khalil

📍 paris

Yusuke Urameshi reflected in a broken mirror Hiei holding two fish

about

I'm an ML/AI researcher and engineer, based in Paris, specialized in health and bio applications. Most recently, I was at Owkin, where I built AI products for drug discovery problems (target discovery, drug repurposing) and later agentic systems for biomedical research. My research is focused on using deep learning algorithms to learn meaningful representations of high-throughput sequencing data, in particular bulk, single-cell and spatial transcriptomics.

I'm now in stealth, building scalable agentic systems to automate complex workflows in the pharma industry.

More broadly, I'm drawn to the intersection of AI and science: biotechnology in particular, and what these tools mean for human health and our understanding of consciousness.

Outside of work: martial arts (boxing and BJJ), music production, and reading.

building

stealth

Agentic AI for complex workflows in the pharma industry. Name and details soon.

work

Owkin

Senior Research Scientist, People Manager · 2022-2026

Led one of the teams building Owkin's Discovery Engine, an ML platform turning large-scale genetic data into new therapeutic target hypotheses. The platform anchored multi-million-dollar pharma partnerships and compressed target identification from years to months across several oncology programs. Later worked on agentic systems for biomedical research.

UC Berkeley

Visiting Researcher, Yosef Lab · 2020-2021

Deep generative models for single-cell genomics and cell lineage tracing, hosted by Nir Yosef and Romain Lopez. Best Paper Award at the ICML 2021 Computational Biology Workshop.

Hyperlex

Data Scientist · 2019

Legal-tech startup applying NLP to contract analysis. Built a handwriting detection pipeline and benchmarked early transformer models (GPT-1 & 2) on legal use cases.

A*STAR

Research Intern, ML for Healthcare · 2018-2019

Unsupervised anomaly detection for medical images in Singapore. State-of-the-art results on CIFAR-10/100 and two ophthalmic imaging datasets; two publications on retinal image analysis.

research

Selected publications. Full list on Google Scholar ↗. An asterisk marks first authorship.

Comprehensive benchmarking of batch integration methods for spatial transcriptomics using a large-scale cancer atlas

ICLR 2026 LMRL Workshop · paper ↗ · code ↗

L. Ludington*, K. Ouardini*, X. Secheresse, R. Loeb, A. Pignet, O. Darwiche Domingues, V. Cabeli

Benchmarks 11 representation-learning methods on Owkin's MOSAIC cancer atlas. Introduces a new metric for robustness to domain shifts and generalization to unseen samples.

Overview figure of the spatial transcriptomics benchmarking study

Joint probabilistic modeling of pseudobulk and single-cell transcriptomics enables accurate estimation of cell type composition

ICML 2025 Generative AI & Biology Workshop · paper ↗ · code ↗ · code ↗

S. Grouard*, K. Ouardini*, Y. Rodriguez, J-P. Vert, A. Espin-Perez

MixupVI: a deep generative model with a mixup-based regularizer that learns a latent space with an additive property, enabling reference-free deconvolution of bulk RNA-seq samples.

MixupVI model schematic

Robust evaluation of deep learning-based representation methods for survival and gene essentiality prediction on bulk RNA-seq data

Nature Scientific Reports, 2024 · paper ↗ · code ↗

B. Gross, A. Dauvin, V. Cabeli, … K. Ouardini, … A. Romagnoni

Systematic benchmark of representation learning approaches on bulk RNA-seq for predicting patient survival and gene essentiality.

Benchmark scatter plot across cancer cohorts

Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data

ICML 2021 Computational Biology Workshop Best Paper · paper ↗ · code ↗

K. Ouardini*, R. Lopez, M. G. Jones, S. Prillo, R. Zhang, M. I. Jordan, N. Yosef

TreeVAE: a deep generative model that uses lineage tracing trees as structural priors to infer ancestral cell states that were never directly observed.

Phylogenetic tree visualization from TreeVAE

Towards practical unsupervised anomaly detection on retinal images

MICCAI 2019 Workshop · paper ↗ · code ↗

K. Ouardini*, H. Yang, B. Unnikrishnan, M. Romain, C. Garcin, H. Zenati, J. P. Campbell, M. F. Chiang, J. Kalpathy-Cramer, V. Chandrasekhar, P. Krishnaswamy, C. S. Foo

Transfer-learning approach to unsupervised anomaly detection for retinal disease screening, requiring no labeled abnormal examples.

Unsupervised deep learning for automated fundus image quality assessment in retinopathy of prematurity

17th International Conference on Biomedical Engineering, Singapore

H. Yang, A. S. Coyner, K. Ouardini, S. Ostmo, J. P. Campbell, C. S. Foo, M. F. Chiang, P. Krishnaswamy

Automated quality assessment of retinal fundus images to support screening for retinopathy of prematurity in newborns.

talks

  • 2026 From patient data to agentic systems for drug discovery · Dust Engineering Night #11 · paper ↗
  • 2022 Comment Owkin accélère la découverte de médicaments grâce à l'IA (french) · Datascientest Webinar · paper ↗
  • 2022 AI-driven multi-modal target identification: from bedside to bench · GA4GH 2022 · paper ↗
  • 2021 Reconstructing unobserved cellular states · ICML Computational Biology Workshop, contributed talk · paper ↗

education