METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

Learning to Schedule Online Tasks with Bandit Feedback

Online task scheduling serves an integral role for task-intensive applications in cloud computing and crowdsourcing. Optimal scheduling can enhance system performance, typically measured by the reward-to-cost ratio, under some task arrival distribution. On one hand, both reward and cost are dependent on task context (e.g., evaluation metric) and remain black-box in practice. These render reward and cost hard to model thus unknown before decision making. On the other hand, task arrival behaviors remain sensitive to factors like unpredictable system fluctuation whereby a prior estimation or the conventional assumption of arrival distribution (e.g., Poisson) may fail. This implies another practical yet often neglected challenge, i.e., uncertain task arrival distribution. Towards effective scheduling under a stationary environment with various uncertainties, we propose a double-optimistic learning based Robbins-Monro (DOL-RM) algorithm. Specifically, DOL-RM integrates a learning module that incorporates optimistic estimation for reward-to-cost ratio and a decision module that utilizes the Robbins-Monro method to implicitly learn task arrival distribution while making scheduling decisions. Theoretically, DOL-RM achieves convergence gap and no regret learning with a sub-linear regret of $O(T^{3/4})$, which is the first result for online task scheduling under uncertain task arrival distribution and unknown reward and cost. Our numerical results in a synthetic experiment and a real-world application demonstrate the effectiveness of DOL-RM in achieving the best cumulative reward-to-cost ratio compared with other state-of-the-art baselines.