MambaMIL+: Modeling Long-Term Contextual Patterns for Gigapixel Whole Slide Image

Whole-slide images (WSIs) are an important data modality in computational pathology, yet their gigapixel resolution and lack of fine-grained annotations challenge conventional deep learning models. Multiple instance learning (MIL) offers a solution by treating each WSI as a bag of patch-level instances, but effectively modeling ultra-long sequences with rich spatial context remains difficult. Recently, Mamba has emerged as a promising alternative for long sequence learning, scaling linearly to thousands of tokens. However, despite its efficiency, it still suffers from limited spatial context modeling and memory decay, constraining its effectiveness to WSI analysis. To address these limitations, we propose MambaMIL+, a new MIL framework that explicitly integrates spatial context while maintaining long-range dependency modeling without memory forgetting. Specifically, MambaMIL+ introduces 1) overlapping scanning, which restructures the patch sequence to embed spatial continuity and instance correlations; 2) a selective stripe position encoder (S2PE) that encodes positional information while mitigating the biases of fixed scanning orders; and 3) a contextual token selection (CTS) mechanism, which leverages supervisory knowledge to dynamically enlarge the contextual memory for stable long-range modeling. Extensive experiments on 20 benchmarks across diagnostic classification, molecular prediction, and survival analysis demonstrate that MambaMIL+ consistently achieves state-of-the-art performance under three feature extractors (ResNet-50, PLIP, and CONCH), highlighting its effectiveness and robustness for large-scale computational pathology

Investigating CoT Monitorability in Large Reasoning Models

Large Reasoning Models (LRMs) have demonstrated remarkable performance on complex tasks by engaging in extended reasoning before producing final answers. Beyond improving abilities, these detailed reasoning traces also create a new opportunity for AI safety, CoT Monitorability: monitoring potential model misbehavior, such as the use of shortcuts or sycophancy, through their chain-of-thought (CoT) during decision-making. However, two key fundamental challenges arise when attempting to build more effective monitors through CoT analysis. First, as prior research on CoT faithfulness has pointed out, models do not always truthfully represent their internal decision-making in the generated reasoning. Second, monitors themselves may be either overly sensitive or insufficiently sensitive, and can potentially be deceived by models' long, elaborate reasoning traces. In this paper, we present the first systematic investigation of the challenges and potential of CoT monitorability. Motivated by two fundamental challenges we mentioned before, we structure our study around two central perspectives: (i) verbalization: to what extent do LRMs faithfully verbalize the true factors guiding their decisions in the CoT, and (ii) monitor reliability: to what extent can misbehavior be reliably detected by a CoT-based monitor? Specifically, we provide empirical evidence and correlation analyses between verbalization quality, monitor reliability, and LLM performance across mathematical, scientific, and ethical domains. Then we further investigate how different CoT intervention methods, designed to improve reasoning efficiency or performance, will affect monitoring effectiveness. Finally, we propose MoME, a new paradigm in which LLMs monitor other models' misbehavior through their CoT and provide structured judgments along with supporting evidence.

MONICA: Real-Time Monitoring and Calibration of Chain-of-Thought Sycophancy in Large Reasoning Models

Large Reasoning Models (LRMs) suffer from sycophantic behavior, where models tend to agree with users' incorrect beliefs and follow misinformation rather than maintain independent reasoning. This behavior undermines model reliability and poses societal risks. Mitigating LRM sycophancy requires monitoring how this sycophancy emerges during the reasoning trajectory; however, current methods mainly focus on judging based on final answers and correcting them, without understanding how sycophancy develops during reasoning processes. To address this limitation, we propose MONICA, a novel Monitor-guided Calibration framework that monitors and mitigates sycophancy during model inference at the level of reasoning steps, without requiring the model to finish generating its complete answer. MONICA integrates a sycophantic monitor that provides real-time monitoring of sycophantic drift scores during response generation with a calibrator that dynamically suppresses sycophantic behavior when scores exceed predefined thresholds. Extensive experiments across 12 datasets and 3 LRMs demonstrate that our method effectively reduces sycophantic behavior in both intermediate reasoning steps and final answers, yielding robust performance improvements.

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.