Hugging Science https://huggingscience.co AI for Science — curated blog posts, datasets, and resources from the Hugging Science community. en Fri, 01 May 2026 14:18:15 GMT Tropical Quivers for Modern AI: A Guided Tour of a Research Program https://huggingface.co/blog/AmelieSchreiber/tropical-quivers-of-archs https://huggingface.co/blog/AmelieSchreiber/tropical-quivers-of-archs Sun, 22 Mar 2026 00:00:00 GMT AmelieSchreiber A tour of tropical quiver representations and how their combinatorial structure connects to modern AI architectures. mathematics Surface Orders, Cyclic Time, and a Concrete Hilbert–Pólya Framework https://huggingface.co/blog/AmelieSchreiber/hilbert-polya-for-grh https://huggingface.co/blog/AmelieSchreiber/hilbert-polya-for-grh Tue, 17 Mar 2026 00:00:00 GMT AmelieSchreiber A concrete construction toward the Hilbert–Pólya conjecture using surface orders and cyclic-time symmetry as a route to the Riemann Hypothesis. mathematics ThermoGFN-IF for Catalysis https://huggingface.co/blog/AmelieSchreiber/thermogfn-if https://huggingface.co/blog/AmelieSchreiber/thermogfn-if Tue, 10 Mar 2026 00:00:00 GMT AmelieSchreiber A protein sequence design model fine-tuned with GFlowNets for thermostable and kinetically-aware enzyme engineering. biology, chemistry, medicine How to Build a Benchmark with a Private Test Set on Hugging Face https://huggingface.co/blog/hugging-science/building-a-benchmark-or-challenge https://huggingface.co/blog/hugging-science/building-a-benchmark-or-challenge Mon, 16 Feb 2026 00:00:00 GMT hugging-science A step-by-step guide to creating, hosting, and managing a benchmark challenge with a hidden test set on Hugging Face. Did GPT-5.2 Make a Breakthrough Discovery in Theoretical Physics? https://huggingface.co/blog/dlouapre/gpt-single-minus-gluons https://huggingface.co/blog/dlouapre/gpt-single-minus-gluons Sun, 01 Feb 2026 00:00:00 GMT dlouapre GPT-5.2 conjectured a compact formula for single-minus gluon tree amplitudes previously assumed to be zero for 40 years — a striking example of AI contributing to original theoretical physics. physics, mathematics A Comprehensive Introduction to AI for Proteins (2026) https://www.tamarind.bio/blog/a-comprehensive-introduction-to-ai-for-proteins https://www.tamarind.bio/blog/a-comprehensive-introduction-to-ai-for-proteins Thu, 01 Jan 2026 00:00:00 GMT a-comprehensive-introduction-to-ai-for-proteins A thorough primer on the state of AI for protein science — covering structure prediction, protein language models, generative design, and the full open-source model landscape. biology, chemistry, medicine SAIR: Accelerating Pharma R&D with AI-Powered Structural Intelligence https://huggingface.co/blog/SandboxAQ/sair-data-accelerating-drug-discovery-with-ai https://huggingface.co/blog/SandboxAQ/sair-data-accelerating-drug-discovery-with-ai Sat, 06 Sep 2025 00:00:00 GMT SandboxAQ How SandboxAQ's SAIR dataset of 1M+ protein–ligand structures is enabling AI-powered drug discovery with unprecedented structural coverage. chemistry, medicine, biology Boltz-2: State of the Art Structure and Binding Affinity Prediction https://www.tamarind.bio/blog/boltz2-state-of-the-art-structure-and-binding-affinity-prediction https://www.tamarind.bio/blog/boltz2-state-of-the-art-structure-and-binding-affinity-prediction Wed, 18 Jun 2025 00:00:00 GMT boltz2-state-of-the-art-structure-and-binding-affinity-prediction Boltz-2 outperforms AlphaFold3 on antibody-antigen interfaces and sets a new state of the art for protein-ligand binding affinity prediction. biology, chemistry, medicine Boltzdesign1: Designing De Novo Binders