved within the empirical window for E3). E1 evaluates two pre-registered stylized facts; E2 conducts counterfactual replay across three engine configurations; E3 isolates the resolution-zone protocol's contribution. Results are mixed. Five pre-registered floors: stylized-fact floors (boundary depth asymmetry, terminal-jump magnitude) PASS; welfare-side directional floors (final-hour liquidation -6%, drawdown -5.1% pooled, median PnL +14%) two FAIL one PASS; E3 mechanic floors (final-hour liquidation -80% by halt construction PASS; bad-debt frequency +2.4% FAIL). Three of five materiality floors fail: the framework as specified does not validate deployment, but the empirical record establishes a halt-versus-margin scope distinction (halt addresses execution-channel risk; terminal-jump bad-debt remains margin-side) and documents a pre-emption trade-off constraining the dynamic-margin component. The paper concludes with structural recommendations and explicit non-deployable status.

  • 1 authors
·
May 10