Deep Learning
10b7e27c8eb9571fbbd2ae6a9f8c3855-Paper-Conference.pdf
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Single GPUTask Adaptation of Pathology Foundation Models for Whole Slide Image Analysis
Pathology foundation models (PFMs) have emerged as powerful tools for analyzing whole slide images (WSIs). However, adapting these pretrained PFMs for specific clinical tasks presents considerable challenges, primarily due to the availability of only weak (WSI-level) labels for gigapixel images, necessitating multiple instance learning (MIL) paradigm for effective WSI analysis. This paper proposes a novel approach for single-GPUTask Adaptation of PFMs (TAPFM) that uses vision transformer (ViT) attention for MIL aggregation while optimizing both for feature representations and attention weights. The proposed approach maintains separate computational graphs for MIL aggregator and the PFM to create stable training dynamics that align with downstream task objectives during end-to-end adaptation. Evaluated on mutation prediction tasks for bladder cancer and lung adenocarcinoma across institutional and The Cancer Genome Atlas (TCGA) cohorts, TAPFM consistently outperforms conventional approaches, with H-Optimus-0 (TAPFM) outperforming the benchmarks. TAPFM effectively handles multi-label classification of actionable mutations as well. Thus, TAPFM makes adaptation of powerful pre-trained PFMs practical on standard hardware for various clinical applications.
Dual-Stage Value-Guided Inference with Margin-Based Reward Adjustment for Fast and Faithful VLMCaptioning
Despite significant advances in inference-time search for vision-language models (VLMs), existing approaches remain both computationally expensive and prone to unpenalized, low-confidence generations which often lead to persistent hallucinations. We introduce Value-guided Inference with Margin-based Reward (ViMaR)1, a two-stage inference framework that improves both efficiency and output fidelity by combining a temporal-difference value model with a marginaware reward adjustment. In the first stage, we perform a single pass to identify the highest-value caption among diverse candidates. In the second stage, we selectively refine only those segments that were overlooked or exhibit weak visual grounding, thereby eliminating frequently rewarded evaluations. A calibrated margin-based penalty discourages low-confidence continuations while preserving descriptive richness. Extensive experiments across multiple VLM architectures demonstrate that ViMaR generates captions that are significantly more reliable, factually accurate, detailed, and explanatory, while achieving over 4 speedup compared to existing value-guided methods. Specifically, we show that ViMaR trained solely on LLaVA Mistral-7B generalizes effectively to guide decoding in stronger unseen models. To further validate this, we adapt ViMaR to steer generation in both LLaVAOneVision-Qwen2-7B and Qwen2.5-VL-3B,
Among Us: ASandbox for Measuring and Detecting Agentic Deception
Prior studies on deception in language-based AI agents typically assess whether the agent produces a false statement about a topic, or makes a binary choice prompted by a goal, rather than allowing open-ended deceptive behavior to emerge in pursuit of a longer-term goal. To fix this, we introduce Among Us1, a sandbox social deception game where LLM-agents exhibit long-term, open-ended deception as a consequence of the game objectives. While most benchmarks saturate quickly, Among Us can be expected to last much longer, because it is a multi-player game far from equilibrium. Using the sandbox, we evaluate 18 proprietary and open-weight LLMs and uncover a general trend: models trained with RL are comparatively much better at producing deception than detecting it. We evaluate the effectiveness of methods to detect lying and deception: logistic regression on the activations and sparse autoencoders (SAEs). We find that probes trained on a dataset of "pretend you're a dishonest model: . . . " generalize extremely well out-of-distribution, consistently obtaining AUROCs over 95% even when evaluated just on the deceptive statement, without the chain of thought. We also find two SAE features that work well at deception detection but are unable to steer the model to lie less. We hope our open-sourced sandbox, game logs, and probes serve to anticipate and mitigate deceptive behavior and capabilities in language-based agents.
MTBBench: AMultimodal Sequential Clinical Decision-Making Benchmark in Oncology
Multimodal Large Language Models (LLMs) hold promise for biomedical reasoning, but current benchmarks fail to capture the complexity of real-world clinical workflows. Existing evaluations primarily assess unimodal, decontextualized question-answering, overlooking multi-agent decision-making environments such as Molecular Tumor Boards (MTBs). MTBs bring together diverse experts in oncology, where diagnostic and prognostic tasks require integrating heterogeneous data and evolving insights over time. Current benchmarks lack this longitudinal and multimodal complexity. We introduce MTBBench, an agentic benchmark simulating MTB-style decision-making through clinically challenging, multimodal, and longitudinal oncology questions. Ground truth annotations are validated by clinicians via a co-developed app, ensuring clinical relevance. We benchmark multiple open and closed-source LLMs and show that, even at scale, they lack reliability--frequently hallucinating, struggling with reasoning from time-resolved data, and failing to reconcile conflicting evidence or different modalities. To address these limitations, MTBBench goes beyond benchmarking by providing an agentic framework with foundation model-based tools that enhance multi-modal and longitudinal reasoning, leading to task-level performance gains of up to 9.0% and 11.2%, respectively. Overall, MTBBench offers a challenging and realistic testbed for advancing multimodal LLM reasoning, reliability, and tool-use with a focus on MTB environments in precision oncology.
