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Sanatan Upmanyu

Sanatan Upmanyu

AI for Biomedicine — Hypothesis to Patient · GenAI · LLM-RAG · Knowledge Graphs · Digital Twins

Summary

Data-science executive with 18+ years spanning wet-lab biology, AI/ML engineering, and cross-site leadership across pharma, biotech, and consumer health. Architect of the AlphaMeld™ platform — an end-to-end AI stack that accelerates target triage and indication selection for global drug-makers. Deep experience in clinical-trial design and enrollment prediction, digital-twin modelling, and large-scale knowledge-graph analytics. Known for converting multimodal data into real business value, scaling cross-functional teams, and forging industry partnerships that redefine R&D.

Experience

Apxora GmbHnow

Dec 2024 – Present
Co-Founder & AI/Data Science Head · Basel, Switzerland
  • Drives development and deployment of the ResearchNexus and Clinical Navigator platforms.
  • Leads strategic AI/ML initiatives for detecting early innovation signals for emerging targets, novel therapeutics, and healthcare solutions.
  • Supports the Asset Lifecycle Manager and Portfolio Management platforms.
PythonLLMsReactAWSNeo4j

RenaissThera Pvt Ltdnow

Sep 2024 – Present
Scientific & AI Advisory Board · Remote
  • Advising on AI-driven strategies for early-stage drug discovery and translational research.
  • Shaping the future of health through regulatory-aware innovation in digital and data sciences.
AI StrategyDrug Discovery

AlphaMeld GmbH (formerly InveniAI GmbH)now

Dec 2020 – Present
Head of Data Sciences – Site Head · Basel, Switzerland
  • Leads development and deployment of the AlphaMeld Platform.
  • Spearheads strategic AI/ML initiatives to enhance AlphaMeld/AlphaCompass capacity.
  • Advises pharma/biotech companies on leveraging data science methodologies.
  • Applied deep molecular biology expertise for MOA analyses and therapeutic target viability.
  • Manages a data science team of 5 members.
PythonNeo4jAWSReactLLMsKnowledge Graphs

ArtiXio Pvt Ltdnow

Sep 2017 – Present
Chief Technology Officer · Remote
  • Owns technology strategy, architecture, and delivery of Artixio's digital product portfolio — from concept to production.
  • Conceptualized and built QuriousRI, a secure role-based regulatory intelligence platform covering pharmaceuticals, biologics, biosimilars, and generics across 12+ agencies (FDA, EMA, PMDA, NMPA, Health Canada, MHRA, Swissmedic, and more), with LLM-powered document analysis.
  • Architected additional technology applications for the company, including an AI assistant that mines global regulatory updates and auto-drafts submission dossiers — opening a new non-pharma revenue channel.
  • Directs enterprise-level data science and AI product development using Agile methodologies, ensuring adherence to global regulatory standards (FDA, EMA, ICH) across the drug development lifecycle.
ReactNext.jsTypeScriptLLMsAgentic AIPostgreSQL

Kstych Pvt Ltd

Jul 2012 – Aug 2023
Co-Founder | Director Data Sciences | Life Science Consultant · Gurgaon, India
  • Co-founded and led data sciences, applying statistical, mathematical, and predictive modeling to build algorithms for life-science research questions.
  • Advised pharma and biotech firms on de novo, reformulation, repurposing, and drug-rescue strategies using real-world data.
  • Built statistical predictive models using NLP and machine learning on RWD; led therapeutic target assessment and MOA analysis.
  • Hands-on expertise in Python, R, KNIME, MongoDB, Hadoop, MySQL/MariaDB, Tableau, Gephi, and Cytoscape.
PythonRNLPMongoDBHadoopTableau

InveniAI LLC

Sep 2017 – Nov 2020
Senior Director of Data Science · Hybrid Gurgaon IN / CT US
  • Conceptualized, built, and executed innovative solutions throughout the drug development lifecycle.
  • Managed enterprise-level data science products using Agile methodologies.
  • Established short- to long-term strategies for Data Science and AI teams.
PythonAgileData ScienceAI/ML

BioXcel Corporation

Nov 2010 – Jul 2017
Director Data Sciences | Life Science Consultant · Gurgaon, India
  • Directed drug repurposing and novel target hypothesis generation using big data and statistical techniques.
  • Advised pharma and biotech firms on diverse scientific strategic projects, surveys, and future opportunity mapping (de novo, reformulation, repurposing, drug rescue) using real-world data.
  • Managed and mentored a team of data scientists; partnered closely with US-based pharma and biotech clients.
  • Led project management and strategy consulting efforts, providing scientific support to business development.
Data ScienceDrug RepurposingBig DataStrategy

Ranbaxy

Jan 2008 – Nov 2010
Research Biologist · Gurgaon, India
  • Conducted siRNA targeted gene silencing for target-based drug discovery.
  • Cloning, expression, purification, and activity analysis of human kinases, cytochrome P450 proteins, GPCRs, and bacterial enzymes — supporting enzyme- and cell-based NCE screening assays.
  • Managed experiments using mammalian, baculovirus, and Dictyostelium expression systems.
Molecular BiologysiRNADrug Discovery

Selected Platforms & Initiatives

AlphaMeld® Operating System

Live
Compresses hypothesis-to-insight cycles from months to weeks, varying by disease area

End-to-end AI stack combining a custom UI layer (Knowledge Graph, ChatAlphaMeld, Bioinformatics, Literature Analysis, AlphaClinMeld) with 12 ML models — including NER, RE, evidence scoring, digital-twin CT predictors and landscape assessment — running on PostgreSQL + Neo4j and self-hosted LLM APIs.

Discovery Navigator

Early access
Hypothesis landscaping compressed from weeks to hours, with traceable evidence at every step

Guided drug-discovery hypothesis-generation platform built on the AlphaMeld Knowledge Graph. Supports four starting points — disease-first, target-first, indication expansion, and combination therapy — through a step-by-step workflow (project → config → exploration → agent scoring → ranking → hypotheses). A project-aware Discovery Copilot accompanies every step. Multi-tenant SaaS with SSO, RBAC, and audit logging.

ChatAlphaMeld Benchmark Suite

Research
97.34% accuracy on 188-question ACM benchmark

Two agentic workflow engines fine-tuned on biomedical tasks; outperformed leading general-purpose frontier LLMs; delivered richer step-by-step rationales critical for complex clinical questions.

SequenceFlow® ResearchNexus & Clinical Navigator

Live
6+ integrated modules

End-to-end AI stack combining Knowledge Graph, Clinical Trial Prediction, Literature Analysis, Patient Digital Twin, TPP, TOP with 12 ML models running on PostgreSQL + Neo4j and self-hosted LLM APIs.

AlphaCompass Portfolio Intelligence

Live
Standardized indication-prioritization across 200 active programs

Clinical-trial–centric SaaS module on AlphaMeld® graph analytics; benchmarks pipeline assets and quantifies comparative risk. Adopted by two BD teams within six months, standardizing evidence-based indication-prioritization across 200 active programs.

Digital Twins for Systemic Sclerosis (EUSTAR)

Research
In-silico control arms over a 23,000+ patient, 200+ center systemic sclerosis registry

Outcome-focused digital-twin framework built on the EUSTAR systemic sclerosis registry — longitudinal records for 23,000+ patients across 200+ centers. A PyTorch deep/generative stack (a mask- and time-aware GRU-D sequence forecaster plus a conditional sequence-VAE twin generator) produces prognostic scores and synthetic placebo trajectories for organ-specific and composite clinical outcomes. Designed as an ML-generated digital control arm — a PROCOVA/ANCOVA covariate that lifts trial power and cuts sample size — aligned with FDA digital-twin and EMA/ICH MIDD guidance.

Clinical-Trial Digital Twins

Research
In-silico placebo arms demonstrated for Phase II Type 2 Diabetes trials

Conditional variational auto-encoder (CVAE) pipeline that synthesizes patient-level digital twins for Phase II Type 2 Diabetes trials. Generated matched placebo trajectories and predicted drug-response curves — proving feasibility of in-silico arms for protocol optimization and hypothesis testing.

Publications

  1. DeAngelis, M., Wilkinson, E., Anant, M., Sharma, S., Vijayadamodar, G., Upmanyu, S., Ganjoo, A., Alesci, S., Kant, A., & Nandabalan, K. (2022). AI-based deconvolution of the gut-brain axis (GBA) and its therapeutic implications. Gastroenterology, 162(7-S), 760.
  2. Rastelli, L., Gupta, S., Dahiya, A., Jagga, Z., Nandabalan, K., & Upmanyu, S. (2017). The synergy between BXCL701, a DPP inhibitor, and immune checkpoint inhibitors discovered using AI and Big Data analytics. AACR; Cancer Res, 77(13 Suppl), Washington, DC.
  3. Sheetal, K., Upmanyu, S., Sharma, H., & Nandabalan, K. (2015). Targeting immune checkpoints: using a big data approach for their identification, prioritization and application. AACR 106th Annual Meeting, Philadelphia, PA.
  4. Tiwari, P., Saini, S., Upmanyu, S., Benjamin, B., Tandon, R., Saini, K. S., & Sahdev, S. (2010). Enhanced expression of recombinant proteins utilizing a modified baculovirus expression vector. Molecular Biotechnology, 46, 80-89.
  5. Tiwari, P., Saini, S., Upmanyu, S., Saini, K. S., & Sahdev, S. (2009). Enhanced expression of kinases and cyp-450 enzymes through a modified Baculovirus expression vector for oncology research. Poster, International Symposium on Cancer Chemoprevention, JNU, New Delhi.

Patents