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Weekly AI/ML & Biotech Digest — Aug 3 to Aug 9, 2026

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ CAFE: A Co-folding Approach for Fragment Exploration of Allosteric and Cryptic Binding Sites — Co-folding models hold immense potential for allosteric drug discovery, but have been severely hampered by their systematic bias toward orthosteric ligand binding. ★ Decoding cancer circulating transcriptomic signatures with language models — Current liquid biopsy methods for multi-cancer detection using plasma cell-free RNA (cfRNA, short RNA fragments circulating in blood that can reflect disease states) typically rely on gene annotations, which can overlook signals from unannotated or repetitive genomic regions. ★ An expanded codebook of human transcription factor DNA-binding specificity — Abstract Gene expression is regulated by transcription factors (TFs), which recognize specific DNA sequence motifs. ★ Generat...
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Weekly AI/ML & Biotech Digest — Jul 27 to Aug 2, 2026

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ A systematic evaluation framework for universal antibody-antigen binding affinity prediction and candidate recommendation ★ Miniaturizing and modifying natural proteins with Raygun ★ Cellular and signalling mechanisms that regulate the blood–brain barrier — The blood-brain barrier (BBB) is a unique specialization of central nervous system (CNS) capillary endothelial cells that controls molecular traffic between the blood and the brain. ★ Structure-free, site-resolved contrastive learningextends small-molecule discovery beyond the reachof structure-based modeling — Virtual screening asks which molecules, among an enormous space of drug-like chemistry, are worth synthesizing and testing against a protein target. ★ Structure and evolution-guided design of minimal RNA-guided nucleases — The design of RNA-guid...
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Weekly AI/ML & Biotech Digest — Jul 20 to Jul 26, 2026

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ AI-redesigned starting points and outcomes enhance protein evolution — Abstract Engineered or laboratory-evolved proteins often have suboptimal stability, activity or specificity. ★ Distributional regression using generalized additive models for location, scale and shape ★ High-throughput machine learning-aided antibody discovery for cell surface antigens — Machine learning (ML) has the potential to revolutionize antibody design and selection, but its success depends on access to well-curated datasets of antibody-antigen interactions.
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Weekly AI/ML & Biotech Digest — Jul 13 to Jul 19, 2026

Curated weekly digest of notable AI/ML and biotech developments. Flagged items are manually selected; remaining items are the week's most recent. 🧬 Biotech ★ Biotech's digital twin dilemma — Nature Biotechnology explores how digital twins — from virtual patients to simulated cells and organs-on-chips — are forecasting disease and guiding drug development. ★ Universal cell embedding provides a foundation model for cell biology — A self-supervised single-cell foundation model (>650M-parameter, 33-layer transformer) trained on 36M cells across eight species, producing a 1,280-dimensional universal embedding that enables zero-shot cross-species cell-type mapping without fine-tuning or annotation. ★ De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging — Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes pr...
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Weekly AI/ML & Biotech Digest — Jul 6 to Jul 12, 2026

Curated weekly digest of notable AI/ML and biotech developments. I really liked the paper " Guiding generative models to uncover diverse and novel crystals via reinforcement learning" by  Hyunsoo Park & Aron Walsh, published in Nature Machine Intelligence. They leveraged RL to guide the generative model to generate novel crystals that differ from the training data distribution, which also showed more stable training behavior. Traditionally model generate new data by sampling in latents space close to the original training data, which limits novelty, and may even hinder the discovery of entirely new structures that are no longer subject to evolutional selection. Very nice work.  Although I do not work on crystal structures, I do feel their work is inspiring for bio-centered AI/ML applications. 🧬 Biotech ★ TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution — A generative foundation model trained on 112 million cells across 12 species ach...
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Weekly AI/ML & Biotech Digest — Jun 29 to Jul 5, 2026

I am starting a series of weekly digest of notable AI/ML and biotech developments related to my own interests. While most of the contents here are published in the past week, I may also add papers that were published earlier but just got my attention. I hope you will find these weekly digests useful. 🧬 Biotech ★ Multivalent mRNA vaccine platform with compatible antigens conferred broad-spectrum protection against orthoebolaviruses' exposure — A multivalent mRNA vaccine platform delivering glycoproteins and nucleoproteins in a single LNP for broad-spectrum protection against EBOV, SUDV, and BDBV. (PNAS) ★ Biomolecular profiling for noninvasive health monitoring — A review highlighting how MS-based molecular discovery and wearable sensing serve as complementary approaches for continuous, noninvasive health monitoring. (Nature Biotechnology) 🤖 AI/ML ★ Evaluating Large Language Models in Scientific Discovery — A scenario-grounded benchmark evaluating LLMs across bi...
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Adding Apple Silicon (MPS) Support to FlashABB

  FlashABB is a fast antibody structure prediction library from the Oxford Protein Informatics Group. (OXPIG) with a preprint here . It predicts paired VH/VL structures, scores, developability (FlashTAP), and produces structure-aware sequence embeddings (FlashABB-SSS) — all from a single "HEAVY|LIGHT" sequence string, with weights bundled in the repo. The library was written for CUDA. Getting it running on Apple Silicon required fixing five separate issues. I worked with Claude Code and got the following fixes:   --- Fix 1 — pip ≥ 26 editable install pip 26 dropped the legacy setup.py-only editable install fallback. A minimal pyproject.toml was all that was needed:   [build-system]   requires = ["setuptools>=64", "wheel"]   build-backend = "setuptools.build_meta"   ---   Fix 2 — Device auto-detection   Three places hardcoded device='cuda'. Replaced with a helper:   def _default_device():       if torch.cuda.is_available(): ...
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