Artificial intelligence publications
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Interpolative Decoding: Exploring the Spectrum of Personality Traits in LLMs
Abstract Recent research has explored using very large language models (LLMs) as proxies for humans in tasks such as simulation, surveys, and studies. While LLMs do not possess a human…
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Building a Virtual Member of a Community of Practice
Abstract We describe a virtual member of a knowledge management Community of Practice (CoP), called ATHENA, that knows an individual, his tasks, his organization, and the community. ATHENA employs an…
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AI as Collaborative Partner: Rethinking Human-AI Teaming for the Real World
Abstract Much work in human-AI teaming today involves collaboration under fairly constrained settings. Humans supervise AI agents, who are relegated to following orders. The division of tasks is relatively superficial,…
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ToMCAT: Theory-of-Mind for Cooperative Agents in Teams via Multiagent Diffusion Policies
We introduce ToMCAT, a framework that integrates Theory-of-Mind (ToM) reasoning with a multiagent diffusion model to generate team-aware plans conditioned on agents' goals and inferred teammate characteristics. Experiments in a…
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Collaborative Metabolic Curation of an Emerging Model Marine Bacterium, Alteromonas macleodii ATCC 27126
A community curation workshop by researchers and students resulted in a new manually-curated genome and metabolic pathway database in BioCyc for the model marine bacterium Alteromonas macleodii ATCC 27126. The…
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Revisiting the y-ome of Escherichia coli
EcoCyc.org, the most comprehensive curated genome database for the model microorganism E. coli K-12, has implemented a new categorization schema that indicates the degree to which a gene has been…
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Visual Analysis of Multi-Omics Data
Abstract We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based…
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The Comparative Genome Dashboard
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms.
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The Genome Explorer Genome Browser
In this paper we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily…
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Automating the Derivation of Unification Algorithms. A Case Study in Deductive Program Synthesis
The unification algorithm has long been a target for program synthesis research, but a fully automatic derivation remains a research goal.
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An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
We evaluate the effectiveness of chatbots in retrieving biological knowledge for curation and research purposes.
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CyanoCyc Cyanobacterial Web Portal
CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools.