Curriculum Vitae
Updated October 2026Summary
AI research scientist and PhD in Computer Science specializing in representation learning, with primary applications in computational biology and drug discovery. Industry experience at Johnson and Johnson and Microsoft, where I developed language models for mRNA and machine learning systems for large scale biomedical data. Strong programming background in Python, and JavaScript, with deep experience in PyTorch, Transformers and graph neural networks. Published in NeurIPS, ICLR and Briefings in Bioinformatics, with work spanning mRNA modeling, drug target interaction prediction and algorithmic fairness.
Research Experience
Senior Research Scientist2026-01 – Present
DeepBio Scientific, Orlando, FL- Lead computational biology and drug discovery research, developing machine learning models and algorithms for analyzing complex biomedical data.
- Collaborate with cross-functional teams to translate research findings into scalable bioinformatics and computational drug discovery workflows.
- Design and implement a state-of-the-art agentic AI system for retrieval and multi-step reasoning across biomedical datasets, enabling faster and more accurate analysis.
- Develop benchmark datasets, evaluation metrics, and testing frameworks to assess model retrieval, reasoning, and predictive performance.
Research Intern, Bio-LLMs2025-06 – 2025-09
Microsoft, Redmond, WA- Built a novel agent orchestration system for planning, tool use, and judgment.
- Explored agentic AI on deidentified clinical datasets with end to end experiments and evaluation.
- Developed a RAG retrieval stack with hybrid dense and sparse search, reranking, and citation attribution.
- Contributed to the development of evaluation metrics and benchmarks for agentic AI systems.
Data Science Intern, AI/ML for Drug Discovery2024-05 – 2024-11
Johnson & Johnson (Janssen R&D)- Developed and trained HELM (Hierarchical Encoding for mRNA Language Modeling), the first mRNA antibody language model, achieving up to 8% increase in prediction accuracy and enabling the generation of more diverse and biologically plausible sequences.
- Explored alternative attention architectures such as Mamba and Hyena, enhancing transformer model efficiency and effectiveness in processing mRNA sequences.
- Implemented large-scale distributed training on Kubernetes, resulting in significant reduction in training time for LLMs on extensive datasets, optimizing resource utilization and scalability.
- Collaborated with cross-functional teams to refine and deploy advanced LLM architectures, enhancing model accuracy and efficiency for large-scale data processing tasks.
Education
PhD in Computer Science2021-01 – 2025-10
University of Central Florida- Thesis: Advancing Drug Discovery with Structural and Representation Learning of Biological Systems Link
- GPA: 3.91/4.0
MS in Computer Science2021-01 – 2023-08
University of Central Florida- GPA: 3.9/4.0
MS in Industrial Engineering2017-09 – 2019-12
Sharif University of Technology- GPA: 3.88/4.0
Selected Publications
Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models2025
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Ozlem Ozmen Garibay · Neurips 2025BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation2025
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay · Advances in BioinformaticsHELM: Hierarchical Encoding for mRNA Language Modeling2024
Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi, Artem Moskalev, Rui Liao · ICLR 2025, Neurips 2024 Workshop on AI for New Drug ModalitiesFair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium2024
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, AmirArsalan Rajabi, Aida Tayebi, Ivan Garibay, Ozlem Ozmen Garibay · Neurips 2024Learning Fair Representations: Mitigating Statistical Dependencies2024
Aida Tayebi, Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Niloofar Yousefi, Ozlem Ozmen Garibay · HCII conference 2023 Oral PresentationFragXsiteDTI: an interpretable transformer-based model for drug-target interaction prediction2024
Ali Khodabandeh Yalabadi*, Mehdi Yazdani-Jahromi*, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Ozlem Ozmen Garibay · Recomb 2024 (Oral), Neurips 2023 Workshop on New Frontiers of AI for Drug Discovery and Development; * equal contributionControlling the misinformation diffusion in social media by the effect of different classes of agents2023
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Sina Abdidizaji, Ivan Garibay, Ozlem Ozmen Garibay · The Computational Social Science Society of the Americas Annual ConferenceAgent-Based Modeling of C. Difficile Spread in Hospitals: Assessing Contribution of High-Touch vs. Low-Touch Surfaces and Inoculations' Containment Impact2023
Sina Abdidizaji, Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay, Ivan Garibay · The Computational Social Science Society of the Americas Annual ConferenceThrough a fair looking-glass: on mitigating bias in image datasets2023
Amirarsalan Rajabi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay, Gita Sukthankar · HCII conference 2023 (Oral), AAAI 2023 Workshop on Representation Learning for Responsible Human-Centric AIBindingSiteAugmented DTA to enable A Next-Generation Pipeline for Interpretable Prediction Models in Drug-Repurposing2023
