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Applications · Health / Medicine

Rohit Dilip, Ayush Varshney, David Van Valen

Tokenization is a promising path to multi-modal models capable of jointly understanding protein sequences, structure, and function. Existing protein structure tokenizers create tokens by pooling information from local neighborhoods, an approach that limits their performance on generative and representation tasks. In this work, we present a method for global tokenization of protein structures in which successive tokens contribute increasing levels of detail to a global representation. This change resolves several issues with generative models based on local protein tokenization: it mitigates error accumulation, provides embeddings without sequence-reduction operations, and allows task-specific adaptation of a tokenized sequence's information content. We validate our method on reconstruction, generative, and representation tasks and demonstrate that it matches or outperforms existing models based on local protein structure tokenizers. We show that our adaptive approach enables inference criteria based on the information content of the generated proteins. We validate representations generated from our tokenizer on CATH classification tasks and demonstrate that non-linear probing on our tokenized sequences outperforms equivalent probing on representations from other tokenizers. Finally, we demonstrate how our method supports zero-shot protein shrinking and affinity maturation.

Social Aspects · Security

Shayne Longpre, Elaine Zhu, Carson Ezell, Avijit Ghosh, Sean McGregor, Kevin Paeth, Kevin Klyman, Sayash Kapoor, Rishi Bommasani, Ruth Elisabeth Appel 等

Flaw reporting for deployed AI systems is fundamental to identifying system failures and improving AI safety. Yet the AI reporting ecosystem is fragmented: researchers who identify flaws often do not know what or where to report, and groups who receive reports rarely share them with other relevant stakeholders. As a result, good-faith reporters duplicate effort by submitting many different forms, and recipients lack standardized, triage-ready information. We audit 12 reporting systems published by AI developers, cybersecurity groups, and AI flaw aggregators, identifying five recurring design challenges spanning discoverability, scope, information collection, coordination, and guidance for strict-liability cases. Building on this analysis and feedback from 49 experts across 32 organizations representing developers, security researchers, and ecosystem coordinators, we introduce FLARE-AI, an open-source AI flaw reporting system designed for interoperability with existing systems. FLARE-AI streamlines flaw report creation by collecting triage-relevant information through conditional logic and early classification, then enables optional dissemination of standardized, machine-readable reports to multiple developers, coordinators, and incident registries from a single submission. By lowering barriers to reporting AI flaws and improving interoperability across stakeholders, FLARE-AI helps break down silos and accelerate remediation across the AI ecosystem.

Optimization · Convex

Xiyuan Wei, Linli Zhou, Bokun Wang, Chih-Jen Lin, Tianbao Yang

This paper studies optimization for a family of problems termed **compositional entropic risk minimization**, in which each data's loss is formulated as a Log-Expectation-Exponential (Log-E-Exp) function. The Log-E-Exp formulation serves as an abstraction of the Log-Sum-Exponential (LogSumExp) function when the explicit summation inside the logarithm is taken over a gigantic number of items and is therefore expensive to evaluate. While entropic risk objectives of this form arise in many machine learning problems, existing optimization algorithms suffer from several fundamental limitations including non-convergence, numerical instability, and slow convergence rates. To address these limitations, we propose a geometry-aware stochastic algorithm, termed **SCENT**, for the dual formulation of entropic risk minimization cast as a min--min optimization problem. The key to our design is a **stochastic proximal mirror descent (SPMD)** update for the dual variable, equipped with a Bregman divergence induced by a negative exponential function that faithfully captures the geometry of the objective. Our main contributions are threefold: (i) we establish an $O(1/\sqrt{T})$ convergence rate of the proposed SCENT algorithm for convex problems; (ii) we theoretically characterize the advantages of SPMD over standard SGD update for optimizing the dual variable; and (iii) we demonstrate the empirical effectiveness of SCENT on extreme classification, partial AUC maximization, contrastive learning and distributionally robust optimization, where it consistently outperforms existing baselines.

