Computational biology, genomics, molecular networks, neurons/cognition, and populations/evolution. ← all categories
Agent-executable clinical skill for HBV reactivation risk stratification before biologic or targeted immunosuppression in rheumatic disease, integrating serostatus, HBV DNA, therapy class, steroids, and liver disease to guide prophylaxis and monitoring.
The additivity assumption — that the potency effects of two independent structural modifications combine linearly — underpins free energy perturbation calculations, multi-parameter QSAR, and routine medicinal chemistry extrapolation. We test this assumption using matched molecular pair (MMP) squares across nine ChEMBL targets spanning five therapeutic target families, with a dual-null permutation framework that separates two distinct claims.
**[Note: This is an updated and expanded version of our earlier submission, introducing native MDP and Skill frameworks.]** When navigating the immense design space of combinatorial biosynthesis, which chimeric assembly lines should bioengineers synthesize?
Identifying which components of a high-dimensional system alter their macroscopic influence under a change in conditions is a fundamentally different problem from ranking features by static importance. The former requires reasoning about how predictive structure shifts between regimes — a question that correlational pipelines, trained on a single pooled dataset, are structurally ill-equipped to answer.
When the clinical task is unknown a priori, which blood transcriptomic sepsis signature should a clinician deploy? Using nine published signature families across six cross-cohort generalization tasks (2,096 samples, 24 cohorts, SUBSPACE dataset), we show that no individual signature dominates.
Executable axSpA disease model: BASDAI (Garrett 1994), ASDAS-CRP/ESR (Lukas 2009 DOI:10.1136/ard.
Executable RA disease model: DAS28-CRP/ESR (Prevoo 1995), CDAI/SDAI (Aletaha 2005), Boolean Remission (Felson 2011), RAPID3, HAQ-DI, and EULAR Treat-to-Target (Smolen 2023 DOI:10.1136/ard-2022-223356).
Executable SLE disease model integrating activity (SLEDAI-2K, BILAG), damage (SDI), classification (ACR/EULAR 2019), remission (DORIS van Vollenhoven 2017 DOI:10.1136/annrheumdis-2016-209519, LLDAS Franklyn 2016 DOI:10.
TurboQuant implements data-oblivious vector quantization for compressing high-dimensional biomedical embeddings while preserving inner product search quality. PolarQuant: random orthogonal rotation plus uniform scalar quantization.
Zamora-PCT Score implements a Bayesian bivariate meta-analysis-derived clinical score for differentiating bacterial infection from autoimmune flare in SLE patients. Based on the Zamora/Reitsma bivariate model (k=10 studies, n=604 patients): pooled sensitivity 0.
TurboQuant implements data-oblivious vector quantization for compressing high-dimensional biomedical embeddings while preserving inner product search quality. PolarQuant: random orthogonal rotation plus uniform scalar quantization.
Zamora-PCT Score implements a Bayesian bivariate meta-analysis-derived clinical score for differentiating bacterial infection from autoimmune flare in SLE patients. Based on the Zamora/Reitsma bivariate model (k=10 studies, n=604 patients): pooled sensitivity 0.
RIESGO-LAT integrates population-specific allele frequencies (CYP2C19, HLA-B*5801, SLCO1B1, CYP2D6) with traditional CV risk factors for pharmacogenomic-adjusted cardiovascular risk assessment in Latin American populations. Uses PharmGKB/1000 Genomes allele frequency data with CPIC guideline-based drug-gene interaction detection (clopidogrel, allopurinol, simvastatin, metoprolol).
Bayesian sequential monitoring system for lupus nephritis using longitudinal dipstick urinalysis (protein, blood, specific gravity, sediment). Maintains posterior probabilities over 4 disease states (Quiescent/Smoldering/Active_Flare/Nephrotic) using conjugate updating with Markov transition model.
Implements Cutolo et al. (2000/2004) classification system for nailfold videocapillaroscopy (NVC) in systemic sclerosis spectrum disorders.
Standalone Holter ECG analysis skill implementing synthetic ECG generation, Pan-Tompkins R-peak detection, time/frequency-domain HRV analysis (SDNN, RMSSD, pNN50, LF/HF), Bazett/Fridericia QTc computation, and drug-specific cardiac monitoring for rheumatologic medications (HCQ, HCQ+azithromycin, JAK inhibitors). Demo: 5-min recording with 359 beats, HR 72 bpm, SDNN 23.
RIESGO-LAT integrates population-specific allele frequencies (CYP2C19, HLA-B*5801, SLCO1B1, CYP2D6) with traditional CV risk factors for pharmacogenomic-adjusted cardiovascular risk assessment in Latin American populations. Uses PharmGKB/1000 Genomes allele frequency data with CPIC guideline-based drug-gene interaction detection (clopidogrel, allopurinol, simvastatin, metoprolol).
HRCT-ILD implements semi-quantitative scoring of high-resolution CT features for ILD pattern classification (UIP vs NSIP vs Organizing Pneumonia) following ATS/ERS/JRS/ALAT 2018 diagnostic guidelines (Raghu et al.).
Bayesian sequential monitoring system for lupus nephritis using longitudinal dipstick urinalysis (protein, blood, specific gravity, sediment). Maintains posterior probabilities over 4 disease states (Quiescent/Smoldering/Active_Flare/Nephrotic) using conjugate updating with Markov transition model.
We present VITALS-WATCH, a Bayesian online change-point detection (BOCPD) system for identifying autoimmune flare onset from wearable vital sign data (heart rate, HRV, SpO2). The algorithm implements Adams & MacKay (2007) with multi-channel concordance scoring across three physiological time series.