SP-Mind: An Autonomous Reasoning Agent for Spatial Proteomics Analysis

[Submitted on 23 Jun 2026 (v1), last revised 6 Aug 2026 (this version, v2)]

View PDF HTML (experimental)

Abstract:Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine. However, current analysis workflows remain fragmented, requiring expert manual orchestration of heterogeneous tools and limiting research scalability and reproducibility. We present SP-Mind, the first autonomous AI agent designed to unify the spatial proteomics analysis pipeline, from raw multiplexed tissue imaging to downstream phenotype discovery. Equipped with expert-curated biological analysis skills and specialized computational tools, SP-Mind converts natural-language queries into end-to-end analytical workflows without task-specific fine-tuning. To rigorously evaluate its capabilities, we introduce SP-Bench, a comprehensive benchmark spanning diverse tissue types, comprising 102 tasks across 18 distinct categories. Through extensive evaluation on SP-Bench and established downstream tasks, SP-Mind achieves state-of-the-art performance compared to existing open-source biomedical agent baselines. Code is publicly available at this https URL.

Submission history

From: YuCheng Yuan [view email]
[v1] Tue, 23 Jun 2026 07:24:23 UTC (9,244 KB)
[v2] Thu, 6 Aug 2026 05:38:58 UTC (9,248 KB)