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 Deep Learning


FlowRefiner: ARobust Traffic Classification Framework against Label Noise

Neural Information Processing Systems

Network traffic classification is essential for network management and security. In recent years, deep learning (DL) algorithms have emerged as essential tools for classifying complex traffic. However, they rely heavily on high-quality labeled training data. In practice, traffic data is often noisy due to human error or inaccurate automated labeling, which could render classification unreliable and lead to severe consequences. Although some studies have alleviated the label noise issue in specific scenarios, they are difficult to generalize to general traffic classification tasks due to the inherent semantic complexity of traffic data.


Simulating Viva Voce Examinations to Evaluate Clinical Reasoning in Large Language Models

Neural Information Processing Systems

Clinical reasoning in medicine is a hypothesis-driven process where physicians refine diagnoses from limited information through targeted history, physical examination, and diagnostic investigations. In contrast, current medical benchmarks for large language models (LLMs) primarily assess knowledge recall through single-turn questions, where complete clinical information is provided upfront. To address this gap, we introduce VivaBench, a multi-turn benchmark that evaluates sequential clinical reasoning in LLM agents. Our dataset comprises 1152 physiciancurated clinical vignettes structured as interactive scenarios that simulate a viva voce examination in medical training, requiring agents to actively probe for relevant findings, select appropriate investigations, and synthesize information across multiple steps to reach a diagnosis. We evaluated several state-of-the-art LLMs and found that while models demonstrate competence in diagnosing conditions within well-described clinical presentations, their performance degrades significantly when required to navigate diagnostic uncertainty. Our analysis identified several failure modes that mirror common issues in clinical practice, including: (1) fixation on initial hypotheses, (2) excessive investigation ordering, (3) premature diagnostic closure, and (4) missing critical conditions. These patterns reveal fundamental limitations in how current LLMs manage uncertainty and gather information sequentially. Through VivaBench, we provide a standardized benchmark for evaluating conversational medical AI systems for real-world clinical decision support. Beyond medical applications, we contribute to the larger corpus of research on agentic AI by demonstrating how sequential reasoning trajectories can diverge in complex decision-making environments.


PRSformer: Disease Prediction from Million-Scale Individual Genotypes

Neural Information Processing Systems

Predicting disease risk from DNA presents an unprecedented emerging challenge as biobanks approach population scale sizes (N > 106 individuals) with ultra-highdimensional features (L > 105 genotypes). Current methods, often linear and reliant on summary statistics, fail to capture complex genetic interactions and discard valuable individual-level information. We introduce PRSformer, a scalable deep learning architecture designed for end-to-end, multitask disease prediction directly from million-scale individual genotypes. PRSformer employs neighborhood attention, achieving linear O(L) complexity per layer, making Transformers tractable for genome-scale inputs. Crucially, PRSformer utilizes a stacking of these efficient attention layers, progressively increasing the effective receptive field to model local dependencies (e.g., within linkage disequilibrium blocks) before integrating information across wider genomic regions. This design, tailored for genomics, allows PRSformer to learn complex, potentially non-linear and long-range interactions directly from raw genotypes. We demonstrate PRSformer's effectiveness using a unique large private cohort (N 5M) for predicting 18 autoimmune and inflammatory conditions using L 140k variants. PRSformer significantly outperforms highly optimized linear models trained on the same individual-level data and state-of-the-art summary-statistic-based methods (LDPred2) derived from the same cohort, quantifying the benefits of non-linear modeling and multitask learning at scale. Furthermore, experiments reveal that the advantage of non-linearity emerges primarily at large sample sizes (N > 1M), and that a multi-ancestry trained model improves generalization, establishing PRSformer as a new framework for deep learning in population-scale genomics.


tial

Neural Information Processing Systems

Series Section Electron Microscopy (ssEM) has emerged as a pivotal technology for deciphering nanoscale biological architectures. Three-dimensional (3D) registration is a critical step in ssEM, tasked with rectifying axial misalignments and nonlinear distortions introduced during serial sectioning. The core scientific challenge lies in achieving distortion mitigation without erasing the natural morphological deformations of biological tissues, thereby enabling faithful reconstruction of 3D ultrastructural organization. In this study, we present a paradigm-shifting optimization framework that rethinks 3D registration through the lens of manifold trajectory optimization. We propose the first continuous trajectory dynamics formulation for 3D registration and introduce a novel optimization strategy. Specifically, we introduce a dual optimization objective that inherently balances global trajectory smoothness with local structural preservation, while developing a solver that combines Gauss-Seidel iteration with Neural ODEs to systematically integrate biophysical priors with data-driven deformation compensation. Extensive experiments on multiple datasets spanning diverse tissue types demonstrate our method's superior performance in structural restoration accuracy and cross-tissue robustness.


Universal Visuo-Tactile Video Understanding for Embodied Interaction

Neural Information Processing Systems

Tactile perception is essential for embodied agents to understand physical attributes of objects that cannot be determined through visual inspection alone. While existing approaches have made progress in visual and language modalities for physical understanding, they fail to effectively incorporate tactile information that provides crucial haptic feedback for real-world interaction.


Reconciling Geospatial Prediction and Retrieval via Sparse Representations

Neural Information Processing Systems

Urban computing harnesses big data to decode complex urban dynamics and revolutionize location-based services. Traditional approaches have treated geospatial prediction tasks (e.g., estimating socio-economic indicators) and retrieval tasks (e.g., querying geographic objects) as isolated challenges, necessitating separate models with distinct training objectives. This fragmentation imposes significant computational burdens and limits cross-task synergy, despite advances in representation learning and multi-task foundation models.



Composing Linear Layers from Irreducibles

Neural Information Processing Systems

Contemporary large models often exhibit behaviors suggesting the presence of low-level primitives that compose into modules with richer functionality, but these fundamental building blocks remain poorly understood. We investigate this compositional structure in linear layers by asking: can we identify/synthesize linear transformations from a minimal set of geometric primitives? Using Clifford algebra, we show that linear layers can be expressed as compositions of bivectors--geometric objects encoding oriented planes--and introduce a differentiable algorithm that decomposes them into products of rotors. This construction uses only O log2 d parameters, versus O(d2) required by dense matrices. Applied to the key, query, and value projections in LLM attention layers, rotor-based layers match the performance of strong baselines such as block-Hadamard and low-rank approximations. Our findings provide an algebraic perspective on how these geometric primitives can compose into higher-level functions within deep models.


Detecting High-Stakes Interactions with Activation Probes

Neural Information Processing Systems

Monitoring is an important aspect of safely deploying Large Language Models (LLMs). This paper examines activation probes for detecting "high-stakes" interactions--where the text indicates that the interaction might lead to significant harm--as a critical, yet underexplored, target for such monitoring. We evaluate several probe architectures trained on synthetic data, and find them to exhibit robust generalization to diverse, out-of-distribution, real-world data. Probes' performance is comparable to that of prompted or finetuned medium-sized LLM monitors, while offering computational savings of six orders-of-magnitude. These savings are enabled by reusing activations of the model that is being monitored. Our experiments also highlight the potential of building resource-aware hierarchical monitoring systems, where probes serve as an efficient initial filter and flag cases for more expensive downstream analysis.


Through the River: Understanding the Benefit of Schedule-Free Methods for Language Model Training

Neural Information Processing Systems

As both model and dataset sizes continue to scale rapidly, conventional pretraining strategies with fixed compute budgets--such as cosine learning rate schedules--are increasingly inadequate for large-scale training.