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Computational Scientist specializing in AI/ML for precision oncology, multi-agent systems, and clinical decision support.

Basics

Name Mujahid Ali Quidwai
Label AI Systems Engineer
Email quidwaiali@gmail.com
Phone (224) 322-6446
Url https://ali-maq.github.io/
Summary AI Systems Engineer with production deployments in clinical oncology — systems actively used by Mount Sinai oncologists for treatment decisions. Architect of multi-agent genomic curation (OncoCITE: 97.8% precision; Submitted to Nature Cancer) and GPU-accelerated pipelines (92.3% time reduction enabling same-day tumor board). Full-stack AI expertise from fine-tuning 7B-235B models to inference optimization on H100/A100 infrastructure. Research includes a widely cited clinical RAG framework (35+ citations) and first-author work at ACL (BEA Workshop).

Work

  • 2024.12 - Present

    New York, NY

    Computational Scientist
    Icahn School of Medicine at Mount Sinai
    Leading AI/ML initiatives for precision oncology including multi-agent genomic systems, GPU-accelerated pipelines, and predictive modeling.
    • OncoCITE (Submitted to Nature Cancer): Performed systematic EDA on CIViC database (11,312 evidence items, 3,083 publications) quantifying 12 structural bottlenecks. Architected 6-agent solution (Claude Agent SDK, 22 MCP tools) with state serialization and vision-based PDF extraction. Validated on 15-paper corpus: 84% ground truth recovery, 97.8% novel discovery precision, 0% critical errors (n=108). Published at ASH 2025.
    • PRIME Model (Blood 2025): Co-developed predictive model for patients receiving BCMA- and GPRC5D-targeting T-cell engagers. Integrated clinical, genomic, and treatment response data. Presented at ASH 2025.
    • MMAP Pipeline (56x Speedup): Engineered production pipeline on Minerva HPC using NVIDIA H100 GPUs with Parabricks and RAPIDS. Orchestrated 57 computational processes across 3 integrated workflows. Achieved 95.8% processing time reduction (7 days → 3 hours), enabling 8 patients/day throughput. Enabled same-day molecular tumor board readiness.
    • Multi-Omics Integration (Clin Lymph Myel Leuk 2025): Applied modified IntegrAO GNN to MMRF COMPASS cohort (N=655). Achieved 50% classification granularity improvement and 258% high-risk detection enhancement. Identified 18 distinct vulnerability profiles with 94% actionable targets.
  • 2023.10 - 2024.12

    New York, NY

    Associate Computational Scientist
    Icahn School of Medicine at Mount Sinai
    Developed production AI systems for clinical decision support, inference optimization, and CAR-T therapy monitoring.
    • LLM Inference Optimization: Designed model-routing gateway for cost-performance optimization. Implemented KV cache optimization and prompt compression. Achieved 60-80% inference cost reduction using vLLM batch inference on HPC. Multi-cloud deployment across AWS and Azure OpenAI.
    • RAG System (medRxiv, 36 citations): Led development using LangGraph orchestration, BAAI/bge-large-en-v1.5 embeddings, and Mistral-7B. Processed 5,000+ documents achieving 88% clinical effectiveness. First prototype deployed and used by 2-3 clinicians for multiple myeloma research. Presented at IMS 2024.
    • CAR-T Adverse Event Prediction (Information MDPI, under review): Led ML development for early CRS detection (N=25 patients). Engineered time-lagged features from wearables and 92-biomarker Olink panel. Achieved 84.62% accuracy (ide-cel), 80.62% (cilta-cel) within 6-hour prediction window. SHAP analysis identified IFN-gamma as cross-product predictor.
    • Voice ASR Prototype for Clinical Terminology: Fine-tuned OpenAI Whisper Small for on-device deployment. Trained on recorded patient voice dataset to reduce word error rate for multiple myeloma terminology. Prototype demonstrated improved recognition accuracy for domain-specific medical terms.
    • Graduate Student Mentorship: Mentored 6 Carnegie Mellon University graduate students on CAR-T therapy monitoring capstone project. Guided experiment design, baselining, and reporting.
  • 2023.07 - 2023.10

