Gautam Ahuja

Senior Scientific Computing Engineer

Nygen Analytics | Lund, Sweden

• AI at Nygen. I build and maintain CyteType and CyteOnto.
• Core contributor to CyteArc and CyteBase: out-of-core single-cell analysis scaling past a hundred million cells, and a catalogue of public datasets served as cloud-hosted stores.

Scientific Computing Engineer

Nygen Analytics | Lund, Sweden

• Built CyteType, a multi-agent system for evidence-based cell-type annotation in single-cell transcriptomics.
• Built CyteOnto, for ontology-aware comparison of cell-type annotations.
• Contributed to scarf: a reader for unfiltered Cell Ranger output, merging of multiple datasets and assays, and integration metrics (LISI, kNN-graph silhouette, ARI/NMI).

Multimodal Biomedical Data Scientist & ML Engineer (part-time)

Koita Centre for Digital Health at Ashoka (KCDH-A) | Remote

• Single-cell: spatial transcriptomics of IPF lung, substantia nigra in Parkinson’s disease, and preeclampsia.
• Imaging: classifying anti-nuclear antibody immunofluorescence patterns.
• Digital health: PRISM, physician rules combined with small language models for abdominal-pain diagnosis.

Research Assistant

Mphasis AI & Applied Tech Lab at Ashoka | Sonipat, India

• An ensemble machine-learning framework to find small-molecule inhibitors of the NS3 serine protease.
• An agent-based workflow for probable abdominal-pain diagnosis; benchmarked open-source LLMs for named-entity recognition and empathy.

Research Assistant

Koita Centre for Digital Health at Ashoka (KCDH-A) | Sonipat, India

• A knowledge graph of the Indian drug landscape, linked to SNOMED CT through NRCeS.
• OMOP standardisation of terms from unstructured clinical text into patient-level data.
• Benchmarked and fine-tuned (QLoRA) open-source LLMs to extract Indian drug brand names.
• NeurIPS SENSORIUM 2023 competition on predicting visual-cortex activity (4th place).
• Diet and physical-activity behaviours in PCOS.

Research Intern

HealthUnity | Remote

• Folk Computing: a speech-enabled, multilingual health chatbot for vernacular languages.

Machine Learning Research Intern

Mphasis AI & Applied Tech Lab at Ashoka | Remote

• FoodComputing@Ashoka: food ontologies and knowledge graphs built with named-entity recognition.

Research Intern

Ashoka University | Sonipat, India

• CODA TB DREAM Challenge (6th place). Deep-learning models that screen for tuberculosis from cough sounds, using MFCC and mel-spectrogram features.

Full-Stack Developer

IEEE Bombay Section | Remote

• Front end in Figma and Svelte; back end in Node.js and Firebase.

Postgraduate Diploma in Advanced Studies and Research (DipASR), Computer Science

Ashoka University | Sonipat, India

• Thesis: Agent-based Conversational Augmented Intelligence System for Probable Abdominal Pain Diagnosis in Outpatient Setting.
• Cum laude. Dean’s List, Spring 2025.

B.Sc. (Hons.) Computer Science, with a concentration in Mathematics

Ashoka University | Sonipat, India

• Magna cum laude. CGPA 3.87; major GPA 3.94.
• Dean’s List in Monsoon 2021, Spring 2022, Monsoon 2022, Spring 2023 and Monsoon 2023.

Summer Opportunity for Academic Research (SOAR) Scholar

Emory University | Remote

Teaching Fellow

Ashoka Horizons Achievers Programme

• Data Science: Solving for Real-World Challenges

Teaching Fellow

Ashoka Horizons Achievers Programme

• Applied Data Science with ML and AI, taught by Dr. Rintu Kutum

Teaching Fellow

Ashoka Horizons Achievers Programme

• Data Science Fundamentals, taught by Dr. Rintu Kutum

Teaching Assistant

Indian Institute of Technology Jodhpur

• CSL2010: Introduction to Machine Learning — A Practical Perspective, with Dr. Richa Singh, Dr. Pankaj Yadav, Dr. Sucharita Dey and Dr. Rintu Kutum

Teaching Fellow, Young Technology Scholars

Plaksha University

• Sessions on the ESP32, electronics, programming and networking for high-school students; mentored AgBot, an agricultural IoT project on Raspberry Pi, Arduino and ESP32.

Undergraduate Teaching Assistant

Ashoka University

• CS-1104: Discrete Mathematics, with Dr. Goutam Paul

Undergraduate Teaching Assistant

Ashoka University

• CS-1101: Introduction to Computer Programming, with Dr. Goutam Paul

PRISM and the Common Data Model for probable abdominal-pain diagnosis (lightning talk)

OHDSI India Symposium 2025 | Bangalore, India

Fundamentals of Machine Learning (two talks)

Young Scholars Programme, Ashoka University

Computational Thinking (four talks)

Young Scholars Programme, Ashoka University

3rd of 49 teams (Step 1), DREAM Target 2035 Drug Discovery Challenge

Team KutumLab

Participant, Research Week with Google

4th place, NeurIPS SENSORIUM 2023 competition

6th place, CODA TB DREAM Challenge

Head of Projects

Ashoka Health Research Club

Computer Science Representative

Department of Computer Science, Ashoka University