to More Than Just Proteins https://www.tamarind.bio/blog/boltzdesign1-small-molecule-rna-dna-protein-metal-binder-design https://www.tamarind.bio/blog/boltzdesign1-small-molecule-rna-dna-protein-metal-binder-design Sun, 01 Jun 2025 00:00:00 GMT boltzdesign1-small-molecule-rna-dna-protein-metal-binder-design BoltzDesign1 extends de novo binder design beyond protein targets to small molecules, RNA, DNA, and metal ions. biology, chemistry, medicine OpenFold3 and The Future of Protein Folding https://www.tamarind.bio/blog/openfold3-fully-open-alphafold3-alternative https://www.tamarind.bio/blog/openfold3-fully-open-alphafold3-alternative Tue, 01 Apr 2025 00:00:00 GMT openfold3-fully-open-alphafold3-alternative OpenFold3 is a fully open-source, commercially available AlphaFold3 alternative backed by the OpenFold Consortium — enabling unrestricted biomolecular structure prediction. biology, chemistry IntFold: A New Best Structure Prediction Protocol https://www.tamarind.bio/blog/intfold-a-new-state-of-the-art https://www.tamarind.bio/blog/intfold-a-new-state-of-the-art Sat, 01 Mar 2025 00:00:00 GMT intfold-a-new-state-of-the-art IntFold establishes a new state-of-the-art protocol for biomolecular complex structure prediction, setting records across standard benchmarks. biology, chemistry Chai-1r: AlphaFold3 Level Performance, Now Completely Open Source https://www.tamarind.bio/blog/chai-1-alphafold3-level-performance-now-completely-open-source https://www.tamarind.bio/blog/chai-1-alphafold3-level-performance-now-completely-open-source Sat, 01 Feb 2025 00:00:00 GMT chai-1-alphafold3-level-performance-now-completely-open-source Chai-1r achieves AlphaFold3-level accuracy on protein-protein and antibody-antigen complexes with fully open weights and no usage restrictions. biology, chemistry, medicine Open-R1: A Fully Open Reproduction of DeepSeek-R1 https://huggingface.co/blog/open-r1 https://huggingface.co/blog/open-r1 Tue, 28 Jan 2025 00:00:00 GMT lvwerra A fully open reproduction of DeepSeek-R1's math reasoning training pipeline — data, code, and models — bringing transparent reasoning model training to the community. mathematics Physics Informed Neural Networks (PINNs): An Intuitive Guide https://towardsdatascience.com/physics-informed-neural-networks-pinns-an-intuitive-guide-fff138069563/ https://towardsdatascience.com/physics-informed-neural-networks-pinns-an-intuitive-guide-fff138069563/ Tue, 28 Jan 2025 00:00:00 GMT towardsdatascience.com A clear, intuitive walkthrough of how PINNs embed physical laws directly into neural network training — bridging traditional PDE-based modeling with data-driven deep learning. physics, mathematics, engineering AI for PDEs https://huggingface.co/blog/hugging-science/pde https://huggingface.co/blog/hugging-science/pde Wed, 01 Jan 2025 00:00:00 GMT hugging-science Exploring AI approaches to solving partial differential equations. physics, mathematics, engineering SARLO-80: SAR Optic Language Dataset https://huggingface.co/blog/hugging-science/sarlo-80-sar-optic-language-dataset https://huggingface.co/blog/hugging-science/sarlo-80-sar-optic-language-dataset Wed, 01 Jan 2025 00:00:00 GMT hugging-science Introducing a large-scale dataset for SAR and optical remote sensing with language descriptions. earth-science, climate Eve Bio: Mapping the Pharmone Drug Interaction https://huggingface.co/blog/hugging-science/eve-bio-mapping-the-pharmone-drug-interaction https://huggingface.co/blog/hugging-science/eve-bio-mapping-the-pharmone-drug-interaction Wed, 01 Jan 2025 00:00:00 GMT hugging-science Understanding drug interactions through