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BondShift: Organic Mechanism Reasoning

Vision-language model for dermatology, pretrained with MAGEN (Multi-Agent data GENeration) and O-MAKE (Ontology-based Multi-Aspect Knowledge-Enhanced pretraining).

A clinical reasoning assistant for early-stage Alzheimer's assessment. It joins a 3D MRI + biomarker classifier (Vbai-2.6AD) to a reasoning LLM (Gemma 4 12B) inside a single forward pass — the diagnosis is passed as vectors, not text.

Contrastively fine-tuned ESM-C 300M producing fixed-length protein embeddings where biological similarity maps to embedding proximity. Intended for retrieval, clustering, and nearest-neighbour transfer.

SERAPH is a deep learning model designed for 3-state (Q3) protein secondary structure prediction. It processes raw single amino acid sequences and predicts residue-level secondary structure states: Alpha Helix (H), Beta Sheet (E), or Coil/Loop (C).

!TVBP Architecture !Parameters !Trainable !Brownian Reservoir !Framework !Biology

Technical Report 🧬

Nesso-1 is a fast, structure-based protein–ligand binding-affinity model. Given a protein sequence and a ligand (SMILES / CCD code / SDF), it predicts a binding affinity scalar along with a binder/non-binder score.

This 1,120,772,224-parameter nucleotide-level causal language model is a member of the eight-model MarinDNA v0.5 parameter-scaling ladder developed with Marin. This repository contains only the final step-215573 checkpoint from run dna-bolinas-scaling-v0.5-h1920-p1B-0dc6f4, with its tokenizer…

MarinDNA m5.1 is a 1.12B-parameter, nucleotide-level causal language model developed with Marin. This is the final m5.1 base-model checkpoint at step 59,158 from run dna-bolinas-mix-v0.9-p1B-i24-exp135-zoonomia-m5.1-bef41e, released with the A 1B standard Transformer rivals Evo 2 40B on variant…

For a convenient overview and download list, visit our model page for this model.

💻 GitHub Repo • 🤗 Model Collections • 📖 MemSFT Paper

HealthGPT-LoRA is a biomedical question-answering model built by fine-tuning Meta Llama 3.2 3B Instruct using QLoRA (PEFT) on the PubMedQA dataset.

ProtSent-V2 35M plus one more contrastive pass on a fresh draw of the corpus, with a DMS/ProteinGym CoSENT target and a Global Orthogonal Regularization term added.

A DINOv2 ViT-S/14-reg fine-tuned so that an image of a molecular structure diagram embeds where its molecule embeds in the frozen MIST-28M embedding space. Objective: smooth-L1 regression onto the frozen target, no negatives (the JEPA move).

A DINOv2 ViT-S/14-reg fine-tuned so that an image of a molecular structure diagram embeds where its molecule embeds in the frozen MIST-28M embedding space. Objective: SigLIP sigmoid pairwise loss.

Contrastively fine-tuned ESM-2 150M producing fixed-length protein embeddings where biological similarity maps to embedding proximity. Intended for retrieval, clustering, and nearest-neighbour transfer.

🩺 HealthGPT-Pro: A High-Performance Multimodal Large Language Model for Medical Understanding and Analysis

A binary healthy hard coral vs bleached hard coral classifier built on top of the ReefNet species LoRA model BobDerBaum/bioclip-2.5-vith14-reefnet-lora, which provides the fine-tuned vision-encoder LoRA adapters. Only a small linear head is trained on top (frozen backbone + LoRA + 2-way linear…

A LoRA fine-tune of imageomics/bioclip-2.5-vith14 trained contrastively on the ReefNet 1.0 coral-reef species dataset (ReefNet/ReefNet-1.0), 92-class global curated split (train 48,312 / image-val 32,792 / image-test 33,090 / source-val 8,074; split cache 56ea94e36f9f).

A lightweight language model designed to answer science questions clearly and accurately in English.

!Nucleus Resynthesis

Winnow recalibrates confidence scores and provides FDR control for de novo peptide sequencing (DNS) workflows. This repository hosts a calibrator trained on the HeLa Single Shot dataset as referenced in our paper: De novo peptide sequencing rescoring and FDR estimation with Winnow.

Winnow recalibrates confidence scores and provides FDR control for de novo peptide sequencing (DNS) workflows. This repository hosts a pretrained, general-purpose calibrator that maps raw InstaNovo model confidences and complementary features (mass error, retention time, beam features, fragment…

ESMFold2 is a state-of-the-art model for protein structure prediction and design that defines a new frontier for speed and accuracy. The model predicts high-resolution, all-atom 3D protein structures directly from amino acid sequences, with optional multiple sequence alignment (MSA) input for…

ESMFold2 is a state-of-the-art model for protein structure prediction and design that defines a new frontier for speed and accuracy. The model predicts high-resolution, all-atom 3D protein structures directly from amino acid sequences, with optional multiple sequence alignment (MSA) input for…

464 fine-tuned DNABERT models for regulatory variant effect prediction

GB.DNA-7B is DNA foundation model trained on 10.6 billion nucleotides from 796 species, enabling genome mining, in silico mutagenesis studies, gene expression prediction, and directed sequence generation.

Trinity-Mini-AI-Scientist

This is the first release of the Cherimoya Accessibility aTlas (CATv1): a collection of over 7,500 Cherimoya models trained on DNase-seq and ATAC-seq experiments from the ENCODE Project. Cherimoya models are state-of-the-art predictors of local chromatin accessibility, mapping a DNA sequence to a…

In search engines, rerankers are crucial for improving the accuracy of your retrieval system.

In search engines, rerankers are crucial for improving the accuracy of your retrieval system.

In retrieval systems, embedding models determine the quality of your search.

MoLFormer is a class of models pretrained on SMILES string representations of up to 1.1B molecules from ZINC and PubChem. This repository is for the model pretrained on 10% of both datasets.

The commands below use the glyph package. Install it from the code repository:

The commands below use the glyph package. Install it from the code repository:

scUNVEIL is a pretrained foundation model for human single-cell RNA sequencing (scRNA-seq).

This is a QLoRA adapter for query-focused structured extraction from one PubMed title and abstract. It was trained as part of BioEvidence Copilot and targets the repository's versioned ModelEvidenceExtraction JSON Schema.