CV

Education

• M.S. in artificial intelligence, Utrecht University, Utrecht, Nehterlands
• B.S. in computer science, Camilo Jose Cela University, Madrid, Spain

Work experience

• Research data scientist @ TatonettiLab, Cedar Sinai
  • Work on 10+ research projects in cancer and adverse drug events through ML and DL models.
  • Design and implement transformer models trained on genomics data to tackle different cancer challenges.
  • Zero shot and few shot approaches on LLMs to extract meaningful information from medical texts.
  • Research and implement novel methods for computational biomedicine based on the latest papers and innovations.
  • Supervise several student groups for DL/ML architecture implementation.
  • System administration for high performance compute
• Research AI engineer @ Massachusetts General Hospital & Harvard Medical School
  • Worked on 8+ research projects developing machine learning and deep learning algorithms. From data preparation to evaluation.
  • Designed and implemented computer vision algorithms for lesion detection, and classification. Architectures included ResNet, EfficientNet, and U‑Net, achieving remarkable results.
  • I developed a registry system of patients including 45.000+ images capable of categorizing x‑rays into 3 different sets of categories. It required the collaboration of several people under my leadership.
  • Supported peer research projects with software architecture implementation and mentored them on machine learning techniques
• AI engineer @ In2A1
  • Addressed clients needs through artificial intelligence solutions, worked on 10+ different projects.
  • Designed and implemented machine learning architectures, met clients weekly, and followed agile methodologies.
  • Managed a group of developers for 2 web development projects based on open‑source frameworks, including APIs and Elasticsearch database.
  • Worked on CI/CD for several machine learning projects using GitLab, Docker, and scalable computing platforms
• Software Engineer @ Avaloq
  • Designed PL/SQL solutions for banks all over Europe. Worked with Avaloq code. Having limited functionalities fostered a creative and ingenious environment to achieve complex tasks in the simplest ways possible.
  • Coded following the best standards to have reusable and scalable code. Implementations were used by 150+ banks worldwide.
  • Worked in a fast‑paced environment adapting to client’s needs and requests where teamwork played an important role
• Software engineer intern @ Telefónica
  • I was part of a team in charge of designing and coding a chatbot supported by machine learning. The aim was to facilitate real‑state advice for the users.
  • Worked as a back‑end developer with APIs and microservicesand designed a CI/CD system with an API broker and docker, using GitLab

Skills

• Programming: Python, shell/bash, C++, R
• AI: Machine Learning, Transformers, Computer Vision, Pattern Recognition
• ML tools: PyTorch, Tensorflow, SciKit learn, pandas, CUDA, Hugginface
• Software: SQL, NoSQL, REST API, Software Design
• Soft Skills: Teamwork, Critical Thinking, Team Management, Public Speaking, Communication
• Languages: Spanish, English

Publications

Enhancing EHR-based pancreatic cancer prediction with LLM-derived embeddings

Park, J., Patterson, J., Acitores Cortina, J.M. et al. Enhancing EHR-based pancreatic cancer prediction with LLM-derived embeddings. npj Digit. Med. 8, 465 (2025). https://doi.org/10.1038/s41746-025-01869-8

Biomedical Text Normalization through Generative Modeling

Jacob S. Berkowitz, Apoorva Srinivasan, Jose Miguel Acitores Cortina, Yasaman Fatapour, Nicholas P Tatonetti, Biomedical text normalization through generative modeling, Journal of Biomedical Informatics, Volume 167, 2025, 104850, ISSN 1532-0464, https://doi.org/10.1016/j.jbi.2025.104850.

Biases in Race and Ethnicity Introduced by Filtering Electronic Health Records for’Complete Data’

Acitores Cortina J, Fatapour Y, Brown K, Gisladottir U, Zietz M, Bear Don’t Walk IV O, Peter D, Berkowitz J, Friedrich N, Kivelson S, Kuchi A, Liu H, Srinivasan A, Tsang K, Tatonetti N Biases in Race and Ethnicity Introduced by Filtering Electronic Health Records for “Complete Data”: Observational Clinical Data Analysis JMIR Med Inform 2025;13:e67591 URL: https://medinform.jmir.org/2025/1/e67591 DOI: 10.2196/67591

Foundation Models for Translational Cancer Biology

Tsang, Kevin K., Kivelson, Sophia, Acitores Cortina, Jose M., Kuchi, Aditi, Berkowitz, Jacob S., Liu, Hongyu, Srinivasan, Apoorva, Friedrich, Nadine A., Fatapour, Yasaman, Tatonetti, Nicholas P. Foundation Models for Translational Cancer Biology, Annual Review of Biomedical Data Science, Volume 8, 2025, https://doi.org/10.1146/annurev-biodatasci-103123-095633

Probing Large Language Model Hidden States for Adverse Drug Reaction Knowledge

Berkowitz, J. et al. (2025). Probing Large Language Model Hidden States for Adverse Drug Reaction Knowledge. In: Bellazzi, R., Juarez Herrero, J.M., Sacchi, L., Zupan, B. (eds) Artificial Intelligence in Medicine. AIME 2025. Lecture Notes in Computer Science(), vol 15734. Springer, Cham. https://doi.org/10.1007/978-3-031-95838-0_6

Generalizable and Automated Classification of TNM Stage from Pathology Reports with External Validation

Kefeli, J., Berkowitz, J., Acitores Cortina, J.M. et al. Generalizable and automated classification of TNM stage from pathology reports with external validation. Nat Commun 15, 8916 (2024). https://doi.org/10.1038/s41467-024-53190-9

TLab at #SMM4H 2024: Retrieval-Augmented Generation for ADE Extraction and Normalization

Jacob Berkowitz, Apoorva Srinivasan, Jose Cortina, and Nicholas Tatonetti1. 2024. TLab at #SMM4H 2024: Retrieval-Augmented Generation for ADE Extraction and Normalization. In Proceedings of the 9th Social Media Mining for Health Research and Applications (SMM4H 2024) Workshop and Shared Tasks, pages 153–157, Bangkok, Thailand. Association for Computational Linguistics.

Automated AI Detection Tool for Ankle Fractures Using X-Rays and Smart Devices

