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 Deep Learning


Cancer Survival Analysis via Zero-shot Tumor Microenvironment Segmentation on Low-resolution Whole Slide Pathology Images

Neural Information Processing Systems

The whole-slide pathology images (WSIs) are widely recognized as the golden standard for cancer survival analysis. However, due to the high-resolution of WSIs, the existing studies require dividing WSIs into patches and identify key components before building the survival prediction system, which is time-consuming and cannot reflect the overall spatial organization of WSIs. Inspired by the fact that the spatial interactions among different tumor microenvironment (TME) components in WSIs are associated with the cancer prognosis, some studies attempt to capture the complex interactions among different TME components to improve survival predictions. However, they require extra efforts for building the TME segmentation model, which involves substantial annotation workloads on different TME components and is independent to the construction of the survival prediction model. To address the above issues, we propose ZTSurv, a novel end-to-end cancer survival analysis framework via efficient zero-shot TME segmentation on low-resolution WSIs. Specifically, by leveraging tumor infiltrating lymphocyte (TIL) maps on the 50x down-sampled WSIs, ZTSurv enables zero-shot segmentation on other two important TME components (i.e., tumor and stroma) that can reduce the annotation efforts from the pathologists. Then, based on the visual and semantic information extracted from different TME components, we construct a heterogeneous graph to capture their spatial intersections for clinical outcome prediction. We validate ZTSurv across four cancer cohorts derived from The Cancer Genome Atlas (TCGA), and the experimental results indicate that our method can not only achieve superior prediction results but also significantly reduce the computational costs in comparison with the state-of-the-art methods.


Advancing Compositional Awareness in CLIP with Efficient Fine-Tuning

Neural Information Processing Systems

Vision-language models like CLIP have demonstrated remarkable zero-shot capabilities in classification and retrieval. However, these models often struggle with compositional reasoning - the ability to understand the relationships between concepts. A recent benchmark, SugarCrepe++ [11], reveals that previous works on improving compositionality have mainly improved lexical sensitivity but neglected semantic understanding. In addition, downstream retrieval performance often deteriorates, although one would expect that improving compositionality should enhance retrieval. In this work, we introduce CLIC (Compositionally-aware Learning in CLIP), a fine-tuning method based on a novel training technique combining multiple images and their associated captions. CLIC improves compositionality across architectures as well as differently pre-trained CLIP models, both in terms of lexical and semantic understanding, and achieves consistent gains in retrieval performance. This even applies to the recent CLIPS [33], which achieves SOTA retrieval performance. Nevertheless, the short fine-tuning with CLIC leads to an improvement in retrieval and to the best compositional CLIP model on SugarCrepe++.


Position: Require Frontier AILabs To Release Small " Analog " Models Shriyash Upadhyay Martian Chaithanya Bandi Martian Narmeen Oozeer Martian Philip Quirke Martian

Neural Information Processing Systems

Recent proposals for regulating frontier AI models have sparked concerns about the cost of safety regulation, and most such regulations have been shelved due to the safety-innovation tradeoff. This paper argues for an alternative regulatory approach that ensures AI safety while actively promoting innovation: mandating that large AI laboratories release small, openly accessible "analog models"--scaled-down versions trained similarly to and distilled from their largest proprietary models. Analog models serve as public proxies, allowing broad participation in safety verification, interpretability research, and algorithmic transparency without forcing labs to disclose their full-scale models. Recent research demonstrates that safety and interpretability methods developed using these smaller models generalize effectively to frontier-scale systems. By enabling the wider research community to directly investigate and innovate upon accessible analogs, our policy substantially reduces the regulatory burden and accelerates safety advancements. This mandate promises minimal additional costs, leveraging reusable resources like data and infrastructure, while significantly contributing to the public good. Our hope is not only that this policy be adopted, but that it illustrates a broader principle supporting fundamental research in machine learning: deeper understanding of models relaxes the safety-innovation tradeoff and lets us have more of both.



Transformer brain encoders explain human high-level visual responses

Neural Information Processing Systems

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring estimation of a large number of linear encoding parameters, this approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives factor the linear mapping into separate sets of spatial and feature weights, thus finding static receptive fields for units, which is appropriate only for early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable as the attention-routing signals for different high-level categorical areas can be easily visualized for any input image. Given its high performance at predicting brain responses to novel images, the model deserves consideration as a candidate mechanistic model of how visual information from retinotopic maps is routed in the human brain based on the relevance of the input content to different category-selective regions.


SwS: Self-aware Weakness-driven Problem Synthesis in Reinforcement Learning for LLMReasoning

Neural Information Processing Systems

Reinforcement Learning with Verifiable Rewards (RLVR) has proven effective for training large language models (LLMs) on complex reasoning tasks, such as mathematical problem solving. A prerequisite for the scalability of RLVR is a high-quality problem set with precise and verifiable answers.


