César Miguel Valdez Córdova

PhD Student, Quantitative Life Sciences, Mila/McGill University

I study how structure emerges in learning systems, both biological and artificial. When we apply methods like dimensionality reduction or train neural networks on data, we're making implicit choices about what patterns matter. I'm interested in understanding how the shape of the data itself, its underlying geometry, guides these discoveries. I'm developing tools and frameworks for agentic AI systems that can reason geometrically about scientific data, learning to make principled analytical choices based on the intrinsic structure of the systems they're analyzing.

GitHub LinkedIn Google Scholar cesar dot valdez at mila dot quebec

Publications

Measure Before You Look: Grounding Embeddings Through Manifold Metrics
César Miguel Valdez Córdova, et al. UniReps/NeurReps @ NeurIPS 2025
Establishing Priors Towards Geomancer: A Geometric Reasoning AI Scientist
César Miguel Valdez Córdova, et al. TAG-DS 2025
PHATE Derived Ancestry Coordinates Can Effectively Capture Continuous Population Structure in Human Genomic Data
Matthew Scicluna, Shuang Ni, César Miguel Valdez Córdova, Jean-Christophe Grenier, Raphael Poujol, Kevin R. Moon, Guy Wolf, Sebastien Lemieux, Smita Krishnaswamy, Julie Hussin. ASHG 2025
Perteval-scfm: benchmarking single-cell foundation models for perturbation effect prediction
A Wenteler, M Occhetta, N Branson, M Huebner, V Curean, WT Dee, ... César Miguel Valdez Córdova (supervising author), et al. ICML 2025
DNA-diffusion: leveraging generative models for controlling chromatin accessibility and gene expression via synthetic regulatory elements
Lucas Ferreira DaSilva, Simon Senan, Zain Munir Patel, ... César Miguel Valdez Córdova, Aaron Wenteler, ... Luca Pinello, et al. ICLR 2024 Workshop on Machine Learning for Genomics Explorations
Towards learning activity cliff-aware molecular representations
César Miguel Valdez Córdova. LatinX in AI (LXAI) @ ICML 2024

Outreach & Service

Co-founder & Host, Multiomics Reading Group
Mila, 2024–Present

Organized and moderated weekly reading group exploring representation learning in biological systems. Open to researchers worldwide, covering foundational papers and emerging work in computational biology.

VP Academic Affairs, McGill Initiative in Computational Medicine (MiCM)
McGill University, 2024–Present

Designed bioinformatics workshop materials, directed qualified instructors, organized and supervised workshop delivery. Conducted code reviews for workshop materials. Coordinated fundraising efforts to support computational medicine initiatives.

Laboratory Representative, Mila Quebec AI Institute
Mila, 2023–2025

Selected as Laboratory Representative (LabRep) to facilitate communication between students, postdocs, faculty, and staff. Organized assemblies, surveyed students on concerns, tracked proposals through to completion to enhance student involvement in decision-making.

Open Source

Latent Reasoning Works
Founder, Lead Developer

Developing frameworks for geometrically intelligent agentic systems. Building tools for reasoning about manifold structure and guiding scientific discovery through geometric profiling and principled workflow selection.

Mila Research Template
Contributor

Contributed to the development of Mila's official research template. Built the NLP module, remote launching with submitit/hydra, and code profiling infrastructure for seamless interaction with SLURM-managed cluster computing.

Reviewing

Education

Ph.D. in Quantitative Life Sciences

McGill University, Montréal, Québec, Canada (Sept. 2023 – Present)

M.Sc. in Artificial Intelligence (Life Sciences Track)

Johannes Kepler Universität Linz, Upper Austria, Austria (Grad. 2024)

Exchange semester at Polytechnique Montréal, Québec, Canada (International Thematic Clusters in Engineering - Software)

M.Sc. in Computer Science

Ensenada Center for Scientific Research and Higher Education (CICESE), Baja California, México (Grad. 2020)

B.Sc. in Chemistry and Nanotechnology Engineering

Tec de Monterrey, Campus Monterrey, Nuevo León, México (Grad. 2016)

Affiliations

Current

Advisors

Thesis Committee