One Stone with Two Birds: ANull-Text-Null Frequency-Aware Diffusion Models for Text-Guided Image Inpainting
Text-guided image inpainting aims at reconstructing the masked regions as per text prompts, where the longstanding challenges lie in the preservation for unmasked regions, while achieving the semantics consistency between unmasked and inpainted masked regions. Previous arts failed to address both of them, always with either of them to be remedied. Such facts, as we observed, stem from the entanglement of the hybrid (e.g., mid-and-low) frequency bands that encode varied image properties, which exhibit different robustness to text prompts during the denoising process. In this paper, we propose a null-text-null frequency-aware diffusion models, dubbed NTN-Diff, for text-guided image inpainting, by decomposing the semantics consistency across masked and unmasked regions into the consistencies as per each frequency band, while preserving the unmasked regions, to circumvent two challenges in a row. Based on the diffusion process, we further divide the denoising process into early (high-level noise) and late (low-level noise) stages, where the mid-and-low frequency bands are disentangled during the denoising process. As observed, the stable mid-frequency band is progressively denoised to be semantically aligned during text-guided denoising process, which, meanwhile, serves as the guidance to the null-text denoising process to denoise low-frequency band for the masked regions, followed by a subsequent text-guided denoising process at late stage, to achieve the semantics consistency for mid-and-low frequency bands across masked and unmasked regions, while preserve the unmasked regions.
Deep Value Benchmark: Measuring Whether Models Generalize Deep Values or Shallow Preferences
We introduce the Deep Value Benchmark (DVB), an evaluation framework that directly tests whether large language models (LLMs) learn fundamental human values or merely surface-level preferences. This distinction is critical for AI alignment: Systems that capture deeper values are likely to generalize human intentions robustly, while those that capture only superficial patterns in preference data risk producing misaligned behavior. The DVB uses a novel experimental design with controlled confounding between deep values (e.g., moral principles) and shallow features (e.g., superficial attributes). In the training phase, we expose LLMs to human preference data with deliberately correlated deep and shallow features--for instance, where a user consistently prefers (non-maleficence, formal language) options over (justice, informal language) alternatives. The testing phase then breaks these correlations, presenting choices between (justice, formal language) and (non-maleficence, informal language) options.
Diffusion Beats Autoregressive in Data-Constrained Settings
Autoregressive (AR) models have long dominated the landscape of large language models, driving progress across a wide range of tasks. Recently, diffusion-based language models have emerged as a promising alternative, though their advantages over AR models remain underexplored. In this paper, we systematically study masked diffusion models in data-constrained settings--where training involves repeated passes over limited data--and find that they significantly outperform AR models when compute is abundant but data is scarce. Diffusion models make better use of repeated data, achieving lower validation loss and superior downstream performance. We find new scaling laws for diffusion models and derive a closedform expression for the critical compute threshold at which diffusion begins to outperform AR. Finally, we explain why diffusion models excel in this regime: their randomized masking objective implicitly trains over a rich distribution of token orderings, acting as an implicit data augmentation that AR's fixed left-toright factorization lacks. Our results suggest that when data, not compute, is the bottleneck, diffusion models offer a compelling alternative to the standard AR paradigm.
Synthetic Series-Symbol Data Generation for Time Series Foundation Models
Foundation models for time series analysis (TSA) have attracted significant attention. However, challenges such as training data scarcity and imbalance continue to hinder their development. Inspired by complex dynamic system theories, we design a series-symbol data generation mechanism, enabling the unrestricted creation of high-quality time series data paired with corresponding symbolic expressions. To leverage series-symbol data pairs with strong correlations, we develop SymTime, a pre-trained foundation model for enhancing time series representation using symbolic information. SymTime demonstrates competitive performance across five major TSA tasks when fine-tunes with downstream tasks, rivaling foundation models pre-trained on real-world datasets. This approach underscores the potential of series-symbol data generation and pretraining mechanisms in overcoming data scarcity and enhancing task performance.