Theory · Deep Learning

Hongkang Li, Songtao Lu, Xiaodong Cui, Pin-Yu Chen, Meng Wang

The Mamba model has gained significant attention for its computational advantages over Transformer-based models, while achieving comparable performance across a wide range of language tasks. Like Transformers, Mamba exhibits in-context learning (ICL) capabilities, i.e., making predictions for new tasks based on a prompt containing input-label pairs and a query, without requiring fine-tuning. Despite its empirical success, the theoretical understanding of Mamba remains limited, largely due to the nonlinearity introduced by its gating mechanism. To the best of our knowledge, this paper presents the first theoretical analysis of the training dynamics of a one-layer Mamba model, which consists of a linear attention component followed by a nonlinear gating layer, and its ICL generalization on unseen binary classification tasks, even when the prompt includes additive outliers. Our analysis shows that Mamba leverages the linear attention layer to select informative context examples and uses the nonlinear gating layer to suppress the influence of outliers. By establishing and comparing to the analysis of linear Transformers under the same setting, we show that although Mamba may require more training iterations to converge, it maintains accurate predictions even when the proportion of outliers exceeds the threshold that a linear Transformer can tolerate. These theoretical findings are supported by empirical experiments.

Applications · Neuroscience, Cognitive Science

Kartikay Agrawal, Vaishnavi N, Abhijeet Vikram, Vedant Sharma, Ayon Borthakur

Spiking neural networks have attracted increasing attention for their energy efficiency, multiplication-free computation, and sparse event-based processing. In parallel, state space models have emerged as a scalable alternative to transformers for long-range sequence modelling by avoiding quadratic dependence on sequence length. We propose here a spiking heterogeneous harmonic resonate-and-fire state space model (S$H^2$RFSSM), a second-order spiking SSM for classification and regression on ultra-long sequences. S$H^2$RFSSM outperforms transformers and first-order SSMs on average while eliminating matrix multiplications, making it highly suitable for resource-constrained applications. Furthermore, we introduce a kernel-based spiking regressor that enables accurate modelling of dependencies in sequences of up to 50k steps. We also observe a reduction in spiking operations and improved performance with heterogeneity and discretisation in harmonic resonate-and-fire neuronal layers. Overall, we evaluate Harmonic Resonate-and Fire layers across 17 diverse datasets, spanning sensors, time series, and classification to long-term forecasting. Our results demonstrate that S$H^2$RFSSM achieves superior long-range modelling capability with energy efficiency, positioning it as a strong candidate for signal processing on resource-constrained devices for human activity recognition, time series classification, and regression.

Probabilistic Methods · Everything Else

Maja Waldron

One-shot prediction enables rapid adaptation of pretrained foundation models to new tasks using only one labeled example, but lacks principled uncertainty quantification. While conformal prediction provides finite-sample coverage guarantees, standard split conformal methods are inefficient in the one-shot setting due to data splitting and reliance on a single predictor. We propose Conformal Aggregation of One-Shot Predictors (CAOS), a conformal framework that adaptively aggregates multiple one-shot predictors and uses a leave-one-out calibration scheme to fully exploit scarce labeled data. Despite violating classical exchangeability assumptions, we prove that CAOS achieves valid marginal coverage using a monotonicity-based argument. Experiments on one-shot facial landmarking and RAFT text classification tasks show that CAOS produces substantially smaller prediction sets than split conformal baselines while maintaining reliable coverage.

Deep Learning · Attention Mechanisms

Zhouzhiming Zhou, Yong He, Qiaoyun Wu, Chaoxu Mu, Ajmal Mian

The unordered nature of point cloud data poses significant challenges to conventional architectures primarily designed for structured data. Spiking neural networks (SNN), by virtue of their inherent sparsity and dynamics, are particularly well-suited for processing point clouds to effectively extract meaningful features. We propose SpikeNet, a novel spiking neural network architecture for energy-efficient and robust point cloud analysis. We introduce spiking-driven sparse attention mechanism coined the Spiking Vector Mask Transformer (SVMT). By dynamically aligning the sparsity of point cloud data through binary spiking masks, SVMT eliminates the need for softmax and multiplication operations, significantly improving computational efficiency. We also propose a Dynamic Sparse Spiking Residual (DSSR) structure and integrate it with SVMT to form the Spiking Neural Network (SpikeNet) for point cloud classification and segmentation. SpikeNet overcomes the trade-off between accuracy and efficiency in previous SNN methods, achieving collaborative optimization of performance and energy-efficiency. Experiments on benchmark datasets show that SpikeNet achieves state-of-the-art performance in shape classification and segmentation tasks, comparable to artificial neural network (ANN) based methods. Our source code is in supplementary material and will be made publicly available.

