PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.

Spreading Depolarization Detection in Electrocorticogram Spectrogram Imaging by Deep Learning: Is It Just About Delta Band?

Prevention of secondary brain injury is a core aim of neurocritical care, with Spreading Depolarizations (SDs) recognized as a significant independent cause. SDs are typically monitored through invasive, high-frequency electrocorticography (ECoG); however, detection remains challenging due to signal artifacts that obscure critical SD-related electrophysiological changes, such as power attenuation and DC drifting. Recent studies suggest spectrogram analysis could improve SD detection; however, brain injury patients often show power reduction across all bands except delta, causing class imbalance. Previous methods focusing solely on delta mitigates imbalance but overlooks features in other frequencies, limiting detection performance. This study explores using multi-frequency spectrogram analysis, revealing that essential SD-related features span multiple frequency bands beyond the most active delta band. This study demonstrated that further integration of both alpha and delta bands could result in enhanced SD detection accuracy by a deep learning model.

RSFR: A Coarse-to-Fine Reconstruction Framework for Diffusion Tensor Cardiac MRI with Semantic-Aware Refinement

Cardiac diffusion tensor imaging (DTI) offers unique insights into cardiomyocyte arrangements, bridging the gap between microscopic and macroscopic cardiac function. However, its clinical utility is limited by technical challenges, including a low signal-to-noise ratio, aliasing artefacts, and the need for accurate quantitative fidelity. To address these limitations, we introduce RSFR (Reconstruction, Segmentation, Fusion & Refinement), a novel framework for cardiac diffusion-weighted image reconstruction. RSFR employs a coarse-to-fine strategy, leveraging zero-shot semantic priors via the Segment Anything Model and a robust Vision Mamba-based reconstruction backbone. Our framework integrates semantic features effectively to mitigate artefacts and enhance fidelity, achieving state-of-the-art reconstruction quality and accurate DT parameter estimation under high undersampling rates. Extensive experiments and ablation studies demonstrate the superior performance of RSFR compared to existing methods, highlighting its robustness, scalability, and potential for clinical translation in quantitative cardiac DTI.

Reason Like a Radiologist: Chain-of-Thought and Reinforcement Learning for Verifiable Report Generation

Radiology report generation is critical for efficiency but current models lack the structured reasoning of experts, hindering clinical trust and explainability by failing to link visual findings to precise anatomical locations. This paper introduces BoxMed-RL, a groundbreaking unified training framework for generating spatially verifiable and explainable radiology reports. Built on a large vision-language model, BoxMed-RL revolutionizes report generation through two integrated phases: (1) In the Pretraining Phase, we refine the model via medical concept learning, using Chain-of-Thought supervision to internalize the radiologist-like workflow, followed by spatially verifiable reinforcement, which applies reinforcement learning to align medical findings with bounding boxes. (2) In the Downstream Adapter Phase, we freeze the pretrained weights and train a downstream adapter to ensure fluent and clinically credible reports. This framework precisely mimics radiologists' workflow, compelling the model to connect high-level medical concepts with definitive anatomical evidence. Extensive experiments on public datasets demonstrate that BoxMed-RL achieves an average 7% improvement in both METEOR and ROUGE-L metrics compared to state-of-the-art methods. An average 5% improvement in large language model-based metrics further underscores BoxMed-RL's robustness in generating high-quality radiology reports.

Unpaired Translation of Chest X-ray Images for Lung Opacity Diagnosis via Adaptive Activation Masks and Cross-Domain Alignment

Chest X-ray radiographs (CXRs) play a pivotal role in diagnosing and monitoring cardiopulmonary diseases. However, lung opac- ities in CXRs frequently obscure anatomical structures, impeding clear identification of lung borders and complicating the localization of pathology. This challenge significantly hampers segmentation accuracy and precise lesion identification, which are crucial for diagnosis. To tackle these issues, our study proposes an unpaired CXR translation framework that converts CXRs with lung opacities into counterparts without lung opacities while preserving semantic features. Central to our approach is the use of adaptive activation masks to selectively modify opacity regions in lung CXRs. Cross-domain alignment ensures translated CXRs without opacity issues align with feature maps and prediction labels from a pre-trained CXR lesion classifier, facilitating the interpretability of the translation process. We validate our method using RSNA, MIMIC-CXR-JPG and JSRT datasets, demonstrating superior translation quality through lower Frechet Inception Distance (FID) and Kernel Inception Distance (KID) scores compared to existing meth- ods (FID: 67.18 vs. 210.4, KID: 0.01604 vs. 0.225). Evaluation on RSNA opacity, MIMIC acute respiratory distress syndrome (ARDS) patient CXRs and JSRT CXRs show our method enhances segmentation accuracy of lung borders and improves lesion classification, further underscoring its potential in clinical settings (RSNA: mIoU: 76.58% vs. 62.58%, Sensitivity: 85.58% vs. 77.03%; MIMIC ARDS: mIoU: 86.20% vs. 72.07%, Sensitivity: 92.68% vs. 86.85%; JSRT: mIoU: 91.08% vs. 85.6%, Sensitivity: 97.62% vs. 95.04%). Our approach advances CXR imaging analysis, especially in investigating segmentation impacts through image translation techniques.

A Comprehensive Survey on Multi-Agent Cooperative Decision-Making: Scenarios, Approaches, Challenges and Perspectives

With the rapid development of artificial intelligence, intelligent decision-making techniques have gradually surpassed human levels in various human-machine competitions, especially in complex multi-agent cooperative task scenarios. Multi-agent cooperative decision-making involves multiple agents working together to complete established tasks and achieve specific objectives. These techniques are widely applicable in real-world scenarios such as autonomous driving, drone navigation, disaster rescue, and simulated military confrontations. This paper begins with a comprehensive survey of the leading simulation environments and platforms used for multi-agent cooperative decision-making. Specifically, we provide an in-depth analysis for these simulation environments from various perspectives, including task formats, reward allocation, and the underlying technologies employed. Subsequently, we provide a comprehensive overview of the mainstream intelligent decision-making approaches, algorithms and models for multi-agent systems (MAS). Theseapproaches can be broadly categorized into five types: rule-based (primarily fuzzy logic), game theory-based, evolutionary algorithms-based, deep multi-agent reinforcement learning (MARL)-based, and large language models(LLMs)reasoning-based. Given the significant advantages of MARL andLLMs-baseddecision-making methods over the traditional rule, game theory, and evolutionary algorithms, this paper focuses on these multi-agent methods utilizing MARL and LLMs-based techniques. We provide an in-depth discussion of these approaches, highlighting their methodology taxonomies, advantages, and drawbacks. Further, several prominent research directions in the future and potential challenges of multi-agent cooperative decision-making are also detailed.

Revisiting Medical Image Retrieval via Knowledge Consolidation

As artificial intelligence and digital medicine increasingly permeate healthcare systems, robust governance frameworks are essential to ensure ethical, secure, and effective implementation. In this context, medical image retrieval becomes a critical component of clinical data management, playing a vital role in decision-making and safeguarding patient information. Existing methods usually learn hash functions using bottleneck features, which fail to produce representative hash codes from blended embeddings. Although contrastive hashing has shown superior performance, current approaches often treat image retrieval as a classification task, using category labels to create positive/negative pairs. Moreover, many methods fail to address the out-of-distribution (OOD) issue when models encounter external OOD queries or adversarial attacks. In this work, we propose a novel method to consolidate knowledge of hierarchical features and optimisation functions. We formulate the knowledge consolidation by introducing Depth-aware Representation Fusion (DaRF) and Structure-aware Contrastive Hashing (SCH). DaRF adaptively integrates shallow and deep representations into blended features, and SCH incorporates image fingerprints to enhance the adaptability of positive/negative pairings. These blended features further facilitate OOD detection and content-based recommendation, contributing to a secure AI-driven healthcare environment. Moreover, we present a content-guided ranking to improve the robustness and reproducibility of retrieval results. Our comprehensive assessments demonstrate that the proposed method could effectively recognise OOD samples and significantly outperform existing approaches in medical image retrieval (p<0.05). In particular, our method achieves a 5.6-38.9% improvement in mean Average Precision on the anatomical radiology dataset.

Is fitting error a reliable metric for assessing deformable motion correction in quantitative MRI?

Quantitative MR (qMR) can provide numerical values representing the physical and chemical properties of the tissues. To collect a series of frames under varying settings, retrospective motion correction is essential to align the corresponding anatomical points or features. Under the assumption that the misalignment makes the discrepancy between the corresponding features larger, fitting error is a commonly used evaluation metric for motion correction in qMR. This study evaluates the reliability of the fitting error metric in cardiac diffusion tensor imaging (cDTI) after deformable registration. We found that while fitting error correlates with the negative eigenvalues, the negative Jacobian Determinant increases with broken cardiomyocytes, indicated by helix angle gradient line profiles. Since fitting error measures the distance between moved points and their re-rendered counterparts, the fitting parameter itself may be adjusted due to poor registration. Therefore, fitting error in deformable registration itself is a necessary but not sufficient metric and should be combined with other metrics.

Topology-Preserving Loss for Accurate and Anatomically Consistent Cardiac Mesh Reconstruction

Accurate cardiac mesh reconstruction from volumetric data is essential for personalized cardiac modeling and clinical analysis. However, existing deformation-based approaches are prone to topological inconsistencies, particularly membrane penetration, which undermines the anatomical plausibility of the reconstructed mesh. To address this issue, we introduce Topology-Preserving Mesh Loss (TPM Loss), a novel loss function that explicitly enforces topological constraints during mesh deformation. By identifying topology-violating points, TPM Loss ensures spatially consistent reconstructions. Extensive experiments on CT and MRI datasets show that TPM Loss reduces topology violations by up to 93.1% while maintaining high segmentation accuracy (DSC: 89.1%-92.9%) and improving mesh fidelity (Chamfer Distance reduction up to 0.26 mm). These results demonstrate that TPM Loss effectively prevents membrane penetration and significantly improves cardiac mesh quality, enabling more accurate and anatomically consistent cardiac reconstructions.

Continuous Online Adaptation Driven by User Interaction for Medical Image Segmentation

Interactive segmentation models use real-time user interactions, such as mouse clicks, as extra inputs to dynamically refine the model predictions. After model deployment, user corrections of model predictions could be used to adapt the model to the post-deployment data distribution, countering distribution-shift and enhancing reliability. Motivated by this, we introduce an online adaptation framework that enables an interactive segmentation model to continuously learn from user interaction and improve its performance on new data distributions, as it processes a sequence of test images. We introduce the Gaussian Point Loss function to train the model how to leverage user clicks, along with a two-stage online optimization method that adapts the model using the corrected predictions generated via user interactions. We demonstrate that this simple and therefore practical approach is very effective. Experiments on 5 fundus and 4 brain MRI databases demonstrate that our method outperforms existing approaches under various data distribution shifts, including segmentation of image modalities and pathologies not seen during training.