AI-powered pharmacogenomics. medicine, biology, chemistry The ExpansionRx OpenADMET Blind Challenge https://huggingface.co/blog/hugging-science/the-expansionrx-openadmet-blind-challenge https://huggingface.co/blog/hugging-science/the-expansionrx-openadmet-blind-challenge Wed, 01 Jan 2025 00:00:00 GMT hugging-science A blind challenge for predicting ADMET properties in drug discovery. medicine, chemistry PromoterGPT https://huggingface.co/blog/hugging-science/promoter-gpt https://huggingface.co/blog/hugging-science/promoter-gpt Wed, 01 Jan 2025 00:00:00 GMT hugging-science AI-powered promoter sequence design and analysis. biology, genomics AI for Food Allergies https://huggingface.co/blog/hugging-science/ai-for-food-allergies https://huggingface.co/blog/hugging-science/ai-for-food-allergies Wed, 01 Jan 2025 00:00:00 GMT hugging-science Applying AI to understand and predict food allergies. medicine, biology GDP: Generative Design for Proteins https://huggingface.co/blog/cgeorgiaw/gdp https://huggingface.co/blog/cgeorgiaw/gdp Wed, 01 Jan 2025 00:00:00 GMT cgeorgiaw Generative models for protein design and engineering. biology, chemistry Constellation Fusion Challenge https://huggingface.co/blog/cgeorgiaw/constellaration-fusion-challenge https://huggingface.co/blog/cgeorgiaw/constellaration-fusion-challenge Wed, 01 Jan 2025 00:00:00 GMT cgeorgiaw A challenge for advancing fusion energy through AI. physics, energy, engineering Making Antibody Embeddings and Predictions https://huggingface.co/blog/ginkgo-datapoints/making-antibody-embeddings-and-predictions https://huggingface.co/blog/ginkgo-datapoints/making-antibody-embeddings-and-predictions Wed, 01 Jan 2025 00:00:00 GMT ginkgo-datapoints How to create and use antibody embeddings for therapeutic applications. biology, medicine, biotechnology Computational De Novo Design of Antibodies and Nanobodies https://www.tamarind.bio/blog/de-novo-antibody-nanobody-vhh-scfv-rfdiffusion https://www.tamarind.bio/blog/de-novo-antibody-nanobody-vhh-scfv-rfdiffusion Wed, 01 Jan 2025 00:00:00 GMT de-novo-antibody-nanobody-vhh-scfv-rfdiffusion A practical guide to designing antibody VHHs and scFvs de novo using RFdiffusion and ProteinMPNN, from target epitope to validated sequence. biology, medicine, chemistry, biotechnology Predicting Antibody Properties & Developability https://www.tamarind.bio/blog/predicting-antibody-properties-developability https://www.tamarind.bio/blog/predicting-antibody-properties-developability Wed, 01 Jan 2025 00:00:00 GMT predicting-antibody-properties-developability ML approaches for predicting key biophysical properties of therapeutic antibody candidates — stability, solubility, and immunogenicity — before wet-lab validation. biology, medicine, chemistry, biotechnology Are Mini Proteins the Next Antibodies? https://www.tamarind.bio/blog/mini-protein-antibodies https://www.tamarind.bio/blog/mini-protein-antibodies Wed, 01 Jan 2025 00:00:00 GMT mini-protein-antibodies Examining the therapeutic potential of computationally designed miniproteins as a next-generation alternative to traditional antibody drugs. biology, medicine, chemistry LeMaterial: An Open-Source Initiative to Accelerate Materials Discovery https://huggingface.co/blog/lematerial https://huggingface.co/blog/lematerial Tue, 10 Dec 2024 00:00:00 GMT lvwerra Introducing LeMaterial, a community effort to build the largest open database of materials and accelerate AI-driven discovery of new compounds and structures. materials-science, chemistry, engineering Computational De Novo Miniproteins As Therapeutics