Applications · Neuroscience, Cognitive Science

Jinhan Liu, Mahsa Shoaran

Affective and cognitive disorders manifest as distributed, time-varying brain network dynamics across regions, channels, and time, challenging robust representation learning from EEG/sEEG for clinical diagnosis. We propose **RECTOR** (Masked **Re**gion–**C**hannel–**T**emp**or**al Modeling), an end-to-end self-supervised framework that unifies joint region-channel-temporal representation learning beyond fixed anatomical priors. At its core, **RECTOR-SA** is a hierarchical, block-sparse self-attention induced by Adaptive Functional Partitioning that evolves region structures from static anatomical definitions to adaptive functional regions. The self-supervision is driven by **Masked Topology and Representation Learning**, which jointly optimizes three complementary objectives: Masked Predictive Modeling, Topological Structure Modeling, and Cross-View Consistency. Across diverse benchmarks, RECTOR sets a new state-of-the-art in EEG emotion recognition and sEEG task-engagement classification. Crucially, its strong robustness to missing channels and cross-montage generalization underscores its potential for large-scale pre-training on heterogeneous EEG/sEEG, providing interpretable insights at both region and channel levels.

Deep Learning · Self-Supervised Learning

Achleshwar Luthra, Yash Salunkhe, Tomer Galanti

Frozen self-supervised representations often transfer well with only a few labels across many semantic tasks. We argue that a single geometric quantity, *directional* CDNV (decision-axis variance), sits at the core of two favorable behaviors: strong few-shot transfer within a task, and low interference across many tasks. We show that both emerge when variability *along* class-separating directions is small. First, we prove sharp non-asymptotic multiclass generalization bounds for downstream classification whose leading term is the directional CDNV. The bounds include finite-shot corrections that cleanly separate intrinsic decision-axis variability from centroid-estimation error. Second, we link decision-axis collapse to multitask geometry: for independent balanced labelings, small directional CDNV across tasks forces the corresponding decision axes to be nearly orthogonal, helping a single representation support many tasks with minimal interference. Empirically, across SSL objectives, directional CDNV collapses during pretraining even when classical CDNV remains large, and our bounds closely track few-shot error at practical shot sizes. Additionally, on synthetic multitask data, we verify that SSL learns representations whose induced decision axes are nearly orthogonal.

General Machine Learning · Methodology

Inés Castilla Rieso

Topological Machine Learning provides strong discriminative power for classification tasks through the use of Topological Data Analysis, and more particularly, Persistent Homology. Although it has strong theoretical appeal, it remains underused by the broader Machine Learning community; criticism often targets the reliance on synthetic data and the absence of shared experimental standards, which makes reported results difficult to compare. Indeed, current empirical evaluations lack a consistent framework for assessing methods: the construction of topological signatures is often opaque, statistical significance testing to validate reported gains, computing times and robustness to perturbations-such as missing data or noise-are often omitted. We assert that **progress in Topological Machine Learning depends on establishing clear and consolidated experimental standards that support meaningful comparison across methods**, articulated through a transparent and reproducible empirical framework including data processing and performance evaluation. We review current practices, highlight their limitations, and propose a set of principles for conducting rigorous and comparable empirical evaluations. Adopting these standards will enable trustworthy studies, clarify the gains of new methods, and ultimately support the broader adoption of Topological Machine Learning by the Machine Learning community.

Applications · Health / Medicine

Maxence Gélard, Hakim Benkirane, Thomas Pierrot, Guillaume Richard, Paul-Henry Cournède

Oncologists are increasingly relying on multiple modalities to model the complexity of diseases. Within this landscape, transcriptomic and epigenetic data have proven to be particularly instrumental and play an increasingly vital role in clinical applications. However, their integration into multimodal models remains a challenge, especially considering their high dimensionality. In this work, we present a novel bimodal model that jointly learns representations of bulk RNA-seq and DNA methylation leveraging self-supervision from masked language modeling. We leverage an architecture that reduces the memory footprint usually attributed to purely transformer-based models when dealing with long sequences. We demonstrate that the obtained bimodal embeddings can be used to fine-tune cancer-type classification and survival models that achieve state-of-the-art performance compared to unimodal models. Furthermore, we introduce a robust learning framework that maintains downstream task performance despite missing modalities, enhancing the model’s applicability in real-world clinical settings.