    New York, NY

    Entrepreneurial Fellow
    AYA
    Conceptualized and built AYA, leveraging RL-optimized NLP model to extract and formulate questions from academic video content.
    • Selected for Summer Sprint at NYU's Entrepreneurial Institute (10 selected from 150 startups)
    • Developed end-to-end product combining speech processing, natural language generation, and educational content analysis
  • 2021.09 - 2023.05

    New York, NY

    Machine Learning Researcher & Teaching Assistant
    New York University
    Research on AI-generated text detection with IBM Research; taught bioinformatics algorithms.
    • AI-Generated Plagiarism Detection (ACL 2023, BEA Workshop): Developed novel multi-faceted NLP approach with Prof. Parijat Dube (IBM Research) achieving 94% accuracy in human-AI text classification. Method employs contrastive loss and LLM-generated paraphrases. [31 citations]
    • Teaching Assistant - Data Structures & Algorithms for Bioinformatics: Supported graduate course under Prof. Manpreet S. Katari for 3 semesters, teaching 130+ master's students. Created assignments bridging CS fundamentals with bioinformatics applications.
  • 2016.08 - 2017.09

    New Delhi, India

    Technical Lead
    Carcrew
    Founding technical team member for automotive marketplace startup.
    • Built MVP using Django, Flask, PostgreSQL
    • Contributed to technical due diligence that secured $2M Series A from TVS Group
    • Scaled to 10,000+ DAU

Education

  • 2021.09 - 2023.05

    New York, NY

    MS (Honors)
    New York University, Tandon School of Engineering
    Computer Engineering
    • Deep Learning
    • Machine Learning
    • High Performance ML
    • Natural Language Processing
    • ML for Cyber-Security
    • Algorithms & Data Structures for Bioinformatics
  • 2012.08 - 2016.05

    Ghaziabad, India

    BTech
    Dr. A.P.J. Abdul Kalam Technical University
    Computer Science

Awards

Publications

Skills

LLM Fine-tuning & Training
Fine-tuned 7B-235B parameter models (Qwen, Qwen VL, Mistral, MedGemma, Whisper Large)
LoRA/QLoRA adapters
Full fine-tuning
DPO (Direct Preference Optimization)
Hugging Face Transformers
Multi-GPU training (H100 NVL, A100)
LSF/SLURM scheduling
Singularity containers
Multi-Agent Systems & Orchestration
Claude Agent SDK
OpenAI Agent SDK
LangChain
LangGraph
DSPy
6-agent collaborative architectures
State Serialization
Pause-Resume Workflows
Deterministic Replay
MCP (22 tools)
Vector databases (OpenSearch, FAISS)
Hallucination prevention
Model Serving & Deployment
vLLM
SGLang
TGI
TensorRT-LLM
Ollama
PagedAttention
KV Cache Optimization
Context Minimization
<100ms TTFT
FP8/INT4 quantization
Model routing for cost optimization
Multimodal AI
Vision (Claude 3.5, Qwen-VL, DeepSeek-OCR)
PDF-to-Image Processing (300 DPI)
Whisper Fine-tuning
Voice Activity Detection (Silero VAD)
Piper TTS
Domain-specific ASR
Distributed Computing
NVIDIA H100 NVL/A100/A10
196-GPU cluster (Minerva)
Multi-GPU (144 GPU-hours)
CUDA
HPC (LSF/SLURM)
NVLink
Parabricks
cuDF/cuML
Spark
Genomics & Bioinformatics
Nextflow
NGS Processing (STAR, BWA-MEM, fastp, GATK)
Variant Calling (Mutect2, Lancet, HaplotypeCaller)
CNV Analysis (FACETS, BEDTools)
Gene Fusion (Arriba)
Annotation (VEP, SnpEff, Funcotator)
Scanpy
Geneformer
IntegrAO
RNA-seq
WES
Clinical AI & Healthcare
Precision Medicine
Clinical NLP
Variant Annotation
EHR Integration (EPIC)
REDCap
HIPAA Compliance
Regulatory validation (CAP/CLIA)
Clinical Decision Support
Cloud & DevOps
AWS (Bedrock, EC2, OpenSearch, SageMaker)
Azure OpenAI
Multi-cloud deployment
Docker
Singularity
Kubernetes
MLflow
CI/CD

Languages

English
Fluent
Hindi
Native speaker
Urdu
Native speaker

Interests

Clinical AI Systems
Precision Oncology
Multi-Agent AI Systems
Real-Time Clinical Decision Support
Genomics
Drug Discovery

Projects

  • 2024.12 - Present
    OncoCITE - Multi-Agent Genomic Evidence Extraction
    6-agent system using Claude Agent SDK with 22 MCP tools for automated genomic curation from scientific literature. Submitted to Nature Cancer.
    • Systematic EDA on CIViC database (11,312 evidence items, 3,083 publications)
    • 84% ground truth recovery, 97.8% novel discovery precision, 0% critical errors
    • State serialization enabling pause-resume for long-running extractions
    • Identified 24.2% curation errors in expert-curated databases
  • 2024.12 - Present
    MMAP - GPU-Accelerated Genomic Pipeline (56x Speedup)
    Production pipeline on Minerva HPC using NVIDIA H100 GPUs with Parabricks, RAPIDS, and DeepVariant.
    • 95.8% processing time reduction (7 days → 3 hours, 56x speedup)
    • 57 computational processes across 3 integrated workflows
    • 8 patients/day throughput vs. 0.14 previously
    • Enabled same-day molecular tumor board readiness
  • 2024.01 - Present
    Voice ASR Prototype for Clinical Terminology
    Fine-tuned ASR for multiple myeloma medical terminology recognition.
    • Fine-tuned Whisper Small for on-device deployment
    • Trained on patient voice recordings
    • Reduced word error rate for myeloma terminology
    • Improved recognition of domain-specific medical terms
  • 2023.10 - Present
    Clinical RAG System
    Production RAG system for multiple myeloma clinical decision support. Deployed and used by clinicians.
    • LangGraph orchestration with Mistral-7B
    • 5,000+ documents processed
    • 88% clinical effectiveness
    • 36 citations on medRxiv

Volunteer

  • 2024.09 - 2024.12

    New York, NY

    Graduate Research Mentor
    Icahn School of Medicine at Mount Sinai
    Mentored 6 Carnegie Mellon University graduate students on CAR-T therapy monitoring capstone project.
    • Guided experiment design, baselining, and reporting for CRS prediction using wearables and cytokines
    • Coordinated with clinical team on project scope and deliverables
    • Students developed ML models for early adverse event detection
  • 2023.10 - Present

    New York, NY

    AI/ML Integration Mentor
    Icahn School of Medicine at Mount Sinai
    Mentored team members on AI/ML integration workflows and best practices.
    • Trained clinical research staff on RAG system usage and interpretation
    • Developed documentation and tutorials for AI tools in clinical workflows
    • Guided junior team members on production ML system development
  • 2022.01 - 2023.05

    New York, NY

    Teaching Assistant - Data Structures & Algorithms for Bioinformatics
    New York University
    Graduate-level course under Prof. Manpreet S. Katari for 3 semesters (Spring 2022, Fall 2022, Spring 2023).
    • Taught data structures, algorithms, and genomic algorithms to 130+ master's students
    • Created assignments bridging computer science fundamentals with bioinformatics applications
    • Held office hours and provided one-on-one support for complex algorithmic concepts
    • Developed course materials covering sequence alignment, graph algorithms, and dynamic programming for genomics