computer vision

EviAnchor: Mitigating Hallucinations in Large Vision-Language Models via Regional Visual Evidence Compensation

Large vision-language models (LVLMs) frequently generate content unsupported by visual inputs. Preliminary experiments show that visual evidence is primarily incorporated into answer-side representations in early-to-middle decoder layers, while its direct influence progressively weakens in later layers. This attenuation suggests that visual evidence acquired earlier may be insufficiently utilized during subsequent generation. Based on this observation, we propose EviAnchor, a training-free and single-branch inference framework that preserves and reactivates visual evidence throughout generation. EviAnchor introduces Regional Evidence Anchor (REA) slots to progressively aggregate dense visual tokens into spatially structured representations. It then strengthens the current decision state's access to these visual anchors through decision-conditioned evidence routing, mitigating excessive dependence on textual context. Finally, the model resumes its native Transformer computation to integrate the retrieved visual evidence with question semantics and generation history. Experiments across POPE, CHAIR, and MMHal-Bench demonstrate consistent improvements in visual grounding.

Disentangling Representation using Attributes-based Gaussian Estimation for Medical Sound Diagnosis

Deep learning has a powerful capability of feature extraction. However, the lack of fairness and interpretability in deep neural networks poses limitations to their adoption in the medical domain. This paper proposes a disentangled representation learning (DisenRL) framework, named the Attributes-based Gaussian Estimation for Disentangled Representation (AGEDR), which incorporates Attribute Mapping Embedding (AME) modules designed to map attributes into vectors and align them with a subset of the latent vectors in a Variational AutoEncoder (VAE). This part of the latent vector will be disentangled from the remaining latent vectors by minimizing mutual information. A classifier is then trained using the mean parameters of the latent vectors from the VAE. Extensive experiments demonstrate that AGEDR outperforms both conventional classification models and existing disentangled representation learning methods. The ablation experiments also indicate the disentangling capability and fairness of AGEDR. The source code is publicly available at https://github.com/ZhaoKe1024/DisentangledRepr.

Explainable Artificial Intelligence (XAI) in Computational Pathology: Definitions, Taxonomy, and Recommendations

Computational pathology (CompPath) is transforming medicine by leveraging artificial intelligence (AI) algorithms to support diagnosis, prognosis, and treatment prediction from gigapixel whole-slide images. Clinical adoption is progressing, but is constrained by concerns about safety, accountability, and regulatory oversight in high-stakes clinical environments. Explainable AI (XAI) systems hold promise for building trust and enabling verification, yet the literature remains fragmented due to inconsistent terminology, overlapping methodological families, ad hoc validation, and current reviews. This review aims to formalize XAI methods in CompPath through the: i) introduction of a pathology-centric vocabulary comprising seven core terms; ii) development of a taxonomy across methodological families and three orthogonal axes (stage, type, scope); and iii) establishment of a task-driven framework that maps five clinical questions to recommended methods, method evaluation, and deployment context. Five key gaps between current XAI capabilities and clinical deployment are identified, and actionable steps are proposed to advance XAI for CompPath.

MedTVL: Harnessing Vision and Language for Medical Time Series Classification

Recent advancements in multimodal learning for medical time series (MedTS) classification highlight the benefits of integrating complementary modalities for clinical decision. However, existing methods typically focus on bi-modal interactions (e.g., time series and text), leaving the tri-modal synergy between time series, vision, and language largely unexplored. Inspired by diagnostic practice synergizing numerical assessment, visual inspection and clinical context, we introduce MedTVL, a text-guided dual-pathway architecture tailored for MedTS classification. Specifically, it synergizes a convolution-based temporal pathway for fine-grained temporal dynamics from raw numerical sequences and a transformer-based visual pathway for holistic morphological structures from time-series-derived images. Such combination of cross-modal and architectural heterogeneity provides a comprehensive diagnostic perspective. To further resolve potential diagnostic ambiguity, both pathways are guided by adaptive medical textual semantics. Finally, a Mixture-of-Experts mechanism dynamically routes each instance to specialized fusion experts, capturing instance-specific reliance on the temporal and visual pathway outputs. In addition, MedTVL supports multimodal contrastive learning to mitigate the clinical label scarcity challenge. Extensive experiments across multiple medical datasets and tasks, spanning supervised, few-shot, and contrastive learning settings, demonstrate the superiority and transferability of MedTVL, highlighting its potential for robust clinical decision support.

