This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

This repository implements speculative sampling for large language model (LLM) decoding, utilizing two models - a target model and an approximation model. The approximation model generates token guesses, corrected by the target model, resulting in improved efficiency. It includes implementations of Google's and Deepmind's versions of speculative sampling, supporting models like llama-7B and llama-1B. The tool is designed for fast inference from transformers via speculative decoding.

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.

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.

Graph-enhanced Large Language Models in Asynchronous Plan Reasoning is a repository containing code and datasets for the ICML-2024 paper. It includes naturalistic datasets, code for generating data, benchmarking experiments, and prototypical experiments. The repository also offers a train/test-split version of the dataset on huggingface. The paper focuses on utilizing large language models with graph enhancements for asynchronous plan reasoning.

Aligner is a model-agnostic alignment tool designed to efficiently correct responses from large language models. It redistributes initial answers to align with human intentions, improving performance across various LLMs. The tool can be applied with minimal training, enhancing upstream models and reducing hallucination. Aligner's 'copy and correct' method preserves the base structure while enhancing responses. It achieves significant performance improvements in helpfulness, harmlessness, and honesty dimensions, with notable success in boosting Win Rates on evaluation leaderboards.

RAG Foundry is a library designed to enhance Large Language Models (LLMs) by fine-tuning models on RAG-augmented datasets. It helps create training data, train models using parameter-efficient finetuning (PEFT), and measure performance using RAG-specific metrics. The library is modular, customizable using configuration files, and facilitates prototyping with various RAG settings and configurations for tasks like data processing, retrieval, training, inference, and evaluation.

OpenSSA is an open-source framework for creating efficient, domain-specific AI agents. It enables the development of Small Specialist Agents (SSAs) that solve complex problems in specific domains. SSAs tackle multi-step problems that require planning and reasoning beyond traditional language models. They apply OODA for deliberative reasoning (OODAR) and iterative, hierarchical task planning (HTP). This "System-2 Intelligence" breaks down complex tasks into manageable steps. SSAs make informed decisions based on domain-specific knowledge. With OpenSSA, users can create agents that process, generate, and reason about information, making them more effective and efficient in solving real-world challenges.

SUQL (Structured and Unstructured Query Language) is a tool that augments SQL with free text primitives for building chatbots that can interact with relational data sources containing both structured and unstructured information. It seamlessly integrates retrieval models, large language models (LLMs), and traditional SQL to provide a clean interface for hybrid data access. SUQL supports optimizations to minimize expensive LLM calls, scalability to large databases with PostgreSQL, and general SQL operations like JOINs and GROUP BYs.

EasyDist is an automated parallelization system and infrastructure designed for multiple ecosystems. It offers usability by making parallelizing training or inference code effortless with just a single line of change. It ensures ecological compatibility by serving as a centralized source of truth for SPMD rules at the operator-level for various machine learning frameworks. EasyDist decouples auto-parallel algorithms from specific frameworks and IRs, allowing for the development and benchmarking of different auto-parallel algorithms in a flexible manner. The architecture includes MetaOp, MetaIR, and the ShardCombine Algorithm for SPMD sharding rules without manual annotations.

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.

The IBM Analog Hardware Acceleration Kit is an open-source Python toolkit for exploring and using the capabilities of in-memory computing devices in the context of artificial intelligence. It consists of two main components: Pytorch integration and Analog devices simulator. The Pytorch integration provides a series of primitives and features that allow using the toolkit within PyTorch, including analog neural network modules, analog training using torch training workflow, and analog inference using torch inference workflow. The Analog devices simulator is a high-performant (CUDA-capable) C++ simulator that allows for simulating a wide range of analog devices and crossbar configurations by using abstract functional models of material characteristics with adjustable parameters. Along with the two main components, the toolkit includes other functionalities such as a library of device presets, a module for executing high-level use cases, a utility to automatically convert a downloaded model to its equivalent Analog model, and integration with the AIHW Composer platform. The toolkit is currently in beta and under active development, and users are advised to be mindful of potential issues and keep an eye for improvements, new features, and bug fixes in upcoming versions.

Marlin is a highly optimized FP16xINT4 matmul kernel designed for large language model (LLM) inference, offering close to ideal speedups up to batchsizes of 16-32 tokens. It is suitable for larger-scale serving, speculative decoding, and advanced multi-inference schemes like CoT-Majority. Marlin achieves optimal performance by utilizing various techniques and optimizations to fully leverage GPU resources, ensuring efficient computation and memory management.

KAG is a logical reasoning and Q&A framework based on the OpenSPG engine and large language models. It is used to build logical reasoning and Q&A solutions for vertical domain knowledge bases. KAG supports logical reasoning, multi-hop fact Q&A, and integrates knowledge and chunk mutual indexing structure, conceptual semantic reasoning, schema-constrained knowledge construction, and logical form-guided hybrid reasoning and retrieval. The framework includes kg-builder for knowledge representation and kg-solver for logical symbol-guided hybrid solving and reasoning engine. KAG aims to enhance LLM service framework in professional domains by integrating logical and factual characteristics of KGs.

pyLLMSearch is an advanced RAG system that offers a convenient question-answering system with a simple YAML-based configuration. It enables interaction with multiple collections of local documents, with improvements in document parsing, hybrid search, chat history, deep linking, re-ranking, customizable embeddings, and more. The package is designed to work with custom Large Language Models (LLMs) from OpenAI or installed locally. It supports various document formats, incremental embedding updates, dense and sparse embeddings, multiple embedding models, 'Retrieve and Re-rank' strategy, HyDE (Hypothetical Document Embeddings), multi-querying, chat history, and interaction with embedded documents using different models. It also offers simple CLI and web interfaces, deep linking, offline response saving, and an experimental API.

