This repository provides training on large language models (LLMs) for genomics, including lecture notes and lab classes covering pretraining, finetuning, zeroshot learning prediction of mutation effect, synthetic DNA sequence generation, and DNA sequence optimization.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

ManipVQA is a framework that enhances Multimodal Large Language Models (MLLMs) with manipulation-centric knowledge through a Visual Question-Answering (VQA) format. It addresses the deficiency of conventional MLLMs in understanding affordances and physical concepts crucial for manipulation tasks. By infusing robotics-specific knowledge, including tool detection, affordance recognition, and physical concept comprehension, ManipVQA improves the performance of robots in manipulation tasks. The framework involves fine-tuning MLLMs with a curated dataset of interactive objects, enabling robots to understand and execute natural language instructions more effectively.

A public repository collecting links to state-of-the-art training sets, QA, benchmarks and other evaluations for various ML and LLM applications in materials science and chemistry. It includes datasets related to chemistry, materials, multimodal data, and knowledge graphs in the field. The repository aims to provide resources for training and evaluating machine learning models in the materials science and chemistry domains.

LLM-RGB is a repository containing a collection of detailed test cases designed to evaluate the reasoning and generation capabilities of Language Learning Models (LLMs) in complex scenarios. The benchmark assesses LLMs' performance in understanding context, complying with instructions, and handling challenges like long context lengths, multi-step reasoning, and specific response formats. Each test case evaluates an LLM's output based on context length difficulty, reasoning depth difficulty, and instruction compliance difficulty, with a final score calculated for each test case. The repository provides a score table, evaluation details, and quick start guide for running evaluations using promptfoo testing tools.

SharpNEAT is a complete implementation of NEAT written in C# and targeting .NET 9. It provides an implementation of an Evolutionary Algorithm (EA) with the specific goal of evolving a population of neural networks towards solving some goal problem task. The framework facilitates research into evolutionary computation and specifically evolution of neural networks, allowing for modular experimentation with genetic coding and evolutionary algorithms.

Parsee AI is a high-level open source data extraction and structuring framework specialized for the extraction of data from a financial domain, but can be used for other use-cases as well. It aims to make the structuring of data from unstructured sources like PDFs, HTML files, and images as easy as possible. Parsee can be used locally in Python environments or through a hosted version for cloud-based jobs. It supports the extraction of tables, numbers, and other data elements, with the ability to create custom extraction templates and run jobs using different models.

LLM-Geo is an AI-powered geographic information system (GIS) that leverages Large Language Models (LLMs) for automatic spatial data collection, analysis, and visualization. By adopting LLM as the reasoning core, it addresses spatial problems with self-generating, self-organizing, self-verifying, self-executing, and self-growing capabilities. The tool aims to make spatial analysis easier, faster, and more accessible by reducing manual operation time and delivering accurate results through case studies. It uses GPT-4 API in a Python environment and advocates for further research and development in autonomous GIS.

Long-Context-Attention (YunChang) is a unified sequence parallel approach that combines the strengths of DeepSpeed-Ulysses-Attention and Ring-Attention to provide a versatile and high-performance solution for long context LLM model training and inference. It addresses the limitations of both methods by offering no limitation on the number of heads, compatibility with advanced parallel strategies, and enhanced performance benchmarks. The tool is verified in Megatron-LM and offers best practices for 4D parallelism, making it suitable for various attention mechanisms and parallel computing advancements.

This repository contains the source code and datasets for Graph Chain-of-Thought: Augmenting Large Language Models by Reasoning on Graphs accepted to ACL 2024. It proposes a framework called Graph Chain-of-thought (Graph-CoT) to enable Language Models to traverse graphs step-by-step for reasoning, interaction, and execution. The motivation is to alleviate hallucination issues in Language Models by augmenting them with structured knowledge sources represented as graphs.

LongRoPE is a method to extend the context window of large language models (LLMs) beyond 2 million tokens. It identifies and exploits non-uniformities in positional embeddings to enable 8x context extension without fine-tuning. The method utilizes a progressive extension strategy with 256k fine-tuning to reach a 2048k context. It adjusts embeddings for shorter contexts to maintain performance within the original window size. LongRoPE has been shown to be effective in maintaining performance across various tasks from 4k to 2048k context lengths.

AI4U is a tool that provides a framework for modeling virtual reality and game environments. It offers an alternative approach to modeling Non-Player Characters (NPCs) in Godot Game Engine. AI4U defines an agent living in an environment and interacting with it through sensors and actuators. Sensors provide data to the agent's brain, while actuators send actions from the agent to the environment. The brain processes the sensor data and makes decisions (selects an action by time). AI4U can also be used in other situations, such as modeling environments for artificial intelligence experiments.

DBRX is a large language model trained by Databricks and made available under an open license. It is a Mixture-of-Experts (MoE) model with 132B total parameters and 36B live parameters, using 16 experts, of which 4 are active during training or inference. DBRX was pre-trained for 12T tokens of text and has a context length of 32K tokens. The model is available in two versions: a base model and an Instruct model, which is finetuned for instruction following. DBRX can be used for a variety of tasks, including text generation, question answering, summarization, and translation.

