Christoph Feinauer

Research Scientist & Acting Director @?

[GenBio AI @genbioai]

1/ 🚀 Introducing AIDO.StructureDiffusion:
A generative model for structural protein design—enabling high-quality, controllable generation of monomers, complexes, and antibodies.
🧵

[Caleb Ellington @probablybots]

Good software should be fast, reliable, reusable, and maintainable. A lot of BioML benchmarking is uh… not.

But biology doesn’t standardize to a few data types like language, audio, or images. We’re constantly inventing new ways to measure life... 1/n

[Euxhen Hasanaj @EuxhenH]

We will be presenting our paper on Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction at two #ICML2025 Workshops this week: FM4LS (https://t.co/w1eGACR6pz) and Generative AI and Biology (https://t.co/hWLiztuoy1).

We systematically benchmarked perturbation embeddings across modalities (expression, protein, DNA, prior knowledge, networks). Embeddings based on network and prior knowledge consistently outperformed expression-based FMs, suggesting that structured biology remains a strong foundation for perturbation modeling.

#SingleCell #FoundationModels #PerturbationModeling

Preprint: https://t.co/kGUSCOsH3b

[Caleb Ellington @probablybots]

AIDO.ModelGenerator v0.1.2 is now on PyPI

Use the mgen CLI for no-code inference, embedding, and finetuning for the new SOTA AIDO models (Tissue, StructurePrediction, Protein-RAG), as well as ESM, Enformer, Borzoi, Geneformer, and scFoundation models.

pip install modelgenerator

[Christoph Feinauer @cfeinau]

@sebastiangoldt @Sissaschool Glückwunsch!

[Francesca Buffa @BuffaFrancesca]

Looking for outstanding computational scientists to work on #multiagents, #gene #networks and #machinelearning in #ERC #computational #biology project MICROC-DATAGENRE at @Unibocconi BIDSA Computing Sciences with @UniofOxford Medical Sciences. To apply https://t.co/8sAUuXidOZ 👇

[bioRxiv Bioinfo @biorxiv_bioinfo]

TULIP - a Transformer based Unsupervised Language model for Interacting Peptides and T-cell receptors that generalizes to unseen epitopes https://t.co/QP4RfCO3Cr #biorxiv_bioinfo

[antisense. @razoralign]

Mean Dimension of Generative Models for Protein Sequences https://t.co/ezCQH72rSt

[bioRxiv @biorxivpreprint]

Mean Dimension of Generative Models for Protein Sequences https://t.co/2gK5WvuJOC #bioRxiv

[bioRxiv Bioinfo @biorxiv_bioinfo]

Context-Aware Generative Models for Multi-Domain Proteins using Transformers https://t.co/y1GgI1qOLk #biorxiv_bioinfo

[Francesca Buffa @BuffaFrancesca]

📣 Looking for 3 experienced computational scientists to work on multi-agent modelling and gene networks in cancer genomics @ERC_Research project @Unibocconi collab with @UniofOxford #MachineLearning #omics #AI #maths #Computational #Biology 👇to apply 👇 https://t.co/wcmy9BWCG2