FRAME-C: A knowledge-augmented deep learning pipeline for classifying multi-electrode array electrophysiological signals

Amyotrophic lateral sclerosis (ALS) diagnosis remains challenging due to heterogeneous symptoms and reliance on clinical assessment, underscoring the need for objective, data-driven approaches that leverage patient-generated physiological signals. We propose Siam-ALS, an explainable Siamese deep learning framework that jointly models synchronized electroencephalography (EEG) and eye-tracking (ET) signals. EEG captures ALS-related changes in brain activity, while ET provides information about oculomotor control, allowing the model to learn complementary patterns associated with ALS. The framework employs two modality-specific encoders: a convolutional EEG encoder that captures spatiotemporal neural patterns and an MLP-based ET encoder that models oculomotor dynamics. These modality-specific features are processed through weight-sharing Siamese branches and fused into a compact 64-dimensional joint embedding. A lightweight classifier is used to predict ALS, while pairwise metric learning helps the model learn more effective patterns from the small, diverse ALS datasets. Performance was evaluated on the public EEGET-ALS dataset using strict subject-level cross-validation, where Siam-ALS achieved an accuracy of 0.988 and an AUROC of 0.998, demonstrating strong performance compared with classical machine learning, DL, and non-Siamese fusion approaches. Cross-dataset evaluation on the independent BigP3BCI dataset achieved an AUROC of approximately 0.98, supporting the generalization capability of Siam-ALS across different BCI paradigms. To enhance interpretability, six XAI methods were evaluated in the learned embedding space, with SHAP achieving the highest, though statistically comparable, fidelity in identifying important EEG and ET patterns that contribute to ALS predictions. Overall, Siam-ALS provides an accurate, generalizable, and explainable framework for multimodal ALS detection.

Machine learning models are increasingly used for automated feature extraction from weakly annotated bioimaging data, such as microscopy and cytomorphology images. Due to the sole dependency of automated feature extraction, existing methods yield inconsistent classification performance across weakly annotated datasets. Here, we propose a model-agnostic knowledge augmentation method that enables ML models to exploit domain knowledge beyond what automated feature extraction can capture. The proposed approach improves classification performance across seven ML architectures. When integrated with masked autoencoder-based self-supervised learning, our method achieves the strongest overall performance, improving precision by 2.9% over the next-best method on three in-house microscopy datasets and by an average of 6.8% across three public cytomorphology benchmarks. We perform nucleus-level classification based on mislocalization of TAR DNA-binding protein 43 (TDP-43) from the nucleus to the cytoplasm, a phenotype linked to Amyotrophic Lateral Sclerosis (ALS), using three independent microscopy datasets of motor neurons derived from human induced pluripotent stem cells. Accurate quantification of this phenotype at scale remains challenging and may contribute to inconsistencies across studies. Application of the best-performing model to these microscopy datasets reveals biological interpretations related to ALS, including dose-dependent effects of the proteasomal stressor, MG132, and the oxidative stressor, sodium arsenite (SA), on TDP-43 mislocalization, variable pathology in motor neurons from sporadic and familial ALS donors, and a lack of protection of the pharmacological compounds, edaravone and niclosamide, against SA-induced TDP-43 mislocalization. Together, our pipeline enables in-vitro cellular image analysis to advance understanding of ALS-associated pathology and potential treatments.

Automated detection of interictal epileptiform discharges in scalp electroencephalography (EEG) is clinically important, but recent high-performing deep-learning models often trade interpretability for accuracy. We introduce EEG-SpikeAgent, a closed-loop program-synthesis framework that uses a large language model (LLM) agentic system to generate signal-processing features for spike detection in scalp EEG. The system iteratively proposes one deterministic EEG feature module at a time, executes the resulting code on EEG to generate tabular features, evaluates performance via a tabular classifier, summarizes run-level metrics, and feeds structured diagnostics back to the model for refinement. Across iterations, EEG-SpikeAgent proposes and refines candidate signal features and decision rules informed by model performance. We evaluated EEG-SpikeAgent on VEPISET, a public 29-channel dataset of 4-second epochs containing 2,516 discharge-containing and 22,933 non-discharge epochs. Across five-fold cross-validation with a gradient-boosted tree classifier, agent-generated features achieved an area under the receiver operating characteristic curve of 0.935, balanced accuracy of 0.699, F1 score of 0.557, sensitivity of 0.401, and specificity of 0.996 at the default operating point. At an operating point with sensitivity 0.80, mean precision was 0.470 and mean specificity was 0.900. Artifact-aware feature generation improved balanced accuracy and F1 score over spike-only feature search. These results indicate that LLM-based program synthesis can automate EEG feature engineering in auditable and inspectable code-driven manner for clinical and methodological review.