Paper List
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Pharmacophore-based design by learning on voxel grids
This paper addresses the computational bottleneck and limited novelty in conventional pharmacophore-based virtual screening by introducing a voxel cap...
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CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design
This paper addresses the critical limitation of current protein structure prediction models (like AlphaFold3) where high-confidence scores (pLDDT) can...
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On the Approximation of Phylogenetic Distance Functions by Artificial Neural Networks
This paper addresses the core challenge of developing computationally efficient and scalable neural network architectures that can learn accurate phyl...
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EcoCast: A Spatio-Temporal Model for Continual Biodiversity and Climate Risk Forecasting
This paper addresses the critical bottleneck in conservation: the lack of timely, high-resolution, near-term forecasts of species distribution shifts ...
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Training Dynamics of Learning 3D-Rotational Equivariance
This work addresses the core dilemma of whether to use computationally expensive equivariant architectures or faster symmetry-agnostic models with dat...
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Fast and Accurate Node-Age Estimation Under Fossil Calibration Uncertainty Using the Adjusted Pairwise Likelihood
This paper addresses the dual challenge of computational inefficiency and sensitivity to fossil calibration errors in Bayesian divergence time estimat...
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Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training
This paper addresses the core challenge of accurately predicting protein fitness with only a handful of experimental observations, where data collecti...
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scCluBench: Comprehensive Benchmarking of Clustering Algorithms for Single-Cell RNA Sequencing
This paper addresses the critical gap of fragmented and non-standardized benchmarking in single-cell RNA-seq clustering, which hinders objective compa...
MCP-AI: Protocol-Driven Intelligence Framework for Autonomous Reasoning in Healthcare
Organizations not explicitly listed in provided content
The 30-Second View
IN SHORT: This paper addresses the critical gap in healthcare AI systems that lack contextual reasoning, long-term state management, and verifiable workflows by introducing a protocol-driven framework that enables autonomous, explainable clinical decision-making.
Innovation (TL;DR)
- Methodology Introduces the Model Context Protocol (MCP) as a structured, version-controlled file format that captures patient state, clinical objectives, and reasoning history, creating reusable and auditable memory objects.
- Methodology Develops a hybrid architecture combining generative AI (for narrative diagnosis and planning) with descriptive AI (for rule validation and scoring) within a persistent reasoning context.
- Biology Demonstrates clinical utility through two complex use cases: Fragile X Syndrome with comorbid depression (rare neurodevelopmental disorder) and Type 2 Diabetes with hypertension (chronic care coordination).
Key conclusions
- MCP-AI enables adaptive, longitudinal reasoning across care settings, demonstrated through successful simulation of complex diagnostic pathways for Fragile X Syndrome with comorbid depression.
- The framework supports secure transitions of AI responsibilities between healthcare providers while maintaining clinical context, validated in chronic disease coordination scenarios for diabetes and hypertension.
- MCP-AI provides traceable, auditable decision-making with built-in physician verification, aligning with regulatory standards including HIPAA and FDA SaMD guidelines for clinical deployment.
Abstract: Healthcare AI systems have historically faced challenges in merging contextual reasoning, long-term state management, and human-verifiable workflows into a cohesive framework. This paper introduces a completely innovative architecture and concept: combining the Model Context Protocol (MCP) with a specific clinical application, known as MCP-AI. This integration allows intelligent agents to reason over extended periods, collaborate securely, and adhere to authentic clinical logic, representing a significant shift away from traditional Clinical Decision Support Systems (CDSS) and prompt-based Large Language Models (LLMs). As healthcare systems become more complex, the need for autonomous, context-aware clinical reasoning frameworks has become urgent. We present MCP-AI, a novel architecture for explainable medical decision-making built upon the Model Context Protocol (MCP) a modular, executable specification for orchestrating generative and descriptive AI agents in real-time workflows. Each MCP file captures clinical objectives, patient context, reasoning state, and task logic, forming a reusable and auditable memory object. Unlike conventional CDSS or stateless prompt-based AI systems, MCP-AI supports adaptive, longitudinal, and collaborative reasoning across care settings. MCP-AI is validated through two use cases: (1) diagnostic modeling of Fragile X Syndrome with comorbid depression, and (2) remote coordination for Type 2 Diabetes and hypertension. In either scenario, the protocol facilitates physician-in-the-loop validation, streamlines clinical processes, and guarantees secure transitions of AI responsibilities between healthcare providers. The system connects with HL7/FHIR interfaces and adheres to regulatory standards, such as HIPAA and FDA SaMD guidelines. MCP-AI provides a scalable basis for interpretable, composable, and safety-oriented AI within upcoming clinical environments.