GenAR: Next-Scale Autoregressive Generation for Spatial Gene Expression Prediction

Spatial Transcriptomics (ST) offers spatially resolved gene expression but remains costly. Predicting expression directly from widely available Hematoxylin and Eosin (H&E) stained images presents a cost-effective alternative. However, most computational approaches (i) predict each gene independently, overlooking co-expression structure, and (ii) cast the task as continuous regression despite expression being discrete counts. This mismatch can yield biologically implausible outputs and complicate downstream analyses. We introduce GenAR, a multi-scale autoregressive framework that refines predictions from coarse to fine. GenAR clusters genes into hierarchical groups to expose cross-gene dependencies, models expression as codebook-free discrete token generation to directly predict raw counts, and conditions decoding on fused histological and spatial embeddings. From an information-theoretic perspective, the discrete formulation avoids log-induced biases and the coarse-to-fine factorization aligns with a principled conditional decomposition. Extensive experimental results on four Spatial Transcriptomics datasets across different tissue types demonstrate that GenAR achieves state-of-the-art performance, offering potential implications for precision medicine and cost-effective molecular profiling. Code is publicly available at https://github.com/oyjr/genar.

Benchmarking and Mitigate Psychological Sycophancy in Medical Vision-Language Models

Vision language models(VLMs) are increasingly integrated into clinical workflows, but they often exhibit sycophantic behavior prioritizing alignment with user phrasing social cues or perceived authority over evidence based reasoning. This study evaluate clinical sycophancy in medical visual question answering through a novel clinically grounded benchmark. We propose a medical sycophancy dataset construct from PathVQA, SLAKE, and VQA-RAD stratified by different type organ system and modality. Using psychologically motivated pressure templates including various sycophancy. In our adversarial experiments on various VLMs, we found that these models are generally vulnerable, exhibiting significant variations in the occurrence of adversarial responses, with weak correlations to the model accuracy or size. Imitation and expert provided corrections were found to be the most effective triggers, suggesting that the models possess a bias mechanism independent of visual evidence. To address this, we propose Visual Information Purification for Evidence based Response (VIPER) a lightweight mitigation strategy that filters non evidentiary content for example social pressures and then generates constrained evidence first answers. This framework reduces sycophancy by an average amount outperforming baselines while maintaining interpretability. Our benchmark analysis and mitigation framework lay the groundwork for robust deployment of medical VLMs in real world clinician interactions emphasizing the need for evidence anchored defenses.

Rate doubly robust estimation for weighted average treatment effects

The weighted average treatment effect (WATE) defines a versatile class of causal estimands for populations characterized by propensity score weights, including the average treatment effect (ATE), treatment effect on the treated (ATT), on controls (ATC), and for the overlap population (ATO). WATE has broad applicability in social and medical research, as many datasets from these fields align with its framework. However, the literature lacks a systematic investigation into the robustness and efficiency conditions for WATE estimation. Although doubly robust (DR) estimators are well-studied for ATE, their applicability to other WATEs remains uncertain. This paper investigates whether widely used WATEs admit DR or rate doubly robust (RDR) estimators and assesses the role of nuisance function accuracy, particularly with machine learning. Using semiparametric efficient influence function (EIF) theory and double/debiased machine learning (DML), we propose three RDR estimators under specific rate and regularity conditions and evaluate their performance via Monte Carlo simulations. Applications to NHANES data on smoking and blood lead levels, and SIPP data on 401(k) eligibility, demonstrate the methods' practical relevance in medical and social sciences.

