Computational biologist working on geometric deep learning for structure-based drug design and longitudinal modeling of clinical cohorts.
B.Sc. Biosciences, Tecnológico de Monterrey (2026)·Guadalajara, Mexico
01 · metal-aware-sbdd
SBDD 3D Diffusion Benchmarking
Published 3D generative models (DiffSBDD, TargetDiff, Pocket2Mol) delete catalytic metal ions during preprocessing, as identified by inspecting their source code. On a curated 133-target zinc benchmark they coordinate zinc validly in 20% of molecules against a 77% native-ligand ceiling, and fine-tuning on more metalloprotein data makes it worse, not better. Analysis plans pre-registered before the data; repair in progress.
02 · strider
Biophysics Thermodynamics PyPI: strider-dna
Nucleic acid thermodynamics and kinetics in pure Python: nearest-neighbor free energies, O(n3) folding (Zuker, McCaskill), strand-displacement rate constants, parallel-tempered sequence design.
03 · cadence
Neural ODE Longitudinal VAE Clinical Cohorts
Latent Neural ODE-VAE over six waves of the Mexican Health and Aging Study; 34 clinical deficits compressed to an 8D manifold with aging velocity as output. Cognitive-decline AUC 0.72 → 0.79, functional 0.67 → 0.75, patient-level 5-fold CV.
04 · ATOMICA-Diffusion
Foundation Models SE(3)-GNN Antibiotic Design
De novo antibiotic design against multidrug-resistant A. baumannii, P. aeruginosa, K. pneumoniae. Conditions DiffSBDD on ATOMICA pocket embeddings through an SE(3)-equivariant cross-graph convolution, with an evolutionary RL loop over ADMET endpoints.
05 · mantis-delta
CRNT Dynamical Systems SymPy
Chemical reaction network theory under mass-action kinetics: network invariants, symbolic ODEs and Jacobians via SymPy, stability certified from topology alone.
- Machine Learning & AI:
PyTorch·Graph Neural Networks·SE(3)-equivariant GNNs (e3nn, EGNN)·Diffusion models (DiffSBDD)·Neural ODEs·VAEs·Reinforcement Learning·Foundation Models (ATOMICA)·Multiple Instance Learning (MIL)·Vision Transformers·scikit-learn·TensorFlow - Drug Discovery & Cheminformatics:
RDKit·Structure-based drug design·AutoDock Vina·Boltz-2·ADMET-AI·CrossDocked curation·SMILES·Tanimoto similarity·REOS filters·Lipinski rules - LLM & RAG Systems:
Retrieval-Augmented Generation (dense/lexical RRF, cross-encoders)·Vector databases (pgvector)·Agentic routing·LangChain·LangGraph·Hugging Face Transformers - Software & Systems:
Python·C++·R·SQL·JavaScript (React)·Flask·Docker·Git·Linux·GPU/HPC clusters·Embedded Systems (Raspberry Pi/ESP32) - Bioinformatics & Wet Lab:
Genomic Data Analysis·ImageJ/Fiji·Chimera·Cell culture·3D spheroids·PCR/qPCR·Flow cytometry·Western blotting·Organic synthesis
- Profiles: 🌐 emiliovenegas.github.io · 💼 LinkedIn · 🆔 ORCID: 0000-0002-7689-9185
- Honors: 🥇 Gold Medal, Iberoamerican Chemistry Olympiad (2021) · 🥉 Bronze Medal, 53rd International Chemistry Olympiad (2021)