Integrating Triaxial IMU Sensors and Ensemble Learning for Effective Parkinson Disease Severity Classification

Parkinson disease PD is a progressive neurodegenerative disease that can have a significant impact on motor performance resulting in the appearance of symptoms such as tremors rigidity postural instabilities and bradykinesia. Timely clinical treatment disease management and quality life of the patients are closely linked to early and appropriate identification of PD. Over the past few years the growth of wearable sensor technology and artificial intelligence AI have made it possible to create noninvasive and data driven disease detection methods. This paper proposes a comparative system using artificial intelligence to detect Parkinsons disease by analyzing the motion and tremor data captured by an inertial measurement unit IMU. The data comprises the signals of the acceleration and gyroscope sensors measuring movement in three directions X Y and Z. The signs and symptoms provide helpful information about subtle motor deficits associated with PD. Several classification models like Support Vector Machine SVM Logistic Regression LR KNearest Neighbors KNN Decision Tree DT Extreme Gradient Boosting XGBoost and Light Gradient Boosting Machine LightGBM were used to compare their effectiveness. The Logistic Regression model had a performance around 75 percent in all evaluation metrics and KNearest Neighbours KNN around 90 percent. The support vector machine SVM performed almost 94 percent whereas the performance of classifiers such as Decision Tree and XGBoost was close to 96 percent and overall classification efficacy respectively. LightGBM model performs consistently at the best rank among all of the evaluated methods having Accuracy, Precision, Recall and F1score of around 97 percent. The results show that the proposed machine learning approach offers an accurate and effective predictive capability in the classification of PD severity.

Hyper3-CLIP: Hierarchy-Conditioned Hyperbolic Vision-Language Training

CLIP-like vision-language models (VLMs) trained with contrastive objectives learn strong global image-text representations, but their Euclidean embeddings and global pooling fail to encode relational structure such as part-whole and parent-child relations. Hyperbolic VLMs address this gap with entailment-based objectives, and text-conditioned variants improve fine-grained alignment through sentence- and phrase-level queries. However, these two lines of work remain separate: hyperbolic VLMs use static image and region features, while query-conditioned methods lack hierarchical geometric structure. We present Hyper3-CLIP, a hierarchy-conditioned hyperbolic VLM that combines global, local, and global-local contrastive learning with query-conditioned visual pooling. To train the model, we construct lightweight query hierarchies from text, comprising full captions, sentence fragments, localized part descriptions, and extracted phrases. Each query conditions the pooling of visual patches, and the resulting representations support image-text, whole-part, and parent-child entailment losses. Query-conditioned pooling is active only during training. Hyper3-CLIP improves R@5 and R@10 retrieval on COCO and Flickr, as well as multi-label classification on VOC and COCO, while remaining competitive on hierarchy metrics. We also audit zero-shot prompt sensitivity under fixed prompt regimes and study the effect of the localized GRIT part budget used during training. Code is available at https://github.com/Hyper3Labs/hyper3-clip.

When Generated Images Look Right and Retrieve Wrong: Coverage-Guided Cross-Scale Re-Indexing for Knowledge-Faithful Generative Perception

Multimodal information systems increasingly route generated visual content back through the same vision-language index that informed its production, so the output must remain retrievable by the queries it was meant to serve. When the scene contains entities at vastly different scales, existing language-guided generators condition on a single, globally pooled text embedding and quietly drop scale-specific concepts, breaking concept-query retrieval even when pixel fidelity is high. We formalise this failure as semantic collapse and propose CERES, a closed-loop multimodal indexing framework that builds a three-level semantic pyramid, mines implicit concepts via a co-occurrence-aware router, performs scale-routed cross-attention into a lightweight U-Net generator, and verifies coverage by re-indexing the generated image with the same frozen VLM. A continuously differentiable soft-Jaccard coverage objective returns dense gradients to the 0.39M-parameter generator under explicit non-degeneracy conditions, and coverage is verified by an independent DINOv2 linear probe trained only on external scene and object labels. On four pansharpening benchmarks across seven settings, CERES delivers the new state of the art with the largest gains where scale variation is most extreme. It also improves concept-query retrieval Recall@5 by +14.0 points and image-text mean reciprocal rank by 0.19 over the strongest baseline, showing that the closed loop preserves queryable content rather than self-referential feature consistency.

PepBAN: A Deep Learning Framework with Bilinear Attention and Adversarial Learning for Peptide-Protein Interaction Prediction

Accurate prediction of the peptide-protein interaction (PepPI) is crucial for developing peptide-based therapeutics and vaccines. However, this computational task has traditionally faced significant challenges, such as the scarcity of structure data along with the corresponding label of the binding affinity for bound complexes. To address these challenges, we introduce PepBAN, a deep learning framework for modeling PepPI predictions. PepBAN incorporates two technical advancements: (1) adopting the protein language model ESM-2 to characterize proteins and ESM-2 or a graph-based foundation model for peptides without structure data and (2) leveraging the conditional domain adversarial learning to enhance generalization across a broad range of protein targets, especially when there are limited binding data. At the core of PepBAN is a bilinear attention network (BAN) that effectively learns the pattern of pairwise local interactions, enables the identification of key residues participating in the peptide-protein interactions, and offers an intuitive approach to interpret the underlying mechanisms of PepPIs via analyzing attention weights. Our numerical experiments demonstrated that PepBAN outperformed the previous state-of-the-art models across several well-established benchmark studies. Furthermore, we evaluated PepBAN's applicability in predicting cyclic peptide-protein interactions, a task that poses significant challenges due to the presence of noncanonical amino acids. These nonstandard residues require specialized handling, which most existing sequence-based PepPI prediction models did not adequately address, and we adopt an atom-resolved molecular graph approach to process cyclic peptides. Despite this complexity, PepBAN demonstrated a clear advantage by achieving a superior prediction performance and offering a distinct edge in tackling the emerging chemical space of cyclic peptides, which has great potential for novel therapeutic development. In summary, PepBAN serves as a valuable tool for advancing peptide-based drug and therapeutic development.

