RFdiffusion VS esm

So I want to install and run RFdiffusion. For reference: https://github.com/RosettaCommons/RFdiffusion

22-Mar-2023 Adobe unveils creative generative AI model, Firefly, to aid content creation Google has begun rolling out early access to its Bard chatbot in the US and UK Data Breach At ChatGPT? Users Report Seeing Unknown Conversations On Their Screens GPT-4 is available in preview in Azure OpenAI Service AI-powered coding assistance REPL that pairs GPT-4 (https://github.com/jiggy-ai/pair) Open source alternative to ChatGPT (https://github.com/nichtdax/awesome-totally-open-chatgpt) Run 100B+ language models at home, BitTorrent‑style (https://petals.ml/) Find the most relevant piece of code context. Hover and highlight blocks of code, the tool will point you to the most relevant pieces of information on git, messaging, and ticketing systems. Finally, it provide a summary with the power of GPT.(https://www.watermelontools.com/) Why AI Won't Replace Software Engineers (https://softwarecomplexity.com/why-ai-wont-replace-software-engineers) 23-Mar-2023 'The iPhone Moment of AI' Nvidia to Rent Out Supercomputers Behind ChatGPT to Businesses for $37,000 a Month Bill Gates calls AI revolutionary, says it can reduce some of the world’s worst inequities AI pics of Donald Trump's arrest by 'cop' Joe Biden go viral. Will we no longer be able to tell what’s real vs what’s fake?” - Eluna AI New research shows we can only accurately identify AI writers about 50% of the time. (https://hai.stanford.edu/news/was-written-human-or-ai-tsu) FauxPilot - an open-source GitHub Copilot server(https://github.com/fauxpilot/fauxpilot) Flower , an open-source framework for training AI on distributed data. We move the model to the data instead of moving the data to the model. (https://flower.dev/) OpenAI-Integrated Microsoft Bing Outperforms Google in Page Visits (https://www.gadgets360.com/internet/news/openai-integrated-microsoft-bing-outperforms-google-page-visits-growth-3885069) GitHub Copilot X: GitHub Copilot is evolving to bring chat and voice interfaces, support pull requests, answer questions on docs, and adopt OpenAI’s GPT-4 for a more personalized developer experience. (https://github.blog/2023-03-22-github-copilot-x-the-ai-powered-developer-experience/) Moonshine – open-source, pretrained ML models for satellite (https://github.com/moonshinelabs-ai/moonshine) Mozilla.ai: A startup — and a community — that will build a trustworthy and independent open-source AI ecosystem. Mozilla.ai’s initial focus? Tools that make generative AI safer and more transparent. And, people-centric recommendation systems that don’t misinform or undermine our well-being. (https://blog.mozilla.org/en/mozilla/introducing-mozilla-ai-investing-in-trustworthy-ai/) OpenAI’s policies hinder reproducible research on language models (https://aisnakeoil.substack.com/p/openais-policies-hinder-reproducible) 24-Mar-2023 Adobe has added AI features to Photoshop and Illustrator, while Nvidia has unveiled ‘Picasso’ AI image generation service. ChatGPT-owner OpenAI fixes 'significant issue' exposing user chat titles.A bug in an open-source library caused ChatGPT to leak user conversation titles. Graphic design platform Canva introduces new generative AI tools Gmail for Android, Google Messages to Soon Get Features for AI-Generated Texts Apple: Transformer architecture optimized for Apple Silicon (https://github.com/apple/ml-ane-transformers) ChatGPT plugins, join waitlist (https://openai.com/blog/chatgpt-plugins) Microsoft's paper on OpenAI's GPT-4 had hidden information (https://twitter.com/DV2559106965076/status/1638769434763608064) how to use LoRA to fine-tune LLaMA using Alpaca training data (https://replicate.com/blog/fine-tune-alpaca-with-lora) Helicone: one-line integration logs the prompts, completions, latencies, and costs of your OpenAI requests (https://github.com/Helicone/helicone) RWKV is an RNN with Transformer-level LLM performance, which can also be directly trained like a GPT transformer (parallelizable). (https://github.com/BlinkDL/RWKV-LM) open-source retrieval plugin The open-source retrieval plugin enables ChatGPT to access personal or organizational information sources (with permission). It allows users to obtain the most relevant document snippets from their data sources, such as files, notes, emails or public documentation, by asking questions or expressing needs in natural language. Security considerations The retrieval plugin allows ChatGPT to search a vector database of content, and add the best results into the ChatGPT session. This means it doesn’t have any external effects, and the main risk is data authorization and privacy. Developers should only add content into their retrieval plugin that they are authorized to use and can share in users’ ChatGPT sessions. https://github.com/openai/chatgpt-retrieval-plugin 27-Mar-2023 Autodoc: Toolkit for auto-generating codebase documentation using LLMs (https://github.com/context-labs/autodoc) March 20 ChatGPT outage: Here’s what happened (https://openai.com/blog/march-20-chatgpt-outage) Facebook is going after LLaMA repos with DMCA's (https://twitter.com/theshawwn/status/1638925249709240322) ChatGPT + Wolfram is INSANE! (https://old.reddit.com/r/ChatGPT/comments/1205omc/chatgpt\_wolfram\_is\_insane/) Reproducing the Stanford Alpaca results using low-rank adaptation (LoRA) (https://github.com/chris-alexiuk/alpaca-lora) GOAT, a decentralized way to publish and download AI models.Powered by BitTorrent and Bitcoin.(https://ipfs.io/ipfs/QmYyucgBQVfs9JXZ2MtmkGPAhgUjNgyGE6rcJT1KybQHhp/index.html) Dolly from databricks (https://www.databricks.com/blog/2023/03/24/hello-dolly-democratizing-magic-chatgpt-open-models.html) AI powered Developer Tools 2.0. https://www.sequoiacap.com/article/ai-powered-developer-tools/ Turn your designs into production-ready front-end code for mobile apps and the web (https://www.locofy.ai/) Using ChatGPT Plugins with LLaMA (https://blog.lastmileai.dev/using-openais-retrieval-plugin-with-llama-d2e0b6732f14) 28-Mar-2023 Bing AI now allows 20 prompts per session and can make images for you ChatGPT Outperforms Crowd-Workers for Text-Annotation Tasks (https://arxiv.org/abs/2303.15056) ChatGPT or Grammarly? Evaluating ChatGPT on Grammatical Error Correction Benchmark (https://arxiv.org/abs/2303.13648) AI-controlled Linux Containers (https://github.com/fafrd/aquarium) Microsoft reportedly orders AI chatbot rivals to stop using Bing’s search data (https://www.theverge.com/2023/3/25/23656336/microsoft-chatbot-rivals-stop-using-bing-search-index) 29-Mar-2023 Text2Video-Zero Code and Weights Released by Picsart AI Research (12G VRAM).(https://github.com/Picsart-AI-Research/Text2Video-Zero) Pause Giant AI Experiments: An Open Letter. Huggingface's SF Open-Source AI Meetup officially has 2000 people registered. Cerebras open sources seven GPT-3 models from 111 million to 13 billion parameters. Trained using the Chinchilla formula, these models set new benchmarks for accuracy and compute efficiency.(https://www.cerebras.net/blog/cerebras-gpt-a-family-of-open-compute-efficient-large-language-models/) Independent implementation of LLaMA that is fully open source under the Apache 2.0 license (https://github.com/Lightning-AI/lit-llama) Bootstrap knowledge of LLMs (https://gist.github.com/rain-1/eebd5e5eb2784feecf450324e3341c8d) OPENFLAMINGO: AN OPEN-SOURCE FRAMEWORK FOR TRAINING VISION-LANGUAGE MODELS WITH IN-CONTEXT LEARNING (https://laion.ai/blog/open-flamingo/) gpt4all: a chatbot trained on a massive collection of clean assistant data including code, stories and dialogue (https://github.com/nomic-ai/gpt4all) 30-Mar-2022 Microsoft Security Copilot is a new GPT-4 AI assistant for cybersecurity (https://www.theverge.com/2023/3/28/23659711/microsoft-security-copilot-gpt-4-ai-tool-features) UK details ‘pro-innovation’ approach to AI regulation (https://www.artificialintelligence-news.com/2023/03/29/uk-details-pro-innovation-approach-ai-regulation/) Employees Are Feeding Sensitive Biz Data to ChatGPT, Raising Security Fears (https://www.darkreading.com/risk/employees-feeding-sensitive-business-data-chatgpt-raising-security-fears) In the Age of AI, Don't Let Your Skills Atrophy (https://www.cyberdemon.org/2023/03/29/age-of-ai-skill-atrophy.html) Now ChatGPT is being (mis)used to do #PeerReview (https://mstdn.science/@ukrio/110100752908161183) Bing Chat now has Ads! (https://twitter.com/debarghya\_das/status/1640892791923572737) Cerebras-GPT vs LLaMA AI Model Comparison (https://www.lunasec.io/docs/blog/cerebras-gpt-vs-llama-ai-model-comparison/) Arthur C. Clarke about the future of AI. — 21 September 1964 (https://twitter.com/Rainmaker1973/status/1640016339011076097) ColossalChat: An Open-Source Solution for Cloning ChatGPT With a Complete RLHF Pipeline (https://medium.com/@yangyou\_berkeley/colossalchat-an-open-source-solution-for-cloning-chatgpt-with-a-complete-rlhf-pipeline-5edf08fb538b) Create and Embed Custom AI Assistants with Libraria (https://libraria.dev/) 31-Mar-2023 Deranged New AI Has No Guardrails Whatsoever, Proudly Praises Hitler (https://futurism.com/deranged-ai-no-guardrails) Midjourney Kills Free AI Image Generator Access After Explosion of Deep Fakes (https://decrypt.co/124972/midjourney-free-ai-image-generation-stopped-over-deepfakes) Judge asks ChatGPT to decide bail in murder trial (https://nypost.com/2023/03/29/judge-asks-chatgpt-for-decision-in-murder-trial/) Should you use OpenAI's embeddings? Probably not, and here's why. (https://iamnotarobot.substack.com/p/should-you-use-openais-embeddings) Visual Studio Code and GitHub Copilot (https://code.visualstudio.com/blogs/2023/03/30/vscode-copilot) Llama Hub (https://llamahub.ai/) Finetuning LLMs on a Single GPU Using Gradient Accumulation (https://lightning.ai/pages/blog/gradient-accumulation/) Open source ETL framework for retrieval augmented generation (RAG). Sync data from your SaaS tools to a vector store, where they can be easily queried by GPT apps (https://github.com/ai-sidekick/sidekick) HALTT4LLM - Hallucination Trivia Test for Large Language Models (https://github.com/manyoso/haltt4llm) Vicuna: An Open-Source Chatbot Impressing GPT-4 with 90%* ChatGPT Quality (https://vicuna.lmsys.org/) Iterate.ai Brings Generative AI Capabilities to Interplay, the Low-Code Platform Accelerating Customers’ Digital Innovation (https://www.indianweb2.com/2023/03/iterateai-brings-generative-ai.html) RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). (https://github.com/RosettaCommons/RFdiffusion) Google denies training Bard on ChatGPT chats from ShareGPT

RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). (https://github.com/RosettaCommons/RFdiffusion)

If you're interested in playing with RFDiffusion any time soon btw, the Baker lab left full instructions to the software on their Github page which works with their Google colab

When evaluating this work, it’s important to remember that the functional labels on each of the 290 million input sequences were originally assigned by HMM as part of the pfam project, so the model is predicting a prediction.

Furthermore, the authors must engage a lot of human curation to ensure the sequences they generate are active. First, they pick an easy target. Second, they employ by-hand classical bioinformatics techniques on their predicted sequences after they are generated. For example, they manually align them and select those which contain specific important amino acids at specific positions which are present in 100% of functional proteins of that class, and are required for function. This is all done by a human bioinformatics expert before they test the “generated” sequences.

One other comment, in protein science, a sequence with 40% identity to another sequence is not “very different” if it is homologous. Since this model is essentially generating homologs from a particular class, it’s no surprise at a pairwise amino acid level, the generated sequences have this degree of similarity. Take proteins in any functional family and compare them. They will have the same overall 3-D structure—called their “fold”—yet have pairwise sequence identities much lower than 30–40%.

Not to be negative. I really enjoyed reading this paper and I think the work is important. Some related work by Meta AI is the ESM series of models [1] trained on the same data (the UniProt dataset [2]).

One thing I wonder is about the vocabulary size of this model. The number of tokens is 26 for the 20 amino acids and some extras, whereas for a LLM like Meta’s LLaMa the vocab size is 32,000. I wonder how that changes training and inference, and how we can adopt the transformer architecture for this scenario.

1. https://github.com/facebookresearch/esm

2. https://www.uniprot.org/help/downloads

What's your input data look like? If you're predicting structures of mutants where there's a wild type structure available you can use variant prediction tools like ESM-IF or some of the protein language models like ESM-2

Such an explosion of protein AI lately. It’s the absolute best time to be a protein scientist with an interest in ML. Every new model type is inevitably tried out on proteins. In this case, by grad students at a very famous protein design lab (Baker Lab at University of Washington). And they usually find some interesting application. Protein design presents tons of interesting challenges.

The very largest plain transformer models trained on protein sequences (analogous to plain text) are about 15B parameters (I am thinking of Meta AI’s ESM-2 [1]). These can do for protein sequences what LLMs do for text (that is, they can “fill in the blank” to design variations, generate new proteins that look like their training data—which consists of all natural protein sequences), and tell you how likely it is that a given sequence exists.

Some cool variations of transformers have applications for protein design, like the now-famous SE(3) equivariant transformer used in the structure prediction module of AlphaFold [2], now appearing in TFA

1. https://github.com/facebookresearch/esm

Likewise PyTorch is seeing a lot of sciml work, in particular to do with protein design. (See e.g. ESM2.)