https://www.tamarind.bio/blog/computationaly-de-novo-minibinders-therapeutic-applications https://www.tamarind.bio/blog/computationaly-de-novo-minibinders-therapeutic-applications Sun, 01 Dec 2024 00:00:00 GMT computationaly-de-novo-minibinders-therapeutic-applications How computationally designed de novo miniproteins and minibinders are being developed as a new class of targeted therapeutics. biology, medicine, chemistry Computational Protein–Protein Interaction Screening https://www.tamarind.bio/blog/ppi-screen https://www.tamarind.bio/blog/ppi-screen Sun, 01 Dec 2024 00:00:00 GMT ppi-screen A practical guide to screening for protein–protein interactions (PPIs) as drug discovery targets using structure prediction and ML scoring. biology, medicine, chemistry Boltz-1: AlphaFold3 Level Performance, Truly Open Source https://www.tamarind.bio/blog/boltz-1-alphafold3-level-performance-truly-open-source-and-commercially-available https://www.tamarind.bio/blog/boltz-1-alphafold3-level-performance-truly-open-source-and-commercially-available Fri, 01 Nov 2024 00:00:00 GMT boltz-1-alphafold3-level-performance-truly-open-source-and-commercially-available Boltz-1 from MIT achieves AlphaFold3-level accuracy on protein and protein-ligand structure prediction with no restrictions on commercial use or input types. biology, chemistry A New Era in Multistep Enzyme Design https://huggingface.co/blog/AmelieSchreiber/a-new-era-of-enzyme-engineering https://huggingface.co/blog/AmelieSchreiber/a-new-era-of-enzyme-engineering Wed, 16 Oct 2024 00:00:00 GMT AmelieSchreiber Exploring generative AI approaches for designing multistep enzymatic pathways for biosynthesis and biocatalysis. biology, chemistry A Guide to Designing New Functional Proteins https://huggingface.co/blog/AmelieSchreiber/protein-optimization-and-design https://huggingface.co/blog/AmelieSchreiber/protein-optimization-and-design Tue, 02 Jul 2024 00:00:00 GMT AmelieSchreiber A comprehensive guide to improving protein function, stability, and diversity using generative AI and ESM-2. biology, chemistry RFDiffusion Potentials https://huggingface.co/blog/AmelieSchreiber/rfdiffusion-potentials https://huggingface.co/blog/AmelieSchreiber/rfdiffusion-potentials Tue, 14 May 2024 00:00:00 GMT AmelieSchreiber Using RFDiffusion with custom guiding potentials to steer protein structure generation toward desired functional properties. biology, chemistry Predicting the Effects of Mutations on Protein Function with ESM-2 https://huggingface.co/blog/AmelieSchreiber/mutation-scoring https://huggingface.co/blog/AmelieSchreiber/mutation-scoring Wed, 13 Dec 2023 00:00:00 GMT AmelieSchreiber Using ESM-2 protein language model embeddings to score and predict the functional impact of point mutations. biology, genomics Faster Persistent Homology Alignment and Protein Complex Clustering https://huggingface.co/blog/AmelieSchreiber/faster-pha https://huggingface.co/blog/AmelieSchreiber/faster-pha Thu, 30 Nov 2023 00:00:00 GMT AmelieSchreiber Accelerating persistent homology alignment with ESM-2 embeddings and persistence landscapes for protein complex clustering. biology, mathematics Clustering Protein Complexes using Persistent Homology https://huggingface.co/blog/AmelieSchreiber/esm-ppi https://huggingface.co/blog/AmelieSchreiber/esm-ppi Wed, 29 Nov 2023 00:00:00 GMT AmelieSchreiber Combining persistent homology with ESM-2 fine-tuning for protein–protein interaction network prediction and complex clustering. biology, chemistry ESM-2 for Generating and Optimizing Peptide Binders https://huggingface.co/blog/AmelieSchreiber/esm-interact https://huggingface.co/blog/AmelieSchreiber/esm-interact Thu, 23 Nov 2023 00:00:00 GMT AmelieSchreiber Generating and optimising peptide binders for target proteins using ESM-2 embeddings and directed evolution. biology, medicine Persistent Homology Alignment: Replacing Multiple Sequence Alignments https://huggingface.co/blog/AmelieSchreiber/plm-persistent-homology-msa-replacement https://huggingface.co/blog/AmelieSchreiber/plm-persistent-homology-msa-replacement Wed, 15 Nov 2023 00:00:00 GMT AmelieSchreiber Replacing traditional multiple sequence alignments with ESM-2 embeddings and persistent homology for structure-aware protein comparison. biology, mathematics In Silico Directed Evolution of Protein Sequences with ESM-2 https://huggingface.co/blog/AmelieSchreiber/directed-evolution-with-esm2 https://huggingface.co/blog/AmelieSchreiber/directed-evolution-with-esm2 Mon, 13 Nov 2023 00:00:00 GMT AmelieSchreiber Using ESM-2 and EvoProtGrad to simulate directed evolution in silico, optimising protein sequences for target properties. biology, chemistry QLoRA for ESM-2 and Post Translational Modification Site Prediction https://huggingface.co/blog/AmelieSchreiber/esm2-ptm https://huggingface.co/blog/AmelieSchreiber/esm2-ptm Sat, 11 Nov 2023 00:00:00 GMT AmelieSchreiber Applying QLoRA fine-tuning to ESM-2 for accurate prediction of post-translational modification sites across protein sequences. biology, genomics Estimating the Intrinsic Dimension of Protein Sequence Embeddings https://huggingface.co/blog/AmelieSchreiber/intrinsic-dimension-of-proteins https://huggingface.co/blog/AmelieSchreiber/intrinsic-dimension-of-proteins Wed, 18 Oct 2023 00:00:00 GMT AmelieSchreiber Measuring the intrinsic dimensionality of ESM-2 protein embeddings to understand the geometric structure of protein sequence space. biology, mathematics Predicting Protein–Protein Interactions Using a Protein Language Model https://huggingface.co/blog/AmelieSchreiber/protein-binding-partners-with-esm2 https://huggingface.co/blog/AmelieSchreiber/protein-binding-partners-with-esm2 Sun, 15 Oct 2023 00:00:00 GMT AmelieSchreiber Using ESM-2 embeddings and linear sum assignment to predict protein–protein binding partners at scale. biology, chemistry ESMBind Ensemble Models https://huggingface.co/blog/AmelieSchreiber/esmbind-ensemble https://huggingface.co/blog/AmelieSchreiber/esmbind-ensemble Fri, 22 Sep 2023 00:00:00 GMT AmelieSchreiber Ensemble methods for ESMBind models to improve binding site prediction accuracy and robustness across protein families. biology, genomics ESMBind: Low Rank Adaptation of ESM-2 for Protein Binding Site Prediction https://huggingface.co/blog/AmelieSchreiber/esmbind https://huggingface.co/blog/AmelieSchreiber/esmbind Fri, 15 Sep 2023 00:00:00 GMT AmelieSchreiber Fine-tuning ESM-2 with LoRA adapters to predict protein binding sites with high accuracy and parameter efficiency. biology, genomics Illustrating Reinforcement Learning from Human Feedback (RLHF) https://huggingface.co/blog/rlhf https://huggingface.co/blog/rlhf Fri, 09 Dec 2022 00:00:00 GMT natolambert A clear, illustrated walkthrough of how RLHF works — the technique behind ChatGPT and modern instruction-following models. One of HF's most-read posts. A Living Review of Machine Learning for Particle Physics https://iml-wg.github.io/HEPML-LivingReview/ https://iml-wg.github.io/HEPML-LivingReview/ Mon, 01 Jun 2020 00:00:00 GMT iml-wg.github.io A continuously updated, near-comprehensive survey of ML techniques applied to experimental, phenomenological, and theoretical high-energy physics — maintained by the Inter-Experimental LHC ML Working Group. physics