RepreGuard: Detecting LLM-Generated Text by Revealing Hidden Representation Patterns

Detecting content generated by large language models (LLMs) is crucial for preventing misuse and building trustworthy AI systems. Although existing detection methods perform well, their robustness in out-of-distribution (OOD) scenarios is still lacking. In this paper, we hypothesize that, compared to features used by existing detection methods, the internal representations of LLMs contain more comprehensive and raw features that can more effectively capture and distinguish the statistical pattern differences between LLM-generated texts (LGT) and human-written texts (HWT). We validated this hypothesis across different LLMs and observed significant differences in neural activation patterns when processing these two types of texts. Based on this, we propose RepreGuard, an efficient statistics-based detection method. Specifically, we first employ a surrogate model to collect representation of LGT and HWT, and extract the distinct activation feature that can better identify LGT. We can classify the text by calculating the projection score of the text representations along this feature direction and comparing with a precomputed threshold. Experimental results show that RepreGuard outperforms all baselines with average 94.92% AUROC on both in-distribution (ID) and OOD scenarios, while also demonstrating robust resilience to various text sizes and mainstream attacks. Data and code are publicly available at: https://github.com/NLP2CT/RepreGuard

Comparative validation of surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation in endoscopy: Results of the PhaKIR 2024 challenge

Reliable recognition and localization of surgical instruments in endoscopic video recordings are foundational for a wide range of applications in computer- and robot-assisted minimally invasive surgery (RAMIS), including surgical training, skill assessment, and autonomous assistance. However, robust performance under real-world conditions remains a significant challenge. Incorporating surgical context - such as the current procedural phase - has emerged as a promising strategy to improve robustness and interpretability. To address these challenges, we organized the Surgical Procedure Phase, Keypoint, and Instrument Recognition (PhaKIR) sub-challenge as part of the Endoscopic Vision (EndoVis) challenge at MICCAI 2024. We introduced a novel, multi-center dataset comprising thirteen full-length laparoscopic cholecystectomy videos collected from three distinct medical institutions, with unified annotations for three interrelated tasks: surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation. Unlike existing datasets, ours enables joint investigation of instrument localization and procedural context within the same data while supporting the integration of temporal information across entire procedures. We report results and findings in accordance with the BIAS guidelines for biomedical image analysis challenges. The PhaKIR sub-challenge advances the field by providing a unique benchmark for developing temporally aware, context-driven methods in RAMIS and offers a high-quality resource to support future research in surgical scene understanding.

Is Long-to-Short a Free Lunch? Investigating Inconsistency and Reasoning Efficiency in LRMs

Large Reasoning Models (LRMs) have achieved remarkable performance on complex tasks by engaging in extended reasoning before producing final answers, yet this strength introduces the risk of overthinking, where excessive token generation occurs even for simple tasks. While recent work in efficient reasoning seeks to reduce reasoning length while preserving accuracy, it remains unclear whether such optimization is truly a free lunch. Drawing on the intuition that compressing reasoning may reduce the robustness of model responses and lead models to omit key reasoning steps, we investigate whether efficient reasoning strategies introduce behavioral inconsistencies. To systematically assess this, we introduce $ICBENCH$, a benchmark designed to measure inconsistency in LRMs across three dimensions: inconsistency across task settings (ITS), inconsistency between training objectives and learned behavior (TR-LB), and inconsistency between internal reasoning and self-explanations (IR-SE). Applying $ICBENCH$ to a range of open-source LRMs, we find that while larger models generally exhibit greater consistency than smaller ones, they all display widespread "scheming" behaviors, including self-disagreement, post-hoc rationalization, and the withholding of reasoning cues. Crucially, our results demonstrate that efficient reasoning strategies such as No-Thinking and Simple Token-Budget consistently increase all three defined types of inconsistency. These findings suggest that although efficient reasoning enhances token-level efficiency, further investigation is imperative to ascertain whether it concurrently introduces the risk of models evading effective supervision.

The Compositional Architecture of Regret in Large Language Models

Regret in Large Language Models refers to their explicit regret expression when presented with evidence contradicting their previously generated misinformation. Studying the regret mechanism is crucial for enhancing model reliability and helps in revealing how cognition is coded in neural networks. To understand this mechanism, we need to first identify regret expressions in model outputs, then analyze their internal representation. This analysis requires examining the model's hidden states, where information processing occurs at the neuron level. However, this faces three key challenges: (1) the absence of specialized datasets capturing regret expressions, (2) the lack of metrics to find the optimal regret representation layer, and (3) the lack of metrics for identifying and analyzing regret neurons. Addressing these limitations, we propose: (1) a workflow for constructing a comprehensive regret dataset through strategically designed prompting scenarios, (2) the Supervised Compression-Decoupling Index (S-CDI) metric to identify optimal regret representation layers, and (3) the Regret Dominance Score (RDS) metric to identify regret neurons and the Group Impact Coefficient (GIC) to analyze activation patterns. Our experimental results successfully identified the optimal regret representation layer using the S-CDI metric, which significantly enhanced performance in probe classification experiments. Additionally, we discovered an M-shaped decoupling pattern across model layers, revealing how information processing alternates between coupling and decoupling phases. Through the RDS metric, we categorized neurons into three distinct functional groups: regret neurons, non-regret neurons, and dual neurons.

