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Willie Neiswanger

@willieneis.bsky.social
7.3K followers 190 following 235 posts

Assistant Professor in CS + AI at USC. Previously at Stanford, CMU. Machine Learning, Decision Making, AI-for-Science, Generative AI, ML Systems, LLMs. willieneis.github.io

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Willie Neiswanger @willieneis.bsky.social · 07/01/2025
​​METAGENE-1 shows state-of-the-art results on pathogen detection, metagenomic embedding, and other genomic tasks. We also release new benchmarks for genomic detection and embedding (eg, Gene-MTEB, based on MTEB for LLMs). See our paper for details: arxiv.org/abs/2501.02045
A subset of results on our Genomic Embedding Benchmark and Pathogen Detection Benchmark.
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Willie Neiswanger @willieneis.bsky.social · 07/01/2025
Our data pipeline is: human microbiome > wastewater > metagenomic sequences > tokens > training data. Wastewater provides a rich source of data from tens of thousands of species across the human-adjacent microbiome. In total we pretrain on over 1.5T base pairs of DNA/RNA.
Overview of the metagenomic data collection and sequencing pipeline for model pretraining.
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Willie Neiswanger @willieneis.bsky.social · 07/01/2025
Metagenomic sequencing of wastewater produces vast amounts of data that can capture public health trends at a societal scale. Our goal is to train a model on this data to help in large-scale wastewater monitoring & detection of novel bio threats.
Overview of METAGENE-1 and applications.
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