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Jeremy Ratcliff

Publications and source records attributed to Jeremy Ratcliff.

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What You Read is What You Classify: Highlighting Attributions to Text and Text-Like Inputs

At present, there are no easily understood explainable artificial intelligence (AI) methods for discrete token inputs, like text. Most explainable AI techniques do not extend well to token sequences, where both local and global features matter, because state-of-the-art models, like transformers, tend to focus on global connections. Therefore, existing explainable AI algorithms fail by (i) identifying disparate tokens of importance, or (ii) assigning a large number of tokens a low value of importance. This method for explainable AI for tokens-based classifiers generalizes a mask-based explainable AI algorithm for images. It starts with an Explainer neural network that is trained to create masks to hide information not relevant for classification. Then, the Hadamard product of the mask and the continuous values of the classifier's embedding layer is taken and passed through the classifier, changing the magnitude of the embedding vector but keeping the orientation unchanged. The Explainer is trained for a taxonomic classifier for nucleotide sequences and it is shown that the masked segments are less relevant to classification than the unmasked ones. This method focused on the importance the token as a whole (i.e., a segment of the input sequence), producing a human-readable explanation.

cs.LG

Accelerating scientific discovery with Co-Scientist

Scientific discovery is driven by scientists generating novel hypotheses for complex problems that undergo rigorous experimental validation. To augment this process, we introduce Co-Scientist, a multi-agent AI system built on Gemini for structured scientific thinking and hypothesis generation. Co-Scientist aims to help scientists discover new original knowledge. Conditioned on their research objectives and prior scientific evidence, it formulates demonstrably novel research hypotheses for experimental verification. The system's design involves agents continuously generating, critiquing and refining hypotheses accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute scaling, improving hypothesis quality over time. While general purpose, we focus the validation in three biomedical applications: drug repurposing, novel target discovery, and explaining mechanisms of anti-microbial resistance. Specifically, Co-Scientist helped identify new drug repurposing candidates and synergistic combination therapies for acute myeloid leukemia, which were validated through in vitro experiments. These real-world validations demonstrate the potential of Co-Scientist to accelerate scientific discovery and usher in an era of AI empowered scientists.

cs.AI