SynGFN: learning across chemical space with generative flow-based molecular discovery

Allosteric Cooperativity Mechanism Investigation of Orthosteric and Allosteric Ligands in Modulating AR Activity: A Molecular Dynamics Study

The androgen receptor (AR) represents a pivotal therapeutic target for prostate cancer. However, existing orthosteric ligand-binding pocket (LBP) antagonists [e.g., enzalutamide (ENZ)] encounter significant obstacles due to resistance-conferring mutations in the LBP. Allosteric antagonists targeting the BF3 site exhibit great potential in overcoming such resistance but have low inhibitory efficacy. In our study, we employed an integrated computational modeling strategy, including Gaussian-accelerated molecular dynamics (GaMD), MM/GBSA free-energy calculations, and elastic network model (ENM)-based signaling communication pathway analyses. This approach is used to probe the cooperativity of allosteric BF3 antagonists [e.g., VPC-13808 (VPC)] with diverse orthosteric LBP ligands [e.g., ENZ and testosterone (TES)] in suppressing AR activity. Herein, four types of AR systems were examined: AR bound to LBP agonist (AR·TES), LBP antagonists (e.g., AR·ENZ), and combinations of LBP agonist/antagonist with BF3 antagonist (e.g., AR·TES·VPC and AR·ENZ·VPC). Results indicate that BF3 antagonists can synergize with the LBP antagonist to amplify conformational flexibility in H12 and induce anticorrelated dynamics of H12 with H3 and H4. This induces the downward movement of H12 and its displacement away from H3/H4, triggering the wide opening of the AF2 binding cleft and substantially reducing the coactivator recruitment. Furthermore, the BF3 antagonist can interact with specific residues (e.g., F673, F826, L830, and Y834) and cooperate with the LBP agonist or antagonist to allosterically perturb the AF2 conformation. Multiple short- and/or long-range BF3→AF2 and LBP→AF2 signaling transition pathways are involved, such as F673→Y834→L722→L812→L744→V746→L873→ENZ→L880/V889/V891. These mechanistic insights establish the foundation for developing novel AR BF3 antagonist and LBP-BF3 combination therapies, suggesting a promising avenue for enhancing the efficacy and overcoming the resistance in castration-resistant prostate cancer treatment.

ChargeNet: E(3) Equivariant Graph Attention Network for Atomic Charge Prediction

Atomic charge is a fundamental quantum chemical property essential for advancing drug design and discovery. Although quantum mechanics (QM) methods offer the highest level of accuracy, their computational demands scale quadratically with the number of atoms, limiting their practicality for large-scale applications. In light of this, empirical and semiempirical methods have been introduced to improve computational efficiency, albeit often at the expense of accuracy. The advent of artificial intelligence has witnessed a growing application of machine learning (ML) techniques to accelerate atomic charge predictions. However, existing ML models often suffer from low accuracy and limited generalization capabilities. To address these challenges, we introduce an advanced equivariant graph attention neural network specifically engineered to model long-range atomic electrostatic interactions with high precision. This model introduces a sophisticated global graph attention mechanism, enabling it to capture charge contributions across multiple scales. By utilizing a combination of structural symmetry-preserving transformations and multiscale attention, our approach not only preserves the inherent symmetries of molecular structures but also substantially improves the model's accuracy, generalization, and robustness in complex scenarios. Our empirical analyses demonstrate that, compared to leading baseline models, the proposed model improves charge prediction accuracy by over 40% on average across various charge-calculation schemes. Remarkably, the model achieves superior performance on the external RESP (restrained electrostatic potential) test data sets, with a 54.6% improvement over the baseline. Additionally, we evaluated our charge model under the setting of virtual screening, where it outperforms both the OPLS3 charges and baseline deep learning models across all evaluation metrics, highlighting its extensive potential for scientific discovery.

PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction

Accurate modeling of protein-peptide interactions is essential for understanding fundamental biological processes and designing peptide-based drugs. However, predicting the complex structures of these interactions remains challenging, primarily due to the high conformational flexibility of peptides. To support a fair and systematic evaluation of recent deep learning (DL) approaches, we introduce PepPCBench, a benchmarking framework tailored to assess protein folding neural networks (PFNNs) in protein-peptide complex prediction. As part of this framework, we curated PepPCSet, a data set of 261 experimentally resolved complexes with peptides ranging from 5 to 30 residues. We benchmark five full-atom PFNNs, including AlphaFold3 (AF3), AlphaFold-Multimer (AFM), Chai-1, HelixFold3 (HF3), and RoseTTAFold-All-Atom (RFAA), using comprehensive evaluation metrics. Our benchmarking reveals meaningful performance differences among these methods and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy. While AF3 shows strong performance in structure prediction, further analysis indicates that confidence metrics correlate poorly with experimental binding affinities, underscoring the need for improved scoring strategies and generalizability. By providing a reproducible and extensible framework, PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction.