William E. Janes

Noah Marchal, William E. Janes, Mihail Popescu et al.

Clinical information for amyotrophic lateral sclerosis (ALS) care documented in unstructured clinical notes limits downstream analysis without extraction into structured formats. Open-source small language models with few-shot prompting for detecting the presence of ALS-relevant clinical terms in patient documentation were evaluated without task-specific training data. The detection task targeted 17 categories spanning functional scores, respiratory measures, medications, and related clinical and non-clinical attributes. Clinical note content was normalized from JSON-encoded discharge summaries and processed with a prompt template having structured JSON outputs. We compared 26 open-source models using aggregate, label-level, and manual-validation multilabel classification metrics. Manual validation showed that a regex rule baseline had higher overall micro-F1 and lower Hamming loss than any single SLM or TF-IDF baseline, while Qwen3-4B-Instruct-2507 was the highest-performing SLM by micro-F1. Model rankings varied by metric and label category, with the TF-IDF baseline showing high recall but low precision, some SLMs showing higher precision but lower recall, and Hammer2.1-7b showing strong performance for ALSFRS-R subscore detection. These findings support targeted hybrid extraction workflows rather than replacement of existing rule-based methods.

Noah Marchal, William E. Janes, Mihail Popescu et al.

Clinical monitoring of functional decline in ALS relies on periodic assessments that may miss critical changes occurring between visits. To address this gap, semi-supervised regression models were developed to estimate rates of decline in a case series cohort by targeting ALSFRS- R scale trajectories with continuous in-home sensor monitoring data. Our analysis compared three model paradigms (individual batch learning and cohort-level batch versus incremental fine-tuned transfer learning) across linear slope, cubic polynomial, and ensembled self-attention pseudo-label interpolations. Results revealed cohort homogeneity across functional domains responding to learning methods, with transfer learning improving prediction error for ALSFRS-R subscales in 28 of 32 contrasts (mean RMSE=0.20(0.04)), and individual batch learning for predicting the composite scale (mean RMSE=3.15(1.25)) in 2 of 3. Self-attention interpolation achieved the lowest prediction error for subscale-level models (mean RMSE=0.19(0.06)), capturing complex nonlinear progression patterns, outperforming linear and cubic interpolations in 20 of 32 contrasts, though linear interpolation proved more stable in all ALSFRS-R composite scale models (mean RMSE=0.23(0.10)). We identified distinct homogeneity-heterogeneity profiles across functional domains with respiratory and speech exhibiting patient-specific patterns benefiting from personalized incremental adaptation, while swallowing and dressing functions followed cohort-level trajectories suitable for transfer models. These findings suggest that matching learning and pseudo-labeling techniques to functional domain-specific homogeneity-heterogeneity profiles enhances predictive accuracy in ALS progression tracking. Integrating adaptive model selection within sensor monitoring platforms could enable timely interventions and scalable deployment in future multi-center studies.