Saman Shafaei
Champaign,IL
Summary
PhD student with a deep interest in integrating novel ML/AI strategies to power means in synthetic biology and protein engineering.
Overview
3
3
years of professional experience
Work History
PhD Research Assistant
University Of Illinois, Urbana-Champaign
08.2021 - Current
- Developed “FermOpt" framework, a semi-automated, data-driven platform for optimizing fermentation conditions, which integrates high-throughput fermentation processes with deep learning modeling and customized fermentation objective functions to enhance efficiency and economic outcome. In four case studies, "FermOpt" demonstrated a 10-65% increase in both production and economic viability of the process.
- Designing two innovative deep learning models for transporter proteins, including a hierarchical metric learning-based model for transporter protein sequence classification (TC numbers) with 0.72 F1 score (state of the art) on TCDB test dataset, and an innovative attention-based model for predicting molecules transported by these proteins, marking a first in the field.
- Building ProtT5Bin, a multi-task, text-to-text transformer model designed for numerical predictions in the realm of protein analysis. Utilizing a binary encoding method and a custom weighted loss function, it excels in predicting protein solubility, stability, and kinetic parameters based on protein sequences and task-specific prompts. This approach capitalizes on the advanced capabilities of transformer architectures, offering a sophisticated solution for detailed protein property analysis.
- Developed new Rubisco photoenzyme variants using AI/ML tools, starting with analyzing structural and sequential data conditions from existing Rubisco forms, then applying conditioned tools like RFDiffusion, EvoDiff, ProteinMPNN, ESM2, ESMIF, and AlphaFold for novel optimized design.
- Created a novel subontology for enzyme commission numbers (EC numbers) using ESM2 embeddings and hierarchical clustering, aimed at accurately describing enzyme protein space.
PhD Teaching Assistant
University Of Illinois, Urbana-Champaign
08.2022 - 08.2023
- Contributed to the syllabus design and end-of-semester project design for students in the Senior Chemical Engineering Design course
- Recipients of the School of Chemical Sciences 2023 Teaching Awards
Education
Ph.D. - Chemical And Biomolecular Engineering
University of Illinois At Urbana-Champaign
Champaign, IL08.2025
Bachelor of Science - Chemical Engineering
Sharif University of Technology
Tehran,Iran08.2020
Skills
- Python, R, Java, SQL programming
- Teamwork and Collaboration
- Algorithm development
- Machine Learning Integration
- Natural Language Processing
Timeline
PhD Teaching Assistant
University Of Illinois, Urbana-Champaign
08.2022 - 08.2023
PhD Research Assistant
University Of Illinois, Urbana-Champaign
08.2021 - Current
Ph.D. - Chemical And Biomolecular Engineering
University of Illinois At Urbana-Champaign
Bachelor of Science - Chemical Engineering
Sharif University of Technology
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