Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design
Cited by (154)
Items 101–154 of 154
- Understanding the host-pathogen evolutionary balance through Gaussian process modeling of SARS-CoV-2Salvatore Loguercio, Ben C. Calverley, Chao Wang, Daniel Shak, Pei Zhao, Shuhong Sun, G. R. Scott Budinger, William E. Balch · 2023 · Patterns
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- Neural network extrapolation to distant regions of the protein fitness landscapeSarah A. Fahlberg, Chase R. Freschlin, Pete Heinzelman, Philip A. Romero · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Optimization of regulatory DNA with active learningYuxin Shen, Grzegorz R. Kudla, Diego A. Oyarzún · 2025 · Computational and Structural Biotechnology Journal
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- Second-generation artificial intelligence approaches for life science researchJürgen Bajorath · 2021 · Artificial Intelligence in the Life Sciences
- Facilitating Machine Learning‐Guided Protein Engineering with Smart Library Design and Massively Parallel AssaysHoi Yee Chu, Alan S.L. Wong · 2021 · Advanced Genetics
- Evaluating point-prediction uncertainties in neural networks for protein-ligand binding predictionYa Ju Fan, Jonathan Allen, Kevin McLoughlin, Da Shi, Brian J. Bennion, Xiaohua Zhang, Felice C. Lightstone · 2023 · Artificial Intelligence Chemistry
- Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencingLena Erlach, Raphael Kuhn, Andreas Agrafiotis, Danielle Shlesinger, Alexander Yermanos, Sai T. Reddy · 2024 · Cell Systems
- Directed Evolution of Proteins via Bayesian Optimization in Embedding SpaceMatouš Soldát, Jǐŕı Kléma · 2024 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Understanding uncertainty in deep learning builds confidenceJürgen Bajorath · 2022 · Artificial Intelligence in the Life Sciences
- Dango: Predicting higher-order genetic interactionsRuochi Zhang, Mihir Bafna, Jianzhu Ma, Jian Ma · 2026 · Cell Systems
- Leveraging conformal prediction to annotate enzyme function space with limited false positivesKerr Ding, Jiaqi Luo, Yunan Luo · 2024 · PLoS Computational Biology
- Nf-Root: A Best-Practice Pipeline for Deep-Learning-Based Analysis of Apoplastic pH in Microscopy Images of Developmental Zones in Plant Root TissueJulian S. Wanner, Luis Kuhn Cuellar, Luiselotte Rausch, Kenneth Wayne Berendzen, Friederike Wanke, Gisela Gabernet, Klaus Harter, Sven Nahnsen · 2024 · Quantitative Plant Biology
- Kermut: Composite kernel regression for protein variant effectsPeter Mørch Groth, Mads Herbert Kerrn, Lars Olsen, Jesper Salomon, Wouter Boomsma · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Advances in computational and data-driven methodologies for accelerating antimicrobial peptide design and discoveryAmal Jayawardena, Andrew Hung, Greg GuangHua Qiao, Elnaz Hajizadeh · 2026 · Progress in Polymer Science
- Challenges and Vision for Standardization of Biopolymer Data Sets for Machine LearningJessica N. Lalonde, Defne Çırcı, Babetta L. Marrone, Stefan Zauscher, L. Catherine Brinson · 2026 · Biomacromolecules
- Specific contributions of artificial intelligence to interdisciplinary life science research – exploring and communicating new opportunitiesJürgen Bajorath · 2022 · Artificial Intelligence in the Life Sciences
- Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad RepeatMaria V. Filsinger Interrante, Shaogeng Tang, Soohyun Kim, Varun R. Shanker, Brian Hie, Theodora U. J. Bruun, Wesley C. H. Wu, John E. Pak, Daniel Fernández, Peter S. Kim · 2025 · ACS Chemical Biology
- Benchmarking Probabilistic Modeling Methods for Protein Fitness Prediction and Uncertainty QuantificationNiketa Penumajji · 2025 · International Conference on Data Science and Information System (ICDSIS)
- Sample-efficient Antibody Design through Protein Language Model for Risk-aware Batch Bayesian OptimizationYanzheng Wang, Boyue Wang, Tianyu Shi, Jie Fu, Yi Zhou, Zhizhuo Zhang · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Evolutionary discovery and characterization of fungal transcriptional activators using active learningLucas M. Waldburger, Hunter M. Nisonoff, Marissa A. Zintel, Liam D. Kirkpatrick, Angelica Lam, Nathan Lanclos, Jay D. Keasling, Max Valentín Staller, Patrick M. Shih · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Systems-level characterization of EGFR kinase inhibitors reveals heterogeneous effects on Mtb-macrophage interactionsCal Gunnarsson, Rachel A. McGinn, Jacob B. Hochfelder, Bryan D. Bryson · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Recent advances in monoclonal antibody development for treatment of B-cell acute lymphoblastic leukemiaHamideh Kamalloo, Mahnaz Fathi, Sobhan Bavandi, Fereshteh Asadi, Sheida Janati, Kumarss Amini · 2025 · Leukemia & lymphoma/Leukemia and lymphoma
- Quantifying uncertainty of tuberculosis drug susceptibility range from single-microplate testEugene B. Postnikov, Anastasia I. Lavrova · 2026 · MethodsX
- Rational design 2.0: transitioning from static structural biology to computational prioritization and iterative vaccine optimization for RSV韦秀龙, Jing Chen, Z Y Li · 2026 · Frontiers in Immunology
- The evaluation crisis in artificial intelligence‐driven computational biology: Pitfalls and solutionsTsung Fei Khang, Joshua W K Ho, Lin Hou, Jiangning Song, Limsoon Wong · 2026 · Quantitative Biology
- Neural Bandits for Protein Sequence OptimizationChenyu Wang, Joseph Kim, Le Cong, Mengdi Wang · 2022 · Conference on Information Sciences and Systems
- Analysis of floor stability in underground coal minesCaio Arthur Santos · 1988 · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)
- Competitive Amplification Networks enable molecular pattern recognition with PCRJohn Goertz, Ruby Sedgwick, Francesca Smith, Myrsini Kaforou, Victoria J. Wright, Jethro Adam Herberg, Zsofia Kote‐Jarai, Rosalind A. Eeles, Michael Levin, Ruth Misener et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Withdrawn: Benchmarking Probabilistic Modeling Methods for Protein Fitness Prediction and Uncertainty QuantificationNiketa Penumajji · 2025 · Preprints.org
- Spatial Clustering of Interface Residues Enhances Few-Shot Prediction of Viral Protein BindingMaxime Basse, Dianzhuo Wang, Eugene I. Shakhnovich · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- TreeGazer: Prospecting Protein Sequence-Function Landscapes via Phylogenetic StructureSebastian Antonio Porras, Samuel J. Davis, Oscar Daniel PAREDES TRUJILLO, Patrick Diep, Gerhard Schenk, Mikael Bodén A · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- A Machine Learning Approach to Identify Small Molecule Inhibitors of Secondary Nucleation in α-Synuclein AggregationRobert I. Horne, Andrea Possenti, Sean Chia, Zacharias Faidon Brotzakis, Roxine Staats, Magdalena Nowinska, Michele Vendruscolo · 2022 · Research Square
- Computer-Aided Synthesis Planning for BiocatalysisWilliam Finnigan · 2023 · Elsevier eBooks
- Detection of Unknown Polymorphic Patterns Using Feature-Extracting Part of a Convolutional AutoencoderPrzemysław Kucharski, Krzysztof Ślot · 2023 · Applied Sciences
- Transfer Learning Bayesian Optimization to Design Competitor DNA Molecules for Use in Diagnostic AssaysRuby Sedgwick, John Goertz, Molly M. Stevens, Ruth Misener, Mark van der Wilk · 2024 · PubMed
- Uncertainty-Aware Discrete Diffusion Improves Protein DesignSazan Mahbub, Christoph Feinauer, Caleb N. Ellington, Le Song, Eric P. Xing · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Phosphines-Nitrogen-Phosphines Chelated CoCl2 Exhibits Potent Antitumor Activity in Pancreatic CancerXuefei Guo, Yang Zhao, Xianle Rong, Xingyu Chen, Xiao Wang, Tian Liu, Yunfei Xie, Yushu Zou, Tian Ming Chu, Xiangxi Wang et al. · 2025 · Research Square
- Optimizing Nominal Current Output in the Elevated Runway Edge Lighting System at Subang Airport through Machine Learning AnalysisW. M. R. Jamaludin, Wan Mazlina Wan Mohamed, N. H. Nik Ali · 2025 · International Conference on Machine Learning Technologies (ICMLT)
- Timeseries transcriptomic profiling workflow of patients-derived colorectal cancer organoids enabling clustering, interpolation, and extrapolationYingao Gao · 2025 · Neurocomputing
- Additional file 1 of A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modelingWang, Dingyan, Yu, Jie, Chen, Lifan, Xutong Li, Jiang, Hualiang, Kaixian Chen, Zheng, Mingyue, Luo, Xiaomin · 2021 · Figshare
- Introduction to Big Data, Artificial Intelligence, and Machine Learning in Computational BiotechnologySerena H. Chen, Yung-Ko Chen · 2025 · Springer handbooks
- Data Diversity and Sequence Length: Key Levers for Powerful Biological AILiam Kozma, Adrienne Hoarfrost · 2026 · NATO science for peace and security series. A, Chemistry and biology
- Application-Specific Measurement Uncertainty Software for Measuring Enrofloxacin Residue in Aquatic Products Using the Quick Quantitative (QQ) MethodBo Rong, Haitao Zhang, Wenjing He, Peilong Song, Yuanyuan Xu, Emmanuel Bob Samuel Simbo, Haizhou Jiang, Liping Qiu, Lei Zhu, Longxiang Fang et al. · 2026 · Biology
- Beyond Exact Matches: Near-Hit Scoring for Protein Binding Site Prediction with Protein Language ModelsYana Podlesna, Vít Škrhák, David Hoksza · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- Uncertainty-aware synthetic lethality prediction with pretrained foundation modelsKailey Hua, Ellie Haber, Jian Ma · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- The landscape of machine learning approaches for modeling protein conformational ensemblesSamuel Sledzieski, Sonya M. Hanson · 2026 · Current Opinion in Structural Biology
- Uncertainty Quantification with Domain Classification Models for Acetylcholinesterase InhibitionJoshua S. Harris, Patricia A. Vignaux, Thomas R. Lane, Sean Ekins · 2026 · Journal of Chemical Information and Modeling
- Uncoupling Type I Interferon Benefits From Inflammatory Toxicity: Transformer‐Prioritized Precision Agonists for Potent and Safer Cancer ImmunotherapyXuefei Guo, Yang Zhao, Xianle Rong, Xingyu Chen, Xiao Wang, Tianyi Liu, Yunfei Xie, Yushu Zou, Pingsen Zhao, Qiang Liu et al. · 2026 · Advanced Science
- Architectural good practices for reproducible benchmarking in protein machine learningJulián Alfonso García - Vinuesa, Diego Fernández Villegas, Michelle Soto-García, Xavier F. Cadet, Mehdi D. Davari, Frédéric Cadet, Juan A. Asenjo, Roberto Uribe-Paredes, David Medina-Ortiz · 2026 · Frontiers in Bioinformatics
- Acquisition Function-Aware Gaussian Process Regression for Airport Visibility Prediction Under Varying Data AvailabilityW. M. R. Jamaludin, Wan Mohamed W. M. · 2026 · International Conference on Machine Learning Technologies (ICMLT)
- Quantitative machine learning of protein interactions reveals the multiscale organization and molecular syntax of signaling networksJulia R. Rogers, Loren P. Cardani, Neel H. Shah, Mohammed AlQuraishi · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Physically Grounded Descriptors for Machine-Learning-Guided Diluent Design in Lithium Metal BatteriesMyeongjun Kim, Chihyun Nam, Hyunmin Lee, Seyeon Shin, Songha Seo, Woojin Chong, Yejin Lee, Munsoo Song, Jongwoo Lim · 2026 · Journal of the American Chemical Society