A good website keeping us all current for biological AI models.
There are not that many open models but the website lists their “openness” and their citation.
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Reinforcement learning
Reinforcement learning is a method that drives learning and memory in primitive species such as birds, humans and other living species to its use in machine learning. It is used to influence the behavior of us humans on social media to its use to train machines. The essential components were initiated by BF Skinner 20th…
Open source protein models
A company called Profluent (profluent.bio) has been developing protein models that can be used for designing new proteins (https://www.nature.com/articles/s41587-022-01618-2), modeling of new CRISPR-Cas sequences (https://www.nature.com/articles/s41586-025-09298-z) and developing LLM for protein generation (https://www.biorxiv.org/content/10.1101/2025.11.12.688125v1.article-info). What is amazing is that they have open sourced all their models and Profluent-E1 is available in GitHub to download and use. (https://github.com/Profluent-AI/E1)…
- AI | Biology | Biomarker | Pharmaceutical
Biotech companies
Small Biotechs: Diagonal Tx: Clustering antibodies that mimic the action of the ligand and bypass the need for the ligand and receptor. This mutation that is created makes standard AI models not useful and so need a new method. This restores new ALK1 signaling in Hereditary Hemorrhagic Telangiectasia. It also treates LoF mutations in ALK1…
Error codes
There is no error code in the answers that are provided by AI prompts. It will return an answer that is the best fit to the prompt or the question, but it does not tell you the probability that it is not correct or that it is low probability of answer. The conversational AI will…
Fitness landscape for antibodies (Flab2)
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DeepSpot
Kalin Klonchev – the winner of a competition for AI based data analysis from Broad in 2024 had also created a tool called DeepSpot. Worth looking at for spot analysis of H&E sections by converting a full H&E slide pictures to “spots” which are analyzed. Some good links: DeepSpot paper: https://www.medrxiv.org/content/10.1101/2025.02.09.25321567v1 DeepSpot GitHub repository: https://github.com/ratschlab/DeepSpot…