Fast attention mechanisms: a tale of parallelism

Neural Information Processing Systems

Transformers have the representational capacity to simulate Massively Parallel Computation (MPC) algorithms, but they suffer from quadratic time complexity, which severely limits their scalability. We introduce an efficient attention mechanism called Approximate Nearest Neighbor Attention (ANNA) with sub-quadratic time complexity. We prove that ANNA-transformers (1) retain the expressive power previously established for standard attention in terms of matching the capabilities of MPC algorithms, and (2) can solve key reasoning tasks such as Match2 and k-hop with near-optimal depth. Using the MPC framework, we further prove that constant-depth ANNA-transformers can simulate constant-depth low-rank transformers, thereby providing a unified way to reason about a broad class of efficient attention approximations.


PSMBENCH: ABenchmark and Dataset for Evaluating LLMs Extraction of Protocol State Machines from RFCSpecifications

Neural Information Processing Systems

Accurately extracting protocol-state machines (PSMs) from the long, densely written Request-for-Comments (RFC) standards that govern Internet-scale communication remains a bottleneck for automated security analysis and protocol testing. In this paper, we introduce RFC2PSM, the first large-scale dataset that pairs 1,580 pages of cleaned RFC text with 108 manually validated states and 297 transitions covering 14 widely deployed protocols spanning the data-link, transport, session, and application layers. Built on this corpus, we propose PSMBENCH, a benchmark that (i) feeds chunked RFC to an LLM, (ii) prompts the model to emit a machine-readable PSM, and (iii) scores the output with structure-aware, semantic fuzzy-matching metrics that reward partially correct graphs. A comprehensive baseline study of nine state-of-the-art open and commercial LLMs reveals a persistent state-transition gap: models identify many individual states (up to 0.82 F1) but struggle to assemble coherent transition graphs ( 0.38 F1), highlighting challenges in long-context reasoning, alias resolution, and action/event disambiguation. We release the dataset, evaluation code, and all model outputs as open-sourced1, providing a fully reproducible starting point for future work on reasoning over technical prose and generating executable graph structures. RFC2PSM and PSMBENCH aim to catalyze cross-disciplinary progress toward LLMs that can interpret and verify the protocols that keep the Internet safe.


d1: Scaling Reasoning in Diffusion Large Language Models via Reinforcement Learning

Neural Information Processing Systems

Recent large language models (LLMs) have demonstrated strong reasoning capabilities that benefits from online reinforcement learning (RL). These capabilities have primarily been demonstrated within the left-to-right autoregressive (AR) generation paradigm. In contrast, non-autoregressive paradigms based on diffusion generate text in a coarse-to-fine manner. Although recent diffusion-based large language models (dLLMs) have achieved competitive language modeling performance compared to their AR counterparts, it remains unclear if dLLMs can also leverage recent advances in LLM reasoning. To this end, we propose d1, a framework to adapt pre-trained masked dLLMs into reasoning models via a combination of supervised finetuning (SFT) and RL. Specifically, we develop and extend techniques to improve reasoning in pretrained dLLMs: (a) we utilize a masked SFT technique to distill knowledge and instill self-improvement behavior directly from existing datasets, and (b) we introduce a novel critic-free, policygradient based RL algorithm called diffu-GRPO, the first integration of policy gradient methods to masked dLLMs. Through empirical studies, we investigate the performance of different post-training recipes on multiple mathematical and planning benchmarks. We find that d1 yields the best performance and significantly improves performance of a state-of-the-art dLLM. Our code is released at https://dllm-reasoning.github.io/.


What Moves the Eyes: Doubling Mechanistic Model Performance Using Deep Networks to Discover and Test Cognitive Hypotheses

Neural Information Processing Systems

Understanding how humans move their eyes to gather visual information is a central question in neuroscience, cognitive science, and vision research. While recent deep learning (DL) models achieve state-of-the-art performance in predicting human scanpaths, their underlying decision processes remain opaque. At an opposite end of the modeling spectrum, cognitively inspired mechanistic models aim to explain scanpath behavior through interpretable cognitive mechanisms but lag far behind in predictive accuracy. In this work, we bridge this gap by using a high-performing deep model--DeepGaze III--to discover and test mechanisms that improve a leading mechanistic model, SceneWalk. By identifying individual fixations where DeepGaze III succeeds and SceneWalk fails, we isolate behaviorally meaningful discrepancies and use them to motivate targeted extensions of the mechanistic framework. These include time-dependent temperature scaling, saccadic momentum and an adaptive cardinal attention bias: Simple, interpretable additions that substantially boost predictive performance. With these extensions, SceneWalk's explained variance on the MIT1003 dataset doubles from 35% to 70%, setting a new state of the art in mechanistic scanpath prediction. Our findings show how performance-optimized neural networks can serve as tools for cognitive model discovery, offering a new path toward interpretable and high-performing models of visual behavior.