Flattery in Motion: Benchmarking and Analyzing Sycophancy in Video-LLMs

As video large language models (Video-LLMs) become increasingly integrated into real-world applications that demand grounded multimodal reasoning, ensuring their factual consistency and reliability is of critical importance. However, sycophancy, the tendency of these models to align with user input even when it contradicts the visual evidence, undermines their trustworthiness in such contexts. Current sycophancy research has largely overlooked its specific manifestations in the video-language domain, resulting in a notable absence of systematic benchmarks and targeted evaluations to understand how Video-LLMs respond under misleading user input. To fill this gap, we propose VISE (Video-LLM Sycophancy Benchmarking and Evaluation), the first dedicated benchmark designed to evaluate sycophantic behavior in state-of-the-art Video-LLMs across diverse question formats, prompt biases, and visual reasoning tasks. Specifically, VISE pioneeringly brings linguistic perspectives on sycophancy into the visual domain, enabling fine-grained analysis across multiple sycophancy types and interaction patterns. In addition, we explore key-frame selection as an interpretable, training-free mitigation strategy, which reveals potential paths for reducing sycophantic bias by strengthening visual grounding.

Mitigating Behavioral Hallucination in Multimodal Large Language Models for Sequential Images

While multimodal large language models excel at various tasks, they still suffer from hallucinations, which limit their reliability and scalability for broader domain applications. To address this issue, recent research mainly focuses on objective hallucination. However, for sequential images, besides objective hallucination, there is also behavioral hallucination, which is less studied. This work aims to fill in the gap. We first reveal that behavioral hallucinations mainly arise from two key factors: prior-driven bias and the snowball effect. Based on these observations, we introduce SHE (Sequence Hallucination Eradication), a lightweight, two-stage framework that (1) detects hallucinations via visual-textual alignment check using our proposed adaptive temporal window and (2) mitigates them via orthogonal projection onto the joint embedding space. We also propose a new metric (BEACH) to quantify behavioral hallucination severity. Empirical results on standard benchmarks demonstrate that SHE reduces behavioral hallucination by over 10% on BEACH while maintaining descriptive accuracy.

Stable Vision Concept Transformers for Medical Diagnosis

Transparency is a paramount concern in the medical field, prompting researchers to delve into the realm of explainable AI (XAI). Among these XAI methods, Concept Bottleneck Models (CBMs) aim to restrict the model's latent space to human-understandable high-level concepts by generating a conceptual layer for extracting conceptual features, which has drawn much attention recently. However, existing methods rely solely on concept features to determine the model's predictions, which overlook the intrinsic feature embeddings within medical images. To address this utility gap between the original models and concept-based models, we propose Vision Concept Transformer (VCT). Furthermore, despite their benefits, CBMs have been found to negatively impact model performance and fail to provide stable explanations when faced with input perturbations, which limits their application in the medical field. To address this faithfulness issue, this paper further proposes the Stable Vision Concept Transformer (SVCT) based on VCT, which leverages the vision transformer (ViT) as its backbone and incorporates a conceptual layer. SVCT employs conceptual features to enhance decision-making capabilities by fusing them with image features and ensures model faithfulness through the integration of Denoised Diffusion Smoothing. Comprehensive experiments on four medical datasets demonstrate that our VCT and SVCT maintain accuracy while remaining interpretable compared to baselines. Furthermore, even when subjected to perturbations, our SVCT model consistently provides faithful explanations, thus meeting the needs of the medical field.