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Biomedical text generation

Usage-Instructions) - A program to visualize reaction networks.

## Model Overview AgroNT is a DNA language model trained on primarily edible plant genomes. More specifically, AgroNT uses the transformer architecture with self-attention and a masked language modeling objective to leverage highly available genotype data from 48 different plant speices to learn…

A benchmarking platform for molecular generation models.

# Medical-Llama3-v2 Fine-Tuned Llama3 for Medical Q&A This repository provides a fine-tuned version of the powerful Llama3 8B model, specifically designed to answer medical questions in an informative way. It leverages the rich knowledge contained in the AI Medical Chatbot dataset…

Diffusion model for scalable protein structure design with multi-motif scaffolding capabilities, achieving state-of-the-art designability, diversity, and novelty through SE(3)-equivariant attention and massive data augmentation (AlQuraishi Lab, 2024)

Partial-Order Alignment for fast alignment and consensus of multiple homologous sequences.

This is an official model checkpoint for Asclepius-Mistral-7B-v0.3 (arxiv). This model is an enhanced version of Asclepius-7B, by replacing the base model with Mistral-7B-v0.3 and increasing the max sequence length to 8192.

This is an official model checkpoint for Asclepius-Llama3-8B (arxiv). This model is an enhanced version of Asclepius-7B, by replacing the base model with Llama-3 and increasing the max sequence length to 8192.

Automated data visualization with minimal code

General-purpose deep learning backbone for molecular modeling

Multi-disciplinary collaboration framework for zero-shot medical reasoning using role-playing LLM agents (ACL 2024)

# MMedLM 💻Github Repo 🖨️arXiv Paper

This model is deprecated. please use the updated sentence transformer model here: https://huggingface.co/nasa-impact/nasa-smd-ibm-st-v2. Alternatively, you can also use distilled version of the model here: https://huggingface.co/nasa-impact/nasa-ibm-st.38m

# JSL-MedLlama-3-8B-v2.0

Generative model for programmable protein design using diffusion modeling, equivariant graph neural networks, and conditional random fields to efficiently sample diverse all-atom structures; supports conditional generation via composable conditioners for substructure, symmetry, shape, and neural-network predictions; validated crystallographically (Generate Biomedicines, Nature 2023)

Large-scale PDF/LaTeX/JATS parsing to standardized JSON for millions of papers

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This model is a fine-tuned version of DeBERTa on the PubMED Dataset.

Circlator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.

Ujjwal Karn.

Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data

MIBiG (Minimum Information about a Biosynthetic Gene Cluster) is a data repository and associated data standard designed to describe biosynthetic gene clusters involved in the production of specialized metabolites. It also stores data on measured biological activities and links to other resources such as NCBI, NPAtlas, and ChEBI. MIBiG is used as a reference database, knowledgebase, and training dataset for machine learning.

file format conversion in Biopython in a convenient way.

Open language model for mathematics (7B/34B) trained on Proof-Pile-2, outperforming Minerva at equal scale on MATH benchmark, with tool use and formal theorem proving in Lean without finetuning (EleutherAI, ICLR 2024)

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AlphaPickle is a Python tool that converts AlphaFold and ColabFold output files into user-friendly CSV files and plots, enabling easy analysis and visualization of protein prediction data without requiring programming expertise. It processes .pkl, .json, and PDB files to extract and visualize metrics like pLDDT and PAE.

Abstract:

This is a merge of pre-trained language models created using mergekit.

Abstract:

This is a merge of pre-trained language models created using mergekit.

k-mer counting, filtering, and graph traversal.

SMILES2IUPAC-canonical-base was designed to accurately translate SMILES chemical names to IUPAC standards.

A package for benchmarking of models for _de novo_ molecular design.

Molecular descriptor calculator based on [RDKit](http://www.rdkit.org/).

# TinyLlama-1.1B

The T5 Large for Medical Text Summarization is a specialized variant of the T5 transformer model, fine-tuned for the task of summarizing medical text. This model is designed to generate concise and coherent summaries of medical documents, research papers, clinical notes, and other…

Huawei's 3D high-resolution global weather forecast model at 0.25° resolution, first AI method to comprehensively outperform traditional NWP across all variables and lead times, integrated into ECMWF operational forecasts (Nature 2023)

This is official model checkpoint for Asclepius-13B (arxiv). This model is the first publicly shareable clinical LLM, trained with synthetic data.

3D Equivariant Diffusion for Target-Aware Molecule Generation (ICLR2023)

Single-cell BERT for gene expression

PINN research collection

Details coming soon

A Vision Transformer (ViT) image classification model. \ Trained on 15M histology patches from PAIP and TCGA. \ Used the MoCo v3 self supervised learning method.

OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.