Selected work
Projects
A sample spanning clinical prediction, biomedical NLP, and core bioinformatics. Full code is on GitHub.
ICU Readmission Prediction from Clinical EHR Data (MIMIC-IV)
A 30-day ICU readmission model built on MIMIC-IV (300K+ critical-care admissions from Beth Israel Deaconess). Complex PostgreSQL queries join demographics, ICD diagnoses, labs, vitals, and medications into 40+ engineered clinical features. Logistic regression, random forest, and XGBoost are compared with cross-validated tuning (AUC 0.78 on held-out test), class imbalance handled with SMOTE and threshold tuning, and SHAP used to surface the top predictive drivers for clinical interpretability.
Spatial Transcriptomics Analysis of Human Brain Tissue
An end-to-end 10x Visium analysis of human dorsolateral prefrontal cortex (spatialLIBD): QC, normalization, and dimensionality reduction with Scanpy and Squidpy; spatially variable genes via Moran's I and SpatialDE; unsupervised clustering to delineate cortical-layer expression domains validated against histology; and a cell2location deconvolution pipeline estimating cell-type proportions per spot from paired scRNA-seq reference.
Bulk RNA-seq Differential Expression Pipeline
A reproducible Nextflow pipeline for bulk RNA-seq: FastQC, Trimmomatic trimming, STAR alignment to GRCh38, and featureCounts quantification, followed by DESeq2 differential expression on a tumor-vs-normal GEO dataset (500+ significant DEGs at FDR < 0.05). GO and KEGG enrichment via clusterProfiler, publication-quality volcano/MA plots and heatmaps, all containerized with Docker for full reproducibility.
Multi-Class Text Classification with Traditional ML and Transformers
An NLP pipeline for news-topic classification on AG News (120K articles), comparing TF-IDF + logistic regression, embeddings + LSTM, and a fine-tuned DistilBERT (94% accuracy vs. 91% baseline). Includes a full preprocessing stack, misclassification analysis with confusion matrices and per-class F1, and deployment as a FastAPI REST service with a simple web interface, containerized with Docker.