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Protein Set Transformer: a protein-based genome language model to power high-diversity viromics Open
Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of …
View article: A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data Open
Computational blind challenges offer critical, unbiased assessment opportunities to assess and accelerate scientific progress, as demonstrated by a breadth of breakthroughs over the last decade. We report the outcomes and key insights from…
MPAC: a computational framework for inferring pathway activities from multi-omic data Open
Motivation Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflic…
View article: A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data Open
Computational blind challenges offer critical, unbiased assessment opportunities to assess and accelerate scientific progress, as demonstrated by a breadth of breakthroughs over the last decade. We report the outcomes and key insights from…
View article: A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data Open
Computational blind challenges offer critical, unbiased assessment opportunities to assess and accelerate scientific progress, as demonstrated by a breadth of breakthroughs over the last decade. We report the outcomes and key insights from…
Chemical Language Model Linker: Blending Text and Molecules with Modular Adapters Open
The development of large language models and multimodal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening…
View article: A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data
A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data Open
Computational blind challenges offer critical, unbiased assessment opportunities to assess and accelerate scientific progress, as demonstrated by a breadth of breakthroughs over the last decade. We report the outcomes and key insights from…
Responsible Biodesign Workshop: AI, Protein Design, and the Biosecurity Landscape – Recommended Actions Open
This report presents Recommended Actions from the January 2025 Responsible Biodesign Workshop, which convened leading experts across AI-enabled biomolecular design and biosecurity policy. Building on existing community commitments for the …
Responsible Biodesign Workshop: AI, Protein Design, and the Biosecurity Landscape – Recommended Actions Open
This report presents Recommended Actions from the January 2025 Responsible Biodesign Workshop, which convened leading experts across AI-enabled biomolecular design and biosecurity policy. Building on existing community commitments for the …
Exploring zero-shot structure-based protein fitness prediction Open
The ability to make zero-shot predictions about the fitness consequences of protein sequence changes with pre-trained machine learning models enables many practical applications. Such models can be applied for downstream tasks like genetic…
Product Manifold Representations for Learning on Biological Pathways. Open
Machine learning models that embed graphs in non-Euclidean spaces have shown substantial benefits in a variety of contexts, but their application has not been studied extensively in the biological domain, particularly with respect to biolo…
Assay2Mol: Large Language Model-based Drug Design Using BioAssay Context Open
Initial release
Protein Set Transformer: A protein-based genome language model to power high diversity viromics Open
Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of …
View article: A renewed call for open artificial intelligence in biomedicine
A renewed call for open artificial intelligence in biomedicine Open
The excitement around and usage of artificial intelligence (AI) tools in scientific research is increasing across fields, but lax publication standards are resulting in papers "like grand mansions of straw, rather than sturdy houses of bri…
Protein Set Transformer: A protein-based genome language model to power high diversity viromics Open
Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of …
MPAC: a computational framework for inferring pathway activities from multi-omic data Open
Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflicting measur…
Biophysics-based protein language models for protein engineering Open
Protein language models trained on evolutionary data have emerged as powerful tools for predictive problems involving protein sequence, structure, and function. However, these models overlook decades of research into biophysical factors go…
View article: Current and future directions in network biology
Current and future directions in network biology Open
Summary Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although t…
View article: Current and future directions in network biology
Current and future directions in network biology Open
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
View article: Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries Open
Traditional small-molecule drug discovery is a time-consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine-learning metho…
HIV-1 virological synapse formation enhances infection spread by dysregulating Aurora Kinase B Open
HIV-1 spreads efficiently through direct cell-to-cell transmission at virological synapses (VSs) formed by interactions between HIV-1 envelope proteins (Env) on the surface of infected cells and CD4 receptors on uninfected target cells. En…
View article: Evaluating scalable supervised learning for synthesize-on-demand chemical libraries
Evaluating scalable supervised learning for synthesize-on-demand chemical libraries Open
Traditional small molecule drug discovery is a time consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine learning metho…
View article: Datasets for evaluating scalable supervised learning for synthesize-on-demand chemical libraries
Datasets for evaluating scalable supervised learning for synthesize-on-demand chemical libraries Open
This repository contains datasets for the manuscript "Evaluating scalable supervised learning for synthesize-on-demand chemical libraries": ams_all_preds.csv.gz: The AMS dataset predictions when using an RF or baseline model trained on the…
View article: Datasets for evaluating scalable supervised learning for synthesize-on-demand chemical libraries
Datasets for evaluating scalable supervised learning for synthesize-on-demand chemical libraries Open
This repository contains datasets for the manuscript "Evaluating scalable supervised learning for synthesize-on-demand chemical libraries": ams_all_preds.csv.gz: The AMS dataset predictions when using an RF or baseline model trained on the…
View article: Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Application of Traditional Vaccine Development Strategies to SARS-CoV-2 Open
The development, production, and distribution of vaccines is imperative to saving lives, preventing illness, and reducing the economic and social burdens caused by the COVID-19 pandemic. Vaccines that use cutting-edge biotechnology have pl…
View article: The Coming of Age of Nucleic Acid Vaccines during COVID-19
The Coming of Age of Nucleic Acid Vaccines during COVID-19 Open
The SARS-CoV-2 pandemic has caused untold damage globally, presenting unusual demands on but also unique opportunities for vaccine development. The development, production, and distribution of vaccines are imperative to saving lives, preve…
A Text-guided Protein Design Framework Open
Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level functionalities. Yet, wheth…
View article: Evaluating scalable supervised learning for synthesize-on-demand chemical libraries
Evaluating scalable supervised learning for synthesize-on-demand chemical libraries Open
Traditional small molecule drug discovery is a time consuming and costly endeavor. High-throughput chemical screening can only assess a tiny fraction of drug-like chemical space. The strong predictive power of modern machine learning metho…
Alternative splicing liberates a cryptic cytoplasmic isoform of mitochondrial MECR that antagonizes influenza virus Open
Viruses must balance their reliance on host cell machinery for replication while avoiding host defense. Influenza A viruses are zoonotic agents that frequently switch hosts, causing localized outbreaks with the potential for larger pandemi…