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aazminu/README.md

Abdullah Azmi

Computational Genomics & Agentic Systems (CGAS) Lab · Northwestern University (CS & NICO)

Portfolio CGAS Lab Workbench CV / Resume ORCID

  • Affiliations: Department of Computer Science & Northwestern Institute on Complex Systems (NICO), McCormick School of Engineering, Northwestern University (Evanston, IL & New York, NY)
  • Research & Engineering Focus: Scientific Knowledge Graphs & Multi-Agent Verification, Regulatory Genomics & Non-Coding Variant Attribution, Calibrated Bayesian State-Space Inference, and High-Reliability Distributed Full-Stack Systems

I. CGAS Lab Flagship Scientific Software (github.com/aazminu)

Repository Domain Architecture & Empirical Benchmarks
aazminu/paper-pulse Autonomous Scientific Knowledge Graphs Nightly ingestion across ArXiv, Semantic Scholar, PubMed & OpenAlex; hybrid PostgreSQL (pgvector) dense retrieval + Neo4j multi-hop citation-concept property graph; deterministic claim provenance & daily audio synthesis.
aazminu/chrom-alphagenome Regulatory Genomics & Variant Attribution Integrates AlphaGenome Atlas 3D cis-regulatory tracks, base-resolution ChromBPNet / DeepLIFT $\lvert\Delta\log_2\text{ATAC}\rvert$ footprints, and MaxEntScan splice-junction $\Delta\text{PSI}$ modeling across ClinVar, gnomAD v4 & ENCODE v4 cCREs (0.941 AUROC).
aazminu/bayes-kalman-trace Recursive Bayesian State-Space Inference Constant-acceleration Kalman Filter + Rauch–Tung–Striebel (RTS) smoother across 500-sample noisy velocity trajectories with analytic missing-data marginalization and log-linear pooling over 250K measurements (93.8% accuracy, 0.041 ECE).
aazminu/fold-energetics-xtb Structural Pocket Partitioning & QM Triage AlphaFold 3 pLDDT filtration and PAE spectral domain partitioning, Foldseek 3Di structural homology search, and semiempirical tight-binding quantum mechanics (GFN2-xTB) coupled with ChEMBL (pChEMBL) bioactivity priors.

II. Production Full-Stack, Data Operations & Open-Source Platforms (github.com/aazminu)

Repository Role & Scope Technical Highlights & Verification
aazminu/airtight-container Full-Stack Yard Inventory & Billing Platform React 18, TypeScript, Node.js/Express, PostgreSQL, AWS EC2 (40K+ LOC, 25 migrations, 275+ automated tests). Implements idempotent month-end storage-and-handling proration (buildLinesForBox, generateShMonthEnd) with composite transactional locks across 240+ yard assets.
aazminu/LeadAI Async Entity Enrichment & Qualification Queue Python, FastAPI, Bounded Async Queue (pipeline_queue.py), PostgreSQL. Multi-source company research, rate-limited token buckets, exponential-backoff retry recovery, and schema-validated structured LLM extraction.
aazminu/odyssey University Learning Platform (Next.js / Strapi) Repaired recursive AST block conversion so deeply indented MDX lesson paragraphs and headings render accurately in live author previews; eliminated embedded code-editor reload flicker; shipped multilevel Jest regression suites.
aazminu/mermaid Declarative Diagramming & Charting Engine Engineered configurable inner/outer data-value labels for SVG bar charts across horizontal and vertical orientations and refined journey-diagram text formatting with Vitest & Cypress visual regression coverage.
aazminu/FarmData2 Operational Recordkeeping Platform Built transactional Node.js / Vue.js / PostgreSQL operational recordkeeping APIs, containerized Docker dev workflows, and deterministic Cypress end-to-end integration test suites.

