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timjm25/README.md
Typing SVG

Python PyTorch Flask FastAPI Docker GitHub Actions


About Me

I build production-grade AI systems at the intersection of Life Sciences, Mathematics, and Computational Intelligence β€” turning complex domain problems into clean, tested, deployable software.

  • Life Sciences focus β€” GxP manufacturing automation, regulatory AI, clinical informatics, pharma knowledge graphs, digital twins
  • Computational intelligence β€” neuro-symbolic reasoning, theorem proving, neurodynamics, cognitive modeling, quantum-classical hybrid systems
  • Applied AI β€” RAG pipelines, NLP, ML imaging, RL agents, graph neural networks
  • Engineering discipline β€” every project ships with a full test suite (pytest), CI/CD (GitHub Actions), REST API, and Docker support

Tech Stack

Languages & Core

Python SQL HTML Bash

AI / ML / NLP

PyTorch NumPy SciPy scikit-learn NetworkX

Web & APIs

Flask FastAPI REST API Pydantic

Quality & Infrastructure

pytest GitHub Actions Docker Git

Pharma / Regulatory

GxP ICH Q10 21 CFR Part 11 FDA


Featured Projects

🧬 Life Sciences & GxP Manufacturing

Project Description Tests
Digital Thread Builder End-to-end knowledge graph connecting R&D through GMP manufacturing. 28 nodes, 35+ edges, ICH Q10 compliance checker, REST API, traceability engine 71
GxP AI Governance Flask platform for pharma AI validation β€” risk classification, 21 CFR Part 11 audit trails, bias detection, CAPA workflows 93
Manufacturing Digital Twin Real-time GMP manufacturing digital twin with process simulation and KPI monitoring
Audit Report Generator Auto-generates structured GxP/regulatory audit reports β€” GMP, ISO 13485, EU GMP β€” with compliance scoring, CAPA tracking, and AI-written narratives
Hepatic Steatosis Imaging ML imaging pipeline for liver fat quantification using radiomics and deep learning 33
DOE Optimization Assistant Design of experiments engine for biopharma process optimization β€” RSM, factorial, Plackett-Burman
Batch Scheduling Optimizer Mixed-integer scheduling for multi-product GMP campaigns with capacity and constraint modeling
CPP/CQA Modeler ICH Q8 critical process parameter and critical quality attribute risk modeling platform

🧠 Computational Intelligence & Neuro-Symbolic AI

Project Description Tests
Neurodynamics & Cognitive Modeling Research platform: 8 neuron models (LIF, HH, AdEx, Izhikevich), brain connectivity, cognitive digital twins, disease models (Alzheimer's, Parkinson's, Epilepsy), multi-agent brain simulation 66
Automated Theorem Proving (ATP+ITP) Neuro-symbolic theorem proving platform β€” 12 specialized agents (PFC, hippocampus, BG, thalamus + math domain agents), interactive proof assistant 104
Quantum Agent Neural network bridge between classical and quantum computing β€” quantum circuit simulation meets neural RL
Algorithmic AI Discovery Neuro-symbolic engine for mathematical discovery β€” conjecture generation, pattern recognition across mathematical domains
Mathematical Philosophy & Appraisals AI-powered mathematical intuition engine β€” predicts conjecture fruitfulness, finds research gaps, bridges 16 mathematical domains

πŸ“Š Applied AI & Analytics

Project Description Tests
Legal Research via RAG Retrieval-Augmented Generation pipeline for legal research β€” case law, statute retrieval, citation graph
Dynamic Tax Loss Harvesting Engine IRS-compliant tax optimization engine β€” wash-sale detection, ST/LT classification, carryforward math, 50-ticker replacement map 70
Win/Loss Analyzer NLP-driven competitive intelligence for B2B pharma/CDMO sales β€” TF-IDF theme extraction, CRM connectors
Outreach Personalizer AI-driven personalized outreach platform β€” prospect profiling, message generation, A/B scoring 168
RFI Semantic Matcher Semantic search engine for RFI/RFP matching β€” embedding-based retrieval, capability scoring
Revenue Reconciliation Automated revenue reconciliation engine for multi-source financial data with discrepancy detection

Domain Expertise

Life Sciences / Pharma          β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ  GMP, GxP, CMC, ICH Q8-Q12, CAPA
Computational Neuroscience      β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘β–‘β–‘  Neural ODEs, spiking networks, cognitive models
Neuro-Symbolic AI               β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘β–‘β–‘β–‘  Theorem proving, logic, knowledge graphs
Applied ML / NLP                β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘  RAG, classification, imaging, NLP pipelines
Financial Analytics             β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘  Tax optimization, revenue, portfolio analytics
Legal / Regulatory AI           β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘β–‘  RAG, case outcome prediction, clause extraction

GitHub Stats


What I'm Building

  • Digital Thread platforms β€” end-to-end traceability systems connecting R&D artifacts through GMP batch records and regulatory submissions
  • Neuro-symbolic reasoning engines β€” systems that combine neural learning with symbolic logic for explainable, verifiable AI
  • Clinical & manufacturing intelligence β€” AI tools that operate inside regulated environments with full audit trails and GxP compliance

Building at the edge of AI Γ— Life Sciences Γ— Mathematics

Pinned Loading

  1. DeepLearning-Quantum-Entaglement DeepLearning-Quantum-Entaglement Public

    Deep learning toolkit for quantum entanglement classification and measure prediction | PyTorch + NumPy | MIT License

    Python 1

  2. LSTM_Robotics LSTM_Robotics Public

    our general LSTM model for training

    Python 1

  3. Dynamic-Tax-Loss-Harvesting-Engine Dynamic-Tax-Loss-Harvesting-Engine Public

    Dynamic Tax-Loss Harvesting Engine

    Python 1

  4. Legal-Research-via-RAG- Legal-Research-via-RAG- Public

    Legal Research via Retrieval-Augmented Generation (RAG)

    Python 1

  5. Mathematical-Philosophy-Computational-Appraisals- Mathematical-Philosophy-Computational-Appraisals- Public

    AI-powered mathematical intuition engine β€” predicts fruitfulness of conjectures, finds research gaps, identifies bridges across 16 mathematical domains | MIT License

    Python 1

  6. Neurodynamics-and-Cognitive-Modeling Neurodynamics-and-Cognitive-Modeling Public

    Neurodynamics and Cognitive Modeling

    Python 1