PromptAgent is a repository for a novel automatic prompt optimization method that crafts expert-level prompts using language models. It provides a principled framework for prompt optimization by unifying prompt sampling and rewarding using MCTS algorithm. The tool supports different models like openai, palm, and huggingface models. Users can run PromptAgent to optimize prompts for specific tasks by strategically sampling model errors, generating error feedbacks, simulating future rewards, and searching for high-reward paths leading to expert prompts.

This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

The 'llm-past-tense' repository contains code related to the research paper 'Does Refusal Training in LLMs Generalize to the Past Tense?' by Maksym Andriushchenko and Nicolas Flammarion. It explores the generalization of refusal training in large language models (LLMs) to the past tense. The code includes experiments and examples for running different models and requests related to the study. Users can cite the work if found useful in their research, and the codebase is released under the MIT License.

This repository contains assets related to AI/ML workloads on Google Kubernetes Engine (GKE). Run optimized AI/ML workloads with Google Kubernetes Engine (GKE) platform orchestration capabilities. A robust AI/ML platform considers the following layers: Infrastructure orchestration that support GPUs and TPUs for training and serving workloads at scale Flexible integration with distributed computing and data processing frameworks Support for multiple teams on the same infrastructure to maximize utilization of resources

Ray is a unified framework for scaling AI and Python applications. It consists of a core distributed runtime and a set of AI libraries for simplifying ML compute, including Data, Train, Tune, RLlib, and Serve. Ray runs on any machine, cluster, cloud provider, and Kubernetes, and features a growing ecosystem of community integrations. With Ray, you can seamlessly scale the same code from a laptop to a cluster, making it easy to meet the compute-intensive demands of modern ML workloads.

Labelbox is a data-centric AI platform for enterprises to develop, optimize, and use AI to solve problems and power new products and services. Enterprises use Labelbox to curate data, generate high-quality human feedback data for computer vision and LLMs, evaluate model performance, and automate tasks by combining AI and human-centric workflows. The academic & research community uses Labelbox for cutting-edge AI research.

Deep Java Library (DJL) is an open-source, high-level, engine-agnostic Java framework for deep learning. It is designed to be easy to get started with and simple to use for Java developers. DJL provides a native Java development experience and allows users to integrate machine learning and deep learning models with their Java applications. The framework is deep learning engine agnostic, enabling users to switch engines at any point for optimal performance. DJL's ergonomic API interface guides users with best practices to accomplish deep learning tasks, such as running inference and training neural networks.

Mojo is a new programming language that bridges the gap between research and production by combining Python syntax and ecosystem with systems programming and metaprogramming features. Mojo is still young, but it is designed to become a superset of Python over time.

TT-NN is a python & C++ Neural Network OP library. It provides a low-level programming model, TT-Metalium, enabling kernel development for Tenstorrent hardware.

The Open MatSci ML Toolkit is a flexible framework for machine learning in materials science. It provides a unified interface to a variety of materials science datasets, as well as a set of tools for data preprocessing, model training, and evaluation. The toolkit is designed to be easy to use for both beginners and experienced researchers, and it can be used to train models for a wide range of tasks, including property prediction, materials discovery, and materials design.

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.

AlphaFold3 is an implementation of the Alpha Fold 3 model in PyTorch for accurate structure prediction of biomolecular interactions. It includes modules for genetic diffusion and full model examples for forward pass computations. The tool allows users to generate random pair and single representations, operate on atomic coordinates, and perform structure predictions based on input tensors. The implementation also provides functionalities for training and evaluating the model.

This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

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.

MD-Agent is a LLM-agent based toolset for Molecular Dynamics. It uses Langchain and a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM. The tool assists in environment setup, installation, and usage by providing detailed steps. It also requires API keys for certain functionalities, such as OpenAI and paper-qa for literature searches. Contributions to the project are welcome, with a detailed Contributor's Guide available for interested individuals.

AIMNet2 Calculator is a package that integrates the AIMNet2 neural network potential into simulation workflows, providing fast and reliable energy, force, and property calculations for molecules with diverse elements. It excels at modeling various systems, offers flexible interfaces for popular simulation packages, and supports long-range interactions using DSF or Ewald summation Coulomb models. The tool is designed for accurate and versatile molecular simulations, suitable for large molecules and periodic calculations.

ADMET-AI is a platform for ADMET prediction using Chemprop-RDKit models trained on ADMET datasets from the Therapeutics Data Commons. It offers command line, Python API, and web server interfaces for making ADMET predictions on new molecules. The platform can be easily installed using pip and supports GPU acceleration. It also provides options for processing TDC data, plotting results, and hosting a web server. ADMET-AI is a machine learning platform for evaluating large-scale chemical libraries.