LLM-Viewer is a tool for visualizing Language and Learning Models (LLMs) and analyzing performance on different hardware platforms. It enables network-wise analysis, considering factors such as peak memory consumption and total inference time cost. With LLM-Viewer, users can gain valuable insights into LLM inference and performance optimization. The tool can be used in a web browser or as a command line interface (CLI) for easy configuration and visualization. The ongoing project aims to enhance features like showing tensor shapes, expanding hardware platform compatibility, and supporting more LLMs with manual model graph configuration.

The xLSTM-jax repository contains code for training and evaluating the xLSTM model on language modeling using JAX. xLSTM is a Recurrent Neural Network architecture that improves upon the original LSTM through Exponential Gating, normalization, stabilization techniques, and a Matrix Memory. It is optimized for large-scale distributed systems with performant triton kernels for faster training and inference.

RAFT (Retrieval-Augmented Fine-Tuning) is a method for creating conversational agents that realistically emulate specific human targets. It involves a dual-phase process of fine-tuning and retrieval-based augmentation to generate nuanced and personalized dialogue. The tool is designed to combine interview transcripts with memories from past writings to enhance language model responses. RAFT has the potential to advance the field of personalized, context-sensitive conversational agents.

This repository provides training on large language models (LLMs) for genomics, including lecture notes and lab classes covering pretraining, finetuning, zeroshot learning prediction of mutation effect, synthetic DNA sequence generation, and DNA sequence optimization.

NoLabs is an open-source biolab that provides easy access to state-of-the-art models for bio research. It supports various tasks, including drug discovery, protein analysis, and small molecule design. NoLabs aims to accelerate bio research by making inference models accessible to everyone.

OpenCRISPR is a set of free and open gene editing systems designed by Profluent Bio. The OpenCRISPR-1 protein maintains the prototypical architecture of a Type II Cas9 nuclease but is hundreds of mutations away from SpCas9 or any other known natural CRISPR-associated protein. You can view OpenCRISPR-1 as a drop-in replacement for many protocols that need a cas9-like protein with an NGG PAM and you can even use it with canonical SpCas9 gRNAs. OpenCRISPR-1 can be fused in a deactivated or nickase format for next generation gene editing techniques like base, prime, or epigenome editing.

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to infectious and neglected disease research. It offers an open-source, low-code solution that provides seamless access to AI/ML models for drug discovery. Models housed in the hub come from two sources: published models from literature (with due third-party acknowledgment) and custom models developed by the Ersilia team or contributors.

OntoGPT is a Python package for extracting structured information from text using large language models, instruction prompts, and ontology-based grounding. It provides a command line interface and a minimal web app for easy usage. The tool has been evaluated on test data and is used in related projects like TALISMAN for gene set analysis. OntoGPT enables users to extract information from text by specifying relevant terms and provides the extracted objects as output.

BIA `bob` is a Jupyter-based assistant for interacting with data using large language models to generate Python code. It can utilize OpenAI's chatGPT, Google's Gemini, Helmholtz' blablador, and Ollama. Users need respective accounts to access these services. Bob can assist in code generation, bug fixing, code documentation, GPU-acceleration, and offers a no-code custom Jupyter Kernel. It provides example notebooks for various tasks like bio-image analysis, model selection, and bug fixing. Installation is recommended via conda/mamba environment. Custom endpoints like blablador and ollama can be used. Google Cloud AI API integration is also supported. The tool is extensible for Python libraries to enhance Bob's functionality.

Scientific Large Language Models (Sci-LLMs) is a repository that collects papers on scientific large language models, focusing on biology and chemistry domains. It includes textual, molecular, protein, and genomic languages, as well as multimodal language. The repository covers various large language models for tasks such as molecule property prediction, interaction prediction, protein sequence representation, protein sequence generation/design, DNA-protein interaction prediction, and RNA prediction. It also provides datasets and benchmarks for evaluating these models. The repository aims to facilitate research and development in the field of scientific language modeling.

Polaris establishes a novel, industry‑certified standard to foster the development of impactful methods in AI-based drug discovery. This library is a Python client to interact with the Polaris Hub. It allows you to download Polaris datasets and benchmarks, evaluate a custom method against a Polaris benchmark, and create and upload new datasets and benchmarks.

The 'awesome-AI4MolConformation-MD' repository focuses on protein conformations and molecular dynamics using generative artificial intelligence and deep learning. It provides resources, reviews, datasets, packages, and tools related to AI-driven molecular dynamics simulations. The repository covers a wide range of topics such as neural networks potentials, force fields, AI engines/frameworks, trajectory analysis, visualization tools, and various AI-based models for protein conformational sampling. It serves as a comprehensive guide for researchers and practitioners interested in leveraging AI for studying molecular structures and dynamics.