PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learning

Designing therapeutic peptides with tailored properties is hindered by the vastness of sequence space, limited experimental data, and poor interpretability of current generative models. To address these challenges, we introduce PepThink-R1, a generative framework that integrates large language models (LLMs) with chain-of-thought (CoT) supervised fine-tuning and reinforcement learning (RL). Unlike prior approaches, PepThink-R1 explicitly reasons about monomer-level modifications during sequence generation, enabling interpretable design choices while optimizing for multiple pharmacological properties. Guided by a tailored reward function balancing chemical validity and property improvements, the model autonomously explores diverse sequence variants. We demonstrate that PepThink-R1 generates cyclic peptides with significantly enhanced lipophilicity, stability, and exposure, outperforming existing general LLMs (e.g., GPT-5) and domain-specific baseline in both optimization success and interpretability. To our knowledge, this is the first LLM-based peptide design framework that combines explicit reasoning with RL-driven property control, marking a step toward reliable and transparent peptide optimization for therapeutic discovery.

Beyond the LUMIR challenge: The pathway to foundational registration models

Medical image challenges have played a transformative role in advancing the field, catalyzing algorithmic innovation and establishing new performance standards across diverse clinical applications. Image registration, a foundational task in neuroimaging pipelines, has similarly benefited from the Learn2Reg initiative. Building on this foundation, we introduce the Large-scale Unsupervised Brain MRI Image Registration (LUMIR) challenge, a next-generation benchmark designed to assess and advance unsupervised brain MRI registration. Distinct from prior challenges that leveraged anatomical label maps for supervision, LUMIR removes this dependency by providing over 4,000 preprocessed T1-weighted brain MRIs for training without any label maps, encouraging biologically plausible deformation modeling through self-supervision. In addition to evaluating performance on 590 held-out test subjects, LUMIR introduces a rigorous suite of zero-shot generalization tasks, spanning out-of-domain imaging modalities (e.g., FLAIR, T2-weighted, T2*-weighted), disease populations (e.g., Alzheimer's disease), acquisition protocols (e.g., 9.4T MRI), and species (e.g., macaque brains). A total of 1,158 subjects and over 4,000 image pairs were included for evaluation. Performance was assessed using both segmentation-based metrics (Dice coefficient, 95th percentile Hausdorff distance) and landmark-based registration accuracy (target registration error). Across both in-domain and zero-shot tasks, deep learning-based methods consistently achieved state-of-the-art accuracy while producing anatomically plausible deformation fields. The top-performing deep learning-based models demonstrated diffeomorphic properties and inverse consistency, outperforming several leading optimization-based methods, and showing strong robustness to most domain shifts, the exception being a drop in performance on out-of-domain contrasts.

ViewSpatial-Bench: Evaluating Multi-perspective Spatial Localization in Vision-Language Models

Vision-language models (VLMs) have demonstrated remarkable capabilities in understanding and reasoning about visual content, but significant challenges persist in tasks requiring cross-viewpoint understanding and spatial reasoning. We identify a critical limitation: current VLMs excel primarily at egocentric spatial reasoning (from the camera's perspective) but fail to generalize to allocentric viewpoints when required to adopt another entity's spatial frame of reference. We introduce ViewSpatial-Bench, the first comprehensive benchmark designed specifically for multi-viewpoint spatial localization recognition evaluation across five distinct task types, supported by an automated 3D annotation pipeline that generates precise directional labels. Comprehensive evaluation of diverse VLMs on ViewSpatial-Bench reveals a significant performance disparity: models demonstrate reasonable performance on camera-perspective tasks but exhibit reduced accuracy when reasoning from a human viewpoint. By fine-tuning VLMs on our multi-perspective spatial dataset, we achieve an overall performance improvement of 46.24% across tasks, highlighting the efficacy of our approach. Our work establishes a crucial benchmark for spatial intelligence in embodied AI systems and provides empirical evidence that modeling 3D spatial relationships enhances VLMs' corresponding spatial comprehension capabilities.

