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P. Freda

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Open access Jul 2026

EcoXAI: Autonomous Agentic Ecosystem for Explainable Artificial Intelligence and Biomedical Discovery

Motivation As biomedical datasets and knowledge graphs continue to grow in size, complexity, and heterogeneity, navigating and extracting actionable insights from them presents a major bottleneck for researchers. There is a clear need for autonomous analytical solutions that can utilize recent advancements in agentic AI such as agent harnessing and loop engineering without introducing hallucination or workflow fragmentation. Researchers, regardless of technical expertise, need tools that streamline complex data analysis and deliver meaningful, actionable insights grounded in both data and established biomedical knowledge. EcoXAI addresses this by introducing a modular, customizable, containerized multi-agent system that structures analysis into explicit pipeline execution stages, lowering the computational barrier for clinical and translational researchers. Result EcoXAI replaces monolithic AI text interfaces with an autonomous execution-driven framework with specialized bioinformatics agents for delivering proactive, data-driven insights grounded in established biological knowledge. Unlike purely LLM-driven or less integrated AI solutions prone to hallucinations or biologically implausible outcomes, EcoXAI’s multi-agent framework, which leverages modern agentic management and explicit knowledge graph integration, provides greater transparency and verifiability in its reasoning. In our use case in drug repurposing for Alzheimer’s Disease, EcoXAI evaluated 103 drug candidates and identified 79 novel candidates whose predictive models exceeded a randomized baseline, including the CCR5 antagonist Maraviroc, whose generated hypothesis was subsequently supported by the literature. These results demonstrate the potential of knowledge graph-grounded AI agents to accelerate hypothesis-driven biomedical research. Availability and implementation EcoXAI is available on GitHub at: https://github.com/EpistasisLab/EcoXAI. Contact jason.moore@csmc.edu

Nicholas Matsumoto, Hyunjun Choi, P. Freda et al. · 0 citations
Open access Aug 2026

ASAREE: An Analytical Sandbox for Agentic AI Research, Engineering, and Experimentation

Summary Agentic AI platforms enable the engineering of autonomous workflows but are not designed for experimentation and hypothesis testing. ASAREE (Analytical Sandbox for Agentic AI Research, Engineering, and Experimentation), is an open-source platform to address this gap. ASAREE creates agents, connects to MCP servers and tools, and designs factorial experiments through a visual interface or Python SDK. It records a full provenance trace for every run and routes all model calls through a provider-agnostic bridge that supports local deployments, ensuring data privacy. As a use-case, we use ASAREE to evaluate key design choices in a mutli-agent machine learning pipeline. Across a 2 × 2 × 2 factorial design, more advanced models, greater reasoning effort, and critic agent use significantly increased compute time, token use, cost, and feature count without improving predictive performance. The lowest-cost baseline, Claude Sonnet 5 with medium effort and no critic, achieved the highest mean PR AUC while Claude Opus 5 with extra high effort and a critic agent cost 15.5× more (USD) and ran 13.1× longer while performing worse on average. These findings highlight ASAREE as a robust framework for evaluating agentic system performance and resource efficiency. Availability and implementation ASAREE is available on GitHub at: https://github.com/EpistasisLab/ASAREE. Contact jason.moore@csmc.edu Supplementary Information Supplementary information is available at https://github.com/EpistasisLab/ASAREE/tree/main/publications/bioinformatics

Jay Moran, P. Freda, Attri Ghosh et al. · 0 citations