001 A collaborative graph-transformer network for spatial transcriptomics data clustering with semantic graph induction Semantic Scholar Paper Jiangkai Long, Yanran Zhu et al. Oct 1 002 Deep learning approaches for microscopic detection and surface localization of leukemic cells Semantic Scholar Paper J. A. Téllez‐Morales, Antoine Ferreira et al. Sep 1 003 Depth-based segment any leaf: A zero-shot pipeline for plant disease detection Semantic Scholar Paper Duygu Sinanc Sep 1 004 Enhancing protein subcellular localization prediction through language model-based knowledge embeddings and machine learning techniques. Semantic Scholar Paper Karthik Avinash, S. Tejas et al. Sep 1 005 Medium-aware multi-task learning for robust bacterial identification using Raman spectroscopy. Semantic Scholar Paper Weibiao Shi, Hao Xie et al. Sep 1 006 NSGA-II enhanced with dual-rank selection and pool-guided mutation for feature selection in microarray data classification Semantic Scholar Paper Min Li, Weicheng Wu et al. Sep 1 007 Odor-evoked modulation of functional network dynamics in the Drosophila brain revealed by pairwise MEM Semantic Scholar Paper Xiaoru Zhang, Jiaqi Fan et al. Sep 1 008 scCCCT: Single-cell RNA-seq data contrastive clustering network with hierarchical cell transformer Semantic Scholar Paper Shan Zhao, Zhongyang Zhou et al. Sep 1 009 Towards scalable deep learning for automated microscopy in harmful algal bloom monitoring: Data-centric workflow and multi-region generalisation. Semantic Scholar Paper Negar Taheriashtiani, Glenn B. McGregor et al. Aug 15 010 Multi-Modal Representation for Spatially Resolved Transcriptomics Based on Global Correlation and Dynamic Cluster Discovery Semantic Scholar Paper Chuanxiu Li, Shengwu Xiong et al. Aug 9 011 SGA: Self-boosting Attributed Graph Alignment via Neighborhood Consistency-based Edge Enhancement Semantic Scholar Paper Chenxu Wang, Wencong Lin et al. Aug 9 012 Antibiotic resistance gene identification using cross-feature transformer from metagenomic data Semantic Scholar Paper S. K., J. Jothi Aug 1 013 Astragalin alleviates ulcerative colitis via FPR1 inhibition and restores Microbiota-Metabolite Homeostasis: A mechanism revealed by deep learning. Semantic Scholar Paper Fang Zhang, Cong Wang et al. Aug 1 014 Hypergraph regularization and reinforcement learning for micro-ribonucleic acid-disease association prediction Semantic Scholar Paper Huaibin Hou, Zhentao Hu et al. Aug 1 015 Overcoming sparsity in micro ribonucleic acid-messenger ribonucleic acid regulatory networks: A graph sample and aggregate framework with learnable virtual nodes Semantic Scholar Paper Zhiping Sun, Ling Guo et al. Aug 1 016 SCTGE infers transformer-based graph embeddings to improve cell-cell interaction identification and cell identity annotations Semantic Scholar Paper Yichong Si, Chenxi Li et al. Aug 1 017 Enhancing Super-Resolution Spatial Transcriptomics Data by Transfer Learning. Semantic Scholar Paper Xiaoyu Li, Lihua Zhang et al. Jul 20 018 MSstatsQC-ML: A Supervised Machine Learning Approach to Monitor System Suitability and Quality Control in Mass Spectrometry-Based Proteomics. Semantic Scholar Paper Eralp Doğu, Shantam Gupta et al. Jul 20 019 Artificial Intelligence and Protein Design: A retrospective study on 20-year emerging trends and core research areas from bibliometric perspectives. Semantic Scholar Paper Wenjuan Zhao, Xiuwu Pan et al. Jul 18 020 Integrating single-cell sQTL mapping with deep-learning splicing prediction identifies causal variants under influenza infection. Semantic Scholar Paper Liuyang Wang, Guinevere G Connelly et al. Jul 18 021 Investigating the mechanisms of malignant progression in colorectal cancer using weighted gene co-expression network analysis and machine learning Semantic Scholar Paper Song Zheng, Lei Meng et al. Jul 18 022 Machine learning meets ecology: XGBoost-based prediction of endangered species habitats using multi-source environmental data Semantic Scholar Paper Aref Hesabi, Seyed Jalil Alavi et al. Jul 18 023 Orientation Reading by Production Vision-Language Models on Optotype Charts: A Controlled Multi-Model Evaluation Across Reasoning Modes, Prompts, and Access Modalities arXiv Paper Shahryar Wasif, A. Sandhu et al. Jul 18 024 Random Forest Modeling to Predict Small Molecule Accumulation in Gram-Negative Bacteria. Semantic Scholar Paper Blake R Levy, P. Hergenrother Jul 18 025 An enzyme-specific protein language model for catalytic property prediction. Semantic Scholar Paper Chong Wang, Mengyao Li et al. Jul 17 026 Artificial intelligence powered decoding of Plasmodium falciparum sporozoite motility patterns. Semantic Scholar Paper C. Naar, K. Pirkovets et al. Jul 17 027 From Optimal Policies to Individual Differences: Rethinking Reinforcement Learning for Biology arXiv Paper Patrick Govoni, P. Bartashevich et al. Jul 17 028 PumpKin: A machine-learning pipeline for automatically tracking localized kinematics in freely moving C. elegans. Semantic Scholar Paper Erin Shappell, Debra Buggs et al. Jul 17 029 SPPIPred: Stacking-based ensemble learning model for identification of protein-protein interaction Semantic Scholar Paper M. Rahman, M. Ali et al. Jul 17 030 STSBench: A Large-Scale Dataset for Modeling Neuronal Activity in the Dorsal Stream of Primate Visual Cortex arXiv Paper Ethan Trepka, Ruobing Xia et al. Jul 17 031 Toward a mechanistic understanding of inference in visual cortex and diffusion models arXiv Paper Zeyu Yun, Alexander Belsten et al. Jul 17 032 scFANCL: Dual contrastive learning with false-negative correction at cell level for single-cell RNA-seq clustering. Semantic Scholar Paper Gunho Choi, Minsik Oh Jul 17 033 A Deterministic Binary Fingerprinting Framework with Zero-Trained Feature Extraction for Sparse Count Matrices arXiv Paper Lei Zhao, Fujin Huang et al. Jul 16 034 A non-linear game for two: genetic parameters and prediction of fertilization success using Bayesian and machine learning frameworks Semantic Scholar Paper Fotis Pappas, P. Debes et al. Jul 16 035 Bioinformatics identification of candidate biomarkers associated with T cell proliferation in atherosclerosis via WGCNA and machine learning. Semantic Scholar Paper Wen Xiong, Xiang Long et al. Jul 16 036 FENNEC: photon-level deep learning for classifying bursts in diffusion-based single-molecule FRET Semantic Scholar Paper B. Schiffrin, J. Crossley Jul 16 037 Follicle Identification in Primate Ovaries Via Machine Learning†. Semantic Scholar Paper James P. Sluka, Riley Israels et al. Jul 16 038 Genomic foundation model embeddings encode higher-order viral genome architecture beyond sequence composition: a benchmark of Evo 2 Semantic Scholar Paper Deyvid E Amgarten, A. Schinaid et al. Jul 16 039 HELMify: A Hybrid Rule- and LLM-Based Generator of Peptide Monomer HELM Names. Semantic Scholar Paper Robert P. Sheridan, Rajvi Shah et al. Jul 16 040 MInt-HDX: Leveraging Hydrogen-Deuterium Exchange Mass Spectrometry and Machine-Learning to Improve Protein-Ligand Docking Semantic Scholar Paper Vincent M. Lowe, Ally K. Smith et al. Jul 16 041 Machine Learning-Guided Engineering of High-Affinity Cross-Reactive Antibodies with Minimal Mutations Semantic Scholar Paper H. Dorison, Anne-Laure Grindel et al. Jul 16 042 Multimodal Semantic-Aware Contrastive Learning For False Negative Mitigation in 3D Medical Imaging arXiv Paper Sara Ketabi, M. Wagner et al. Jul 16 043 Multimodality as Supervision: Self-Supervised Specialization to the Test Environment via Multimodality arXiv Paper Kunal Pratap Singh, Ali Garjani et al. Jul 16 044 ORBIT: Oncogenic Representation Learning via Bi-Prototype Contrastive Learning in Hyperbolic Space for cancer driver gene identification. Semantic Scholar Paper Sang-Pil Cho, Young-Rae Cho Jul 16 045 Shifu: an integrated framework for deep learning of RNA secondary structure Semantic Scholar Paper Gabriel Galvez, Quentin Vicens Jul 16 046 SpaVCCA Identifies Spatial Transcriptomics Domains Across Slices by Coupling Variational Autoencoder with Canonical Correlation Analysis. Semantic Scholar Paper Zhen-Hao Guo, Yanbin Wang et al. Jul 16 047 What Do Generative Models Learn About Adaptive Immune Receptor Repertoires? A Benchmark Study Semantic Scholar Paper Charlotte Würtzen, Maria Mamica et al. Jul 16 048 A Deep Learning Framework for Biomarker Segmentation and Classification in Traumatic Brain Injury Semantic Scholar Paper Rohan Dash, K. Mayilsamy et al. Jul 15 049 A deep neural network for automatic prediction of mouse behavior from ultrasonic vocalizations emitted during social interaction test. Semantic Scholar Paper Alessandro Gnutti, M. Premoli et al. Jul 15 050 A geometric and dynamical theory of latent computations in biological neural networks Semantic Scholar Paper Fatih Dinç, M. Blanco-Pozo et al. Jul 15 051 A modular state-space model of human perception, cognition, and decision dynamics arXiv Paper Sven Schoonebeek, C. Cenedese et al. Jul 15 052 A vision foundation model for single-cell biology via spatial gene cartography arXiv Paper Ridvan Yesiloglu, Sakib Mostafa et al. Jul 15 053 Automated comet assay analysis using YOLOv5-based deep learning. Semantic Scholar Paper Adna Softić, Faruk Bećirović et al. Jul 15 054 Automatic Ordinary Differential Equations Discovery For Biological Systems Using Large Language Model Powered Agentic System arXiv Paper D. Krongauz, A. Zulti et al. Jul 15 055 Evaluating Encoding Strategies for Closed-Loop Classification in Biological Neural Networks arXiv Paper Martin Schottlender, V. Volkova et al. Jul 15 056 Gradient-Guided Graph Contrastive Learning for Mass Spectrometry-Based Proteomics Clustering. Semantic Scholar Paper Yan Liu, Tai-Yuan Xia et al. Jul 15 057 Identifying Potential Exosome-Derived mRNA Biomarkers for Diagnosis and Prediction of Breast Cancer Using Machine-Learning Approaches. Semantic Scholar Paper Chen-Hao Li, Chunyan Wei et al. Jul 15 058 LATTICE: Graph Self-Supervised Learning for Multimodal Spatial Omics Integration arXiv Paper J. Dwarampudi, V. Kochat et al. Jul 15 059 MetaPerch: Learning from metadata for bioacoustics foundation models arXiv Paper Mustafa Chasmai, Vincent Dumoulin et al. Jul 15 060 MiGenPro: A linked data workflow for phenotype-genotype prediction of microbial traits using machine learning Semantic Scholar Paper M. Loomans, M. Suárez-Diez et al. Jul 15