The Hitchhiker's Guide to Program Analysis, Part II: Deep Thoughts by LLMs

Static analysis is a cornerstone for software vulnerability detection, yet it often struggles with the classic precision-scalability trade-off. In practice, such tools often produce high false positive rates, particularly in large codebases like the Linux kernel. This imprecision can arise from simplified vulnerability modeling and over-approximation of path and data constraints. While large language models (LLMs) show promise in code understanding, their naive application to program analysis yields unreliable results due to inherent reasoning limitations. We introduce BugLens, a post-refinement framework that significantly improves static analysis precision. BugLens guides an LLM to follow traditional analysis steps by assessing buggy code patterns for security impact and validating the constraints associated with static warnings. Evaluated on real-world Linux kernel bugs, BugLens raises precision from 0.10 (raw) and 0.50 (semi-automated refinement) to 0.72, substantially reducing false positives and revealing four previously unreported vulnerabilities. Our results suggest that a structured LLM-based workflow can meaningfully enhance the effectiveness of static analysis tools.

Embodied-Reasoner: Synergizing Visual Search, Reasoning, and Action for Embodied Interactive Tasks

Recent advances in deep thinking models have demonstrated remarkable reasoning capabilities on mathematical and coding tasks. However, their effectiveness in embodied domains which require continuous interaction with environments through image action interleaved trajectories remains largely -unexplored. We present Embodied Reasoner, a model that extends o1 style reasoning to interactive embodied search tasks. Unlike mathematical reasoning that relies primarily on logical deduction, embodied scenarios demand spatial understanding, temporal reasoning, and ongoing self-reflection based on interaction history. To address these challenges, we synthesize 9.3k coherent Observation-Thought-Action trajectories containing 64k interactive images and 90k diverse thinking processes (analysis, spatial reasoning, reflection, planning, and verification). We develop a three-stage training pipeline that progressively enhances the model's capabilities through imitation learning, self-exploration via rejection sampling, and self-correction through reflection tuning. The evaluation shows that our model significantly outperforms those advanced visual reasoning models, e.g., it exceeds OpenAI o1, o3-mini, and Claude-3.7 by +9\%, 24\%, and +13\%. Analysis reveals our model exhibits fewer repeated searches and logical inconsistencies, with particular advantages in complex long-horizon tasks. Real-world environments also show our superiority while exhibiting fewer repeated searches and logical inconsistency cases.

Evaluating Bias in Retrieval-Augmented Medical Question-Answering Systems

Medical QA systems powered by Retrieval-Augmented Generation (RAG) models support clinical decision-making but may introduce biases related to race, gender, and social determinants of health. We systematically evaluate biases in RAG-based LLM by examining demographic-sensitive queries and measuring retrieval discrepancies. Using datasets like MMLU and MedMCQA, we analyze retrieval overlap and correctness disparities. Our findings reveal substantial demographic disparities within RAG pipelines, emphasizing the critical need for retrieval methods that explicitly account for fairness to ensure equitable clinical decision-making.

Think Twice, Click Once: Enhancing GUI Grounding via Fast and Slow Systems

Humans can flexibly switch between different modes of thinking based on task complexity: from rapid intuitive judgments to in-depth analytical understanding. However, current Graphical User Interface (GUI) grounding systems which locate interface elements based on natural language instructions rely solely on immediate prediction without reasoning, struggling to understand complex interface layouts with nested structures and hierarchical relationships, limiting their effectiveness on complex interfaces. Inspired by human dual-system cognition, we present Focus, a novel GUI grounding framework that combines fast prediction with systematic analysis. The framework dynamically switches between rapid and deliberate processing through an adaptive system switching based on task complexity, optimizing both efficiency and accuracy. Focus decomposes grounding into progressive stages: interface summarization, visual focused analysis, and precise coordinate prediction. This structured decomposition enables systematic understanding of both interface layouts and visual relationships. Extensive experiments show that Focus achieves state-of-the-art performance using only 300K of the training data with a 2B parameter model compared to existing approaches. Focus demonstrates superior performance particularly in complex GUI scenarios, achieving 77.4% average accuracy on ScreenSpot and 13.3% on the more challenging ScreenSpot-Pro. Our analysis reveals the effectiveness of this dual-system approach while demonstrating its potential for improving complex GUI interaction scenarios.