Jing Yang, Jusheng Zhang, Keze Wang

Long-tailed multi-label text classification is often treated as a data scarcity problem, addressed by re-sampling or fixed re-weighting. We argue that a central failure mode is \textit{dominant coalition capture}: frequent labels, amplified by spurious co-occurrences, form dominant coalitions that dominate shared representations and gradient allocation during optimization. As a result, rare labels are learned via superficial shortcuts, yielding brittle generalization under distribution shifts. We propose \textbf{NBCG}, a Nash-Bargained Causal Game that reformulates multi-label learning as a cooperative bargaining process among label coalitions. NBCG first leverages Neural Structural Equation Models to learn a directed dependency structure, inducing causally coherent coalitions---rather than random partitions---and coalition-specific communication masks. We then optimize a Nash bargaining objective over coalition utilities relative to an adaptive disagreement point, which serves as a principled credit-allocation mechanism: it adaptively prioritizes under-served coalitions while maintaining a Pareto-efficient trade-off among all players.

General Machine Learning · Representation Learning

Yang Li, Yuchen Fang, Tingjin Luo

Incomplete multi-view multi-label classification addresses scenarios where views and labels are partially missing. While existing methods treat labels solely as supervision signals, they overlook the semantic structure inherent in partial annotations. We propose Label-Guided Representation Learning (LGRL) that systematically exploits label semantics as structural priors throughout learning. Our framework constructs a semantic-informed mixture prior via learnable category prototypes to guide representation extraction, and introduces category-specific conditional posteriors where prototypes act as Bayesian experts for multi-view fusion. We further derive a principled label-driven information bottleneck objective balancing reconstruction sufficiency with cross-view consistency, enabling category-conditional reasoning. Extensive experimental results demonstrate the effectiveness of LGRL across benchmark datasets as well as real-world applications in sports analytics and medical imaging.

Yuchen Fang, Zhiming Liu, Wei Luo, Tingjin Luo, Chenping Hou

Multimodal large language models (MLLMs) frequently suffer from object hallucinations, yet the visual perceptual mechanism underlying this failure remains poorly understood. In this work, we reveal that hallucinations are strongly associated with a human-like attention distraction phenomenon, where humans under divided focus experience degraded visual clarity and produce inaccurate descriptions, while in models the same mechanism manifests as spatial inconsistency in multi-head attention and temporal fading of attention to image tokens during decoding. We further provide theoretical insights that attention dispersion increases model complexity and degrades classification generalization. Motivated by these findings, we propose an Attention-Focused Approach for Improved Image Perception (AFIP), which corrects attention distraction via cross-head attention enrichment and reinforces visual grounding through dynamic historical attention enhancement. Extensive experiments on multiple benchmarks and models validate the effectiveness of AFIP without additional training.

General Machine Learning · Representation Learning

Jinping Wang, Zixin Tong, Zhiwu Xie, Zhiqiang Gao

Loss reweighting is a widely used strategy for long-tailed classification, but existing reweighting strategies often rely on heuristics and rarely define a well-specified target. Inspired by Neural Collapse (NC), the ideal simplex Equiangular Tight Frame (ETF) terminal geometry suggests equal per-class average loss as a reasonable target for reweighting. Based on the ideal equal loss objective, we consider loss reweighting as an inverse problem and propose an inverse-view reweighting strategy that infers class weights dynamically to match this ideal objective. Empirically, NC metrics suggest our method can effectively reduce the loss imbalance coefficient and closer alignment with NC geometry while consistently outperforms strong long-tailed baselines on different datasets.

Deep Learning · Large Language Models

Na Di, Ling Li, Zhe Tang, Hao Cheng, Jinlong Pang, Jiaheng Wei, Zhaowei Zhu

Large language models (LLMs) and vision-language models (VLMs) have emerged as efficient annotators for tasks such as generation and classification. While these models offer significant cost and speed advantages over human annotation, a critical challenge remains: existing self-evaluation methods, such as LLM-as-judge, often lack reliable calibration signals for error detection. We address this limitation by introducing **SAGE** (**S**emantic-**A**nchored Jud**G**m**E**nt), a method that leverages semantically similar samples retrieved via $k$-nearest-neighbor as references for annotation verification. We provide a theoretical framework that derives a closed-form expression for the error detection AUROC, which can be decomposed into three factors: intrinsic separability, reference-induced mean shift, and noise reduction through averaging. This decomposition reveals *when* semantic neighbors help (when references are both semantically matched and correct) and *why* (by providing calibration signals that raise scores for correct annotations and lower scores for incorrect ones). Experiments on LLM generation, VLM captioning, and classification tasks validate our theoretical framework: SAGE improves error detection when semantic neighbors provide reliable calibration signals, and our decomposition offers insights into when direct scoring or alternative strategies may be preferred.

Deep Learning · Generative Models and Autoencoders

Gilad Nurko, Roi Benita, Yehoshua Dissen, Tomohiro Nakatani, Marc Delcroix, Shoko Araki, Joseph Keshet

Robust classification in noisy environments remains a fundamental challenge in machine learning. Standard approaches typically treat signal enhancement and classification as separate, sequential stages: first enhancing the signal and then applying a classifier. This approach fails to leverage the semantic information in the classifier's output during denoising. In this work, we propose a general, domain-agnostic framework that integrates two interacting diffusion models: one operating on the input signal and the other on the classifier's output logits, without requiring any retraining or fine-tuning of the classifier. This coupled formulation enables mutual guidance, where the enhancing signal refines the class estimation and, conversely, the evolving class logits guide the signal reconstruction towards discriminative regions of the manifold. We introduce three strategies to effectively model the joint distribution of the input and the logit. We evaluated our joint enhancement method for image classification and automatic speech recognition. The proposed framework surpasses traditional sequential enhancement baselines, delivering robust and flexible improvements in classification accuracy under diverse noise conditions.

Social Aspects · Accountability, Transparency, and Interpretability

Keying Kuang, Iain Carmichael, Elizabeth Purdom

Saliency maps are widely used to interpret image classification models and build trust in their predictions; however, their reliability remains a central concern, as randomized networks can produce saliency maps that closely resemble those of trained models. We identify a previously underappreciated architectural contributor to this phenomenon: a *center-focused saliency bias* induced by common convolutional design choices. Through controlled ablations, we show that this bias arises from architectural components such as zero padding and receptive field growth, and persists even in randomly initialized convolutional neural networks (CNNs) and under randomized inputs. In contrast, this behavior is largely absent in non-convolutional architectures such as Vision Transformers (ViTs) and multilayer perceptrons (MLPs). To investigate the interaction between architectural priors and learning, we introduce a corner-shift benchmark and a Center-Shift Index that quantify how saliency redistributes under object relocation. We show that training can partially shift saliency toward object regions, while randomized models remain dominated by architectural priors, helping explain the previously observed similarity between trained and random saliency maps and clarify how architectural priors can confound standard saliency evaluations.

Deep Learning · Foundation Models

Chunlei Meng, Pengbin Feng, Rong Fu, Hoi Leong Lee, Xiaojing Du, Yuying Li, Zeyu Zhang, Weilin Zhou, Chun Ouyang, Zhongxue Gan

Centralized multimodal learning commonly compresses language, acoustic, and visual signals into a single fused representation for prediction. While effective, this paradigm suffers from two limitations: modality dominance, where optimization gravitates towards the path of least resistance, ignoring weaker but informative modalities, and spurious modality coupling, where models overfit to incidental cross-modal correlations. To address these, we propose \textbf{Group Cognition Learning (GCL)}, a governed collaboration paradigm that applies a two-stage protocol after modality-specific encoding. In Stage 1 (Selective Interaction), a Routing Agent proposes directed interaction routes, and an Auditing Agent assigns sample-wise gates to emphasize exchanges that yield positive marginal predictive gain while suppressing redundant coupling. In Stage 2 (Consensus Formation), a Public-Factor Agent maintains an explicit shared factor, and an Aggregation Agent produces the final prediction through contribution-aware weighting while keeping each modality representation as a specialization channel. Extensive experiments on CMU-MOSI, CMU-MOSEI, and MIntRec demonstrate that GCL mitigates dominance and coupling, establishing state-of-the-art results across both regression and classification benchmarks. Analysis experiments further demonstrate the effectiveness of the design.

General Machine Learning · Evaluation

Kabir Kang, Steve Mussmann

Standard classification treats all errors equally, but in content moderation, medical screening, and safety-critical applications, mistakes on clear-cut cases are far more costly than errors on ambiguous ones. We propose normalized excess cost (NEC), a metric that weights classification errors by per-example costs and reduces to standard error rate when costs are uniform. Costs can derive from annotator vote margins, distance from decision thresholds, or confidence ratings. Across text, image, and tabular benchmarks, we find that NEC is often substantially lower than error rate—models with 5% error rate can achieve 1.8% NEC—revealing that most mistakes concentrate on ambiguous, low-cost examples. However, incorporating costs into training via loss weighting, sampling strategies, or regression yields inconsistent benefits: improvements appear only when costs are predictable from input features, as in our synthetic control, while real-world datasets show mixed or negligible gains. Our framework provides a practical methodology for deriving and evaluating instance-level misclassification costs, even when cost-sensitive training offers limited benefit.