MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design
The growing capabilities of synthetic biology and organic chemistry demand tools to guide syntheses toward useful molecules. Here, we present Molecular AutoenCoding Auto-Workaround (MACAW), a tool that uses a novel approach to generate molecules predicted to meet a desired property specification (e.g., a binding affinity of 50 nM or an octane number of 90). MACAW describes molecules by embedding them into a smooth multidimensional numerical space, avoiding uninformative dimensions that previous methods often introduce. The coordinates in this embedding provide a natural choice of features for accurately predicting molecular properties, which we demonstrate with examples for cetane and octane numbers, flash points, and histamine H1 receptor binding affinity. The approach is computationally efficient and well-suited to the small- and medium-size datasets commonly used in biosciences. We showcase the utility of MACAW for virtual screening by identifying molecules with high predicted binding affinity to the histamine H1 receptor and limited affinity to the muscarinic M2 receptor, which are targets of medicinal relevance. Combining these predictive capabilities with a novel generative algorithm for molecules allows us to recommend molecules with a desired property value (i.e., inverse molecular design). We demonstrate this capability by recommending molecules with predicted octane numbers of 40, 80, and 120, which is an important characteristic of biofuels. Thus, MACAW augments classical retrosynthesis tools by providing recommendations for molecules on specification.
More than an OpenAI Wrapper: Perplexity Pivots to Open Source
Perplexity CEO Aravind Srinivas is a big Larry Page fan. But he thinks he's found a way to compete not only with Google search, but with OpenAI's GPT too.
How to Build a Retrieval Augmented Generative AI Application
RAG AI is a cutting-edge application that marries a Flask backend with a Streamlit frontend, creating a dynamic and interactive user experience. At its core,...
You Can Build an App in 60 Minutes with ChatGPT - Ep. 5 with Geoffrey Litt
This show might be a first in the history of podcasts:
Researcher Geoffrey Litt and I built an app together using ChatGPTapp and Replit in under 60 minutes—while we talked.
We wanted to show how AI and ChatGPT change who gets to build software and how they usher in a world where everyone can modify and remix the apps they use every day.
So we did it live, and ChatGPT delivered a working prototype at the end of the episode.
It was a tiny glimpse of the future—and it pushes the boundaries of what a show can be. It honestly left me speechless and it'll change the way you think about software. If it does, make sure to subscribe, share, and leave us a review!
Timestamps:
00:01:03 - Intro
00:01:36 - What is malleable software?
00:08:06 - Who gets to make software on the web?
00:14:50 - Deciding what app to build
00:22:06 - Starting on our app
00:31:07 - Don’t read the code first
00:47:55 - Starting from scratch could soon be a thing of the past
00:55:50 - Getting past those final error messages
01:03:31 - Voila! An app
01:04:50 - Effortless flow
Links:
https://www.geoffreylitt.com/2023/03/25/llm-end-user-programming.html
https://every.to/chain-of-thought/what-comes-after-saas
https://chat.openai.com/g/g-qPeu5SFW6-micro-web-app-coder
All computer users may soon have the ability to author small bits of code. What structural changes does this imply for the production and distribution of software?
This year has felt distinctly different. I've been working in, on, and with machine learning and AI for over a decade, yet I can't recall a time when these fields were as popular and rapidly evolving as they have been this year. To conclude an eventful 2023 in machine learning and AI research, I'm excited to share 10 noteworthy papers I've read this year. My personal focus has been more on large language models, so you'll find a heavier emphasis on large language model (LLM) papers than computer vision papers this year.
Explore the intriguing history of Eliza, a pioneering chatbot, and learn how to implement a basic version in Go, unraveling the roots of conversational AI.
AI/ML has been witnessing a rapid acceleration in model improvement in the last few years. The majority of the state-of-the-art models in the field are based on the Transformer architecture. Examples include models like BERT (which when applied to Google Search, resulted in what Google calls "one of the biggest leaps forward in the history of Search") and OpenAI's GPT2 and GPT3 (which are able to generate coherent text and essays).
This video by the author of the popular "Illustrated Transformer" guide will introduce the Transformer architecture and its various applications. This is a visual presentation accessible to people with various levels of ML experience.
Intro (0:00)
The Architecture of the Transformer (4:18)
Model Training (7:11)
Transformer LM Component 1: FFNN (10:01)
Transformer LM Component 2: Self-Attention(12:27)
Tokenization: Words to Token Ids (14:59)
Embedding: Breathe meaning into tokens (19:42)
Projecting the Output: Turning Computation into Language (24:11)
Final Note: Visualizing Probabilities (25:51)
The Illustrated Transformer:
https://jalammar.github.io/illustrated-transformer/
Simple transformer language model notebook:
https://github.com/jalammar/jalammar.github.io/blob/master/notebooks/Simple_Transformer_Language_Model.ipynb
Philosophers On GPT-3 (updated with replies by GPT-3):
https://dailynous.com/2020/07/30/philosophers-gpt-3/
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Twitter: https://twitter.com/JayAlammar
Blog: https://jalammar.github.io/
Mailing List: https://jayalammar.substack.com/
More videos by Jay:
Jay's Visual Intro to AI
https://www.youtube.com/watch?v=mSTCzNgDJy4
How GPT-3 Works - Easily Explained with Animations
https://www.youtube.com/watch?v=MQnJZuBGmSQ
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Discussions:
Hacker News (65 points, 4 comments), Reddit r/MachineLearning (29 points, 3 comments)
Translations: Arabic, Chinese (Simplified) 1, Chinese (Simplified) 2, French 1, French 2, Italian, Japanese, Korean, Persian, Russian, Spanish 1, Spanish 2, Vietnamese
Watch: MIT’s Deep Learning State of the Art lecture referencing this post
Featured in courses at Stanford, Harvard, MIT, Princeton, CMU and others
In the previous post, we looked at Attention – a ubiquitous method in modern deep learning models. Attention is a concept that helped improve the performance of neural machine translation applications. In this post, we will look at The Transformer – a model that uses attention to boost the speed with which these models can be trained. The Transformer outperforms the Google Neural Machine Translation model in specific tasks. The biggest benefit, however, comes from how The Transformer lends itself to parallelization. It is in fact Google Cloud’s recommendation to use The Transformer as a reference model to use their Cloud TPU offering. So let’s try to break the model apart and look at how it functions.
The Transformer was proposed in the paper Attention is All You Need. A TensorFlow implementation of it is available as a part of the Tensor2Tensor package. Harvard’s NLP group created a guide annotating the paper with PyTorch implementation. In this post, we will attempt to oversimplify things a bit and introduce the concepts one by one to hopefully make it easier to understand to people without in-depth knowledge of the subject matter.
2020 Update: I’ve created a “Narrated Transformer” video which is a gentler approach to the topic:
A High-Level Look
Let’s begin by looking at the model as a single black box. In a machine translation application, it would take a sentence in one language, and output its translation in another.