Comparative Analysis of Large Language Models for Context-Aware Code Completion using SAFIM Framework

The advent of Large Language Models (LLMs) has revolutionized code completion, transforming it into a more intelligent and context-aware feature in modern integrated development environments. These advancements have significantly enhanced developers' ability to write efficient and error-free code. This study evaluates the performance of several chat-based LLMs, including Gemini 1.5 Flash, Gemini 1.5 Pro, GPT-4o, GPT-4o-mini, and GPT-4 Turbo, using the Syntax-Aware Fill-in-the-Middle (SAFIM) dataset. This benchmark is specifically designed to assess models' capabilities in syntax-sensitive code generation. Performance metrics, such as cosine similarity with ground-truth completions and latency, were employed to measure both accuracy and efficiency. The findings reveal substantial differences in the models' code completion abilities, offering valuable insights into their respective strengths and weaknesses. This work provides a comparative analysis that underscores the trade-offs between accuracy and speed, establishing a benchmark for future advancements in LLM-based code completion.

Qwen2.5-VL Technical Report

We introduce Qwen2.5-VL, the latest flagship model of Qwen vision-language series, which demonstrates significant advancements in both foundational capabilities and innovative functionalities. Qwen2.5-VL achieves a major leap forward in understanding and interacting with the world through enhanced visual recognition, precise object localization, robust document parsing, and long-video comprehension. A standout feature of Qwen2.5-VL is its ability to localize objects using bounding boxes or points accurately. It provides robust structured data extraction from invoices, forms, and tables, as well as detailed analysis of charts, diagrams, and layouts. To handle complex inputs, Qwen2.5-VL introduces dynamic resolution processing and absolute time encoding, enabling it to process images of varying sizes and videos of extended durations (up to hours) with second-level event localization. This allows the model to natively perceive spatial scales and temporal dynamics without relying on traditional normalization techniques. By training a native dynamic-resolution Vision Transformer (ViT) from scratch and incorporating Window Attention, we reduce computational overhead while maintaining native resolution. As a result, Qwen2.5-VL excels not only in static image and document understanding but also as an interactive visual agent capable of reasoning, tool usage, and task execution in real-world scenarios such as operating computers and mobile devices. Qwen2.5-VL is available in three sizes, addressing diverse use cases from edge AI to high-performance computing. The flagship Qwen2.5-VL-72B model matches state-of-the-art models like GPT-4o and Claude 3.5 Sonnet, particularly excelling in document and diagram understanding. Additionally, Qwen2.5-VL maintains robust linguistic performance, preserving the core language competencies of the Qwen2.5 LLM.

Deep Semantic Graph Learning via LLM based Node Enhancement

Graph learning has attracted significant attention due to its widespread real-world applications. Current mainstream approaches rely on text node features and obtain initial node embeddings through shallow embedding learning using GNNs, which shows limitations in capturing deep textual semantics. Recent advances in Large Language Models (LLMs) have demonstrated superior capabilities in understanding text semantics, transforming traditional text feature processing. This paper proposes a novel framework that combines Graph Transformer architecture with LLM-enhanced node features. Specifically, we leverage LLMs to generate rich semantic representations of text nodes, which are then processed by a multi-head self-attention mechanism in the Graph Transformer to capture both local and global graph structural information. Our model utilizes the Transformer's attention mechanism to dynamically aggregate neighborhood information while preserving the semantic richness provided by LLM embeddings. Experimental results demonstrate that the LLM-enhanced node features significantly improve the performance of graph learning models on node classification tasks. This approach shows promising results across multiple graph learning tasks, offering a practical direction for combining graph networks with language models.