Niloofar Yousefi*, Mehdi Yazdani-Jahromi*, Aida Tayebi, Elayaraja Kolanthai, Craig J Neal, Tanumoy Banerjee, Agnivo Gosai, Ganesh Balasubramanian, Sudipta Seal, Ozlem Ozmen Garibay · Briefings in Bioinformatics; * equal contributionAttentionSiteDTI: Attention Based Model for Predicting Drug-Target Interaction Using 3D Structure of Protein Binding Sites2022
Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Elayaraja Kolanthai, Craig J Neal, Sudipta Seal, Ozlem Ozmen Garibay · Briefings in BioinformaticsUnbiasedDTI: Mitigating Real-World Bias of Drug-Target Interaction Prediction2022
Aida Tayebi, Niloofar Yousefi, Mehdi Yazdani-Jahromi, Elayaraja Kolanthai, Craig J Neal, Sudipta Seal, Ozlem Ozmen Garibay · MDPI MoleculesAwards
Nominated for Best Dissertation Award at University of Central Florida
2025Top Reviewer Award from NeuRIPS 2025
2025Received 30000 dollar Amazon Research Credit Award
2023Nominated for Order of Pegasus award
2023Invited to Golden Key International Honor Society
2022Outstanding Graduate Fellowship University of Central Florida
2021Ranked 1st among 25000 competitors in Iranian national entrance exam for M.Sc. of industrial engineering
2017Ranked 2nd in “Kharazmi” national Prize for Programming
2012Teaching Experience
Teaching Assistant - PHI 6679 - Digital Ethics2025-08 – 2025-12
University of Central Florida, Orlando, FLTeaching Assistant - STA 5206 - Statistical Analysis2025-05 – 2025-08
University of Central Florida, Orlando, FLTeaching Assistant - CAP 6737 - Interactive Data Visualization2025-01 – 2025-05
University of Central Florida, Orlando, FLTeaching Assistant - CAP 5610 - Machine Learning2024-08 – 2024-12
University of Central Florida, Orlando, FLTeaching Assistant - STA 6714 - Data Preparation2023-08 – 2023-12
University of Central Florida, Orlando, FLTeaching Assistant - STA 5206 - Statistical Analysis2023-05 – 2023-08
University of Central Florida, Orlando, FLGuest Lecturer (Project in Data Analytics)2022-08 – 2022-12
University of Central Florida, Orlando, FLTeaching Assistant - Data Mining2018-09 – 2019-12
Sharif University of Technology, Tehran, IranDevelopment Experience
Blockchain Developer2020-06 – 2020-12
ZTech Team- Developed blockchain applications on the Ethereum network using Solidity, including implementing ERC20 token standards and smart contracts for financial ICOs.
Lead Software Developer2019-01 – 2020-12
BerimCafe- Developed software for cafe and restaurant management with Django and Flutter.
Lead Software Developer2019-01 – 2020-03
TAEPO- Created TOEFL Online Practice and Exam Platform using Django, Vue.js, and Electron.js.
Lead Software Developer2018-02 – 2019-12
MrZoro.ir- Developed an automated solution for reserving meals in university, a Django based project.
Projects
DeepDrugDomain: Easy-to-use drug-target affinity/interaction prediction package for architecture design
- Developed an open source Python package for drug-target affinity/interaction prediction using deep learning models, including transformers and graph neural networks, for computational drug discovery.
- Implemented a user-friendly API for easy-to-use drug-target affinity/interaction prediction.
- Published on GitHub
COVID-19 Data Collection and Screening Project
Cache Simulator
- Developed a cache simulator to evaluate the performance of different cache management strategies, including LRU, FIFO, and LFU. Implemented in C++.
Academic Services
Reviewer of Journal Briefings in Bioinformatics
Reviewer of Computational and Structural Biotechnology Journal
Reviewer of IEEE Transactions on Neural Networks and Learning Systems Journal
Program Committee Member of AAAI Artificial Intelligence for Social Impact 2025 & 2026.
Reviewer of Neurips 2025 (The Thirty-Ninth Annual Conference on Neural Information Processing Systems)
Skills
Programming Languages
Python, Dart, JavaScript, C++, C#, SQL, Solidity, MATLABPython Packages
Pytorch, Numpy, Pandas, Keras, TensorFlow, Scikit-learn, Scipy, Networkx, iGraph, dgl, matplotlib, seabornJavaScript Frameworks
Vue.js, Electron, NativeScriptTools
Kubernetes, Docker, Git, HTML, CSS, LATEX, AWS, Azure, SlurmQuantitative Research
Machine Learning Methods, Artificial Intelligence, Large Language Models, Generative AI, Genomics Sequence Modeling, Drug Discovery, Graph Neural Networks, Transformers, Recurrent Neural Networks, LSTMs, Mathematical Optimization, Mathematical ModelingSoft Skills
Research team coordination, Student mentoring, Technical writing, Conference presentations, Resource allocation, Strategic planning, Analytical thinking, Complex problem resolution, International team collaboration, Multicultural communication, Self-directed learning, Professional networkingCertificates
References
Dr. Ozlem Ozmen (Advisor)
- Assistant Professor at University of Central Florida Email
Dr. Mangal Prakash
- Senior Scientist, AI/ML at Johnson & Johnson (Janssen R&D) Email
Dr. Artem Moskalev
- Research Scientist at Johnson & Johnson (Janssen R&D) Email
Dr. Ivan Garibay
- Associate Professor at University of Central Florida Email