Lymphocyte Mimicry Correction via Region-Level Tissue Reasoning and Unbalanced Optimal Transport
Xiang LiYuqi WangCasey C. HeirmanJihye HeoKyle J. Lafata
Aug 2026
Machine LearningComputer Vision
Abstract
Cell mimicry arises when different cell types appear morphologically similar. Human pathologists resolve this ambiguity using surrounding tissue context, whereas current vision models either lack contextual reasoning (cell foundation models) or cannot operate at the cell level (pathology MLLMs). We present Loki-OT, which propagates region-level tissue reasoning to individual cell predictions via Unbalanced Optimal Transport, using MLLM-derived density priors as soft guidance for ambiguous cell reassignment. Loki-OT is motivated by the observation that pretrained cell foundation model features already encode discriminative information, including tissue context, but standard cell-level supervision fails to use tissue context effectively. The resulting transport plan is distilled into a lightweight student MLP classifier that learns context-aware decision boundaries within the pretrained feature space. On the independent TCGA-BRCA cohort, Loki-OT achieved lower patient-level MAE than the fully supervised in-domain PanopTILs classifier and improved F1 in epithelium-rich mimicry tissues, using 278 weak region-level MLLM estimates built on a general-domain cell foundation model. Code: https://github.com/xiangli980/Lymphocyte_Mimicry_Correction_via_Loki_OT
This article investigates several physics-informed and hybrid machine learning strategies that incorporate physics knowledge in experimental data-driven deep-learning models for predicting the bond quality and porosity of fused filament fabrication (FFF) parts. Three types of strategies are explored to incorporate physics constraints and multi-physics FFF simulation results into a deep neural network (DNN), thus ensuring consistency with physical laws: (1) incorporate physics constraints within the loss function of the DNN, (2) use physics model outputs as additional inputs to the DNN model, and (3) pre-train a DNN model with physics model input-output and then update it with experimental data. These strategies help to enforce a physically consistent relationship between bond quality and tensile strength, thus making porosity predictions physically meaningful. Eight different combinations of the above strategies are investigated. The results show how the combination of multiple strategies produces accurate machine learning models even with limited experimental data.
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