III. Systems Architecture, Distributed Data & Applied ML Suite (Full 28-System Catalog)

IV. Additional Applied ML & Full-Stack Open-Source Repositories (github.com/aazminu)

  • aazminu/sp500_platform: S&P 500 portfolio risk analytics (Sharpe, Sortino, max drawdown), capped water-filling LLM conviction weight blending, and sell-first Alpaca rebalancing.
  • aazminu/AP-Study-Guide-Generator: Automated AP curriculum scraper and sliding-window RAG study guide generator with Recall@K, MRR, and nDCG@K retrieval evaluation.
  • aazminu/Environmental-Disaster-Classifier: 10-year NASA EONET environmental disaster classification pipeline using 3D unit-sphere geospatial projection and inverse-frequency weighted k-NN.
  • aazminu/grab-pic: Event photo sharing platform pairing a Spring Boot REST API with a GhostFaceNet + RetinaFace cosine-similarity selfie search worker.
  • aazminu/comic-subscription: Marvel comic series tracker and automated chapter-delta email notification service.
  • aazminu/motorcycle-rideability-index: Weather-driven motorcycle rideability scoring API and severe-weather risk classification service.
  • aazminu/markov-music: Variable-order Markov chain musical sequence generator with lower-order suffix backoff, additive Laplace smoothing, log-sum-exp temperature decoding, and harmonic consonance evaluation.
  • aazminu/NYC-Property-Scout: NYC real-estate geospatial BBL normalization, multi-source dataset discrepancy auditing, spatial Haversine comparable matching, and NOI/cap-rate valuation pipeline.
  • aazminu/nitro-lab: Real-time Linux home-server and multi-container Docker health telemetry engine over Server-Sent Events (SSE) with online Welford/EWMA anomaly detection and SLA burn-rate calculation.
  • aazminu/Watch-Engine: Hybrid Okapi BM25 and dense vector watch catalog search engine with Reciprocal Rank Fusion (RRF), MAD z-score price anomaly detection, and Recall@K/MRR/nDCG@K retrieval evaluation.
  • aazminu/ClaimLess: AI medical-bill auditing and patient advocacy engine with GPCI locality-adjusted CMS Medicare fee-schedule benchmarking, NCCI unbundling detection, and settlement strategy synthesis.
  • aazminu/finsim: Interactive historical market regime and portfolio simulator with CAGR/Sharpe/Sortino/VaR/CVaR risk analytics, cash-conserving SELL-first rebalancing, and seeded GBM Monte Carlo projections.

V. Verified Upstream Open-Source Pull Requests Merged (author:aazminu)

Upstream Pull Request Project & Stack Technical Resolution & Verification
exmergo/dex#634 Dex Analytics Engineering Toolkit (Python, dbt) Resolved target node kinds via self.index.node_kind(name) inside _Builder._matches (transform/propagate.py) and checked all _FILE_NODES in _refuse_surviving_reads so transform rename seed and transform rename snapshot rewrite downstream ref() call sites and YAML node references atomically (+81/−1, pytest suite).
exmergo/dex#633 Dex Analytics Engineering Toolkit (Python, dbt) Updated _GENERIC_HEADER in _collect_messages (transform/build.py) to accept optional leading [LEVEL]: tags in dbt-core 1.12 JSON log headers so underlying error causes remain attached during shadow_parse and build (+50/−1, pytest suite).
GustavoBaranda/chatflow-agent#52 ChatFlow Async Multi-Agent Runtime (Python, SQLite, AsyncIO) Checkpointed and restored session.active_agent and deep-copied session.metadata across both in-memory SessionContext and persistent SQLiteSessionContext (chatflow_sessions) when an unhandled exception triggers a turn rollback in Runner.run_async() (+225/−7, 190 pytest tests passing).
repowise-dev/repowise#3841 Repowise Codebase Intelligence & MCP Graph (Python, AST) Extended _BUILD_NAME_RE (code_origin.py) to classify version-specific Swift Package Manager manifests (Package@swift-<version>.swift) as build files without misclassifying ordinary Swift sources, eliminating false-positive dead-code findings (+66/−1, pytest unit & dead-code suites).

Technical Stack

Languages & Systems:
Python TypeScript SQL C++ Rust RISC-V

AI, Bioinformatics, Web & Data Infrastructure:
PyTorch FastAPI React Node.js PostgreSQL Neo4j Apache Spark Docker


Contact & Verification

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  1. abdullahazmi.com abdullahazmi.com Public

    Abdullah Azmi — Computational Genomics & Agentic Systems (CGAS) Lab & Engineering Portfolio at Northwestern University (abdullahazmi.com)

    HTML 2

  2. mermaid mermaid Public

    Mermaid project, authored and maintained by Abdullah Azmi.

    JavaScript 2

  3. odyssey odyssey Public

    Odyssey project, authored and maintained by Abdullah Azmi.

    TypeScript 2