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- AI | Biology | Pharmaceutical
New Molecule generation
There are many tools for generating new molecules needed for new drugs. Some are open source and other’s are made by companies as paid subscriptions or paid collaborations. These AI tools help in docking of a new chemical entity to the protein of interest, or they can also help in designing the chemical compound, DNA/RNA…
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)…
Explainable AI
A very traditional problem solving method is the following: given a set of features or variables, can we understand the features to form a conclusion. This could be something like a treatment strategy wherein the strategy is built on a series of data and then ingesting the data helps make a conclusion. However, an equally…
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…
Functional prediction of microbial sequences
Even with E.coli and M.tuberculosis we only know ½ of them. Can you use ML model to define function: as natural language, or molecular interaction or chemical reaction. Function as molecular interaction: protein – protein interaction. Genomics: Learn association between genes (just like words). It is called gLM2. A multi-modal single residue resolution gLM. GLM2…
Opencell
Discussion by Manu Leonetti at Chan Zuckerberg hub. Self driving cars are taught in simulation. Similar biology should be also done as simulations. The cell needs to be thought as devices. How does information flow within a cell and do that in cells. Use GFP to tag the cells but also later use it for…
