About Me
As a Chemical Engineer with a strong foundation in computer science, I am dedicated to applying artificial intelligence (AI) to advance life sciences, particularly drug discovery. My research focuses on molecular simulations (docking & dynamics), generative modeling, and protein-ligand interactions within computational drug discovery and materials science.
I hold a B.Sc. in Chemical Engineering from ESPOL, Ecuador, and strengthened my computer science skills through coursework at UC Berkeley. My experience includes developing molecular simulation workflows and energy prediction models at Deep Forest Sciences and CIDNA (Ecuador), and contributing to open-source projects like DeepChem. Currently, I am expanding equivariant capabilities for molecular data in DeepChem, specifically developing SE(3)-Transformers.
Publications
Published
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"Exergoeconomic Analysis and Multi-objective Optimization of Biodiesel Production from Waste Cooking Oil Using Genetic Algorithm" — E2DT Conference - Chemical Engineering Transactions - 2025.
Siguenza-Polo J.A., Ajoy-Rendón K.V., Mero-Benavides M.B., Beltrán-Borbor K.K., Barcia-Quimi A.F., Tinoco-Caicedo D.L.
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"DeepChem Equivariant: SE (3)-Equivariant Support in an Open-Source Molecular Machine Learning Library" - arXiv - 2025.
Jose Siguenza, Bharath Ramsundar
arXiv -
"Molecular docking and dynamics simulations of 4-heteroarylidenamino-4, 5-dihydro-1H-1, 2, 4-triazol-5-one derivatives as potential anticancer agents" - Computational Biology and Chemistry - 2025.
Jose Siguenza, Haci Baykara
Journal -
"DeepChem-Variant: A Modular Open Source Framework for Genomic Variant Calling" — Championing Open-source DEvelopment in Machine Learning (CODEML) Workshop at ICML - 2025.
Ankita Vaishnobi Bisoi, V Shreyas, Jose Siguenza, Bharath Ramsundar
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"Open-Source Molecular Processing Pipeline for Generating Molecules" — Machine Learning and Physical Sciences (ML4PS) Workshop at NeurIPS, Molecular Machine Learning Conference (MoML), BayLearn - 2024.
V Shreyas, Jose Siguenza, Karan Bania, Bharath Ramsundar
arXiv -
"Molecular docking of triazole-based ligands with KDM5A to identify potential inhibitors" — International Workshop on Innovative Simulation for Healthcare (IWISH) Workshop at I3M - 2024.
IWISH 2024 Best Paper Award.Jose Siguenza, Haci Baykara
PDF, Scopus
Under Review
"Synthesis, characterization, and mechanical property prediction of microcellulose-reinforced polyvinyl alcohol composites" — ACS Applied Polymer Materials, 2025. Link not yet available
Other Works
Projects
Normalizing Flows Implementation in Deepchem
Used to generate new molecules using nonlinear transformations. Based on datasets like QM9.
SourceBERT-Powered Question Answering for ESPOL
A chatbot built with BERT and web scraping to answer ESPOL-related questions in real time.
GitHubEssential Oils Optimization
Optimization of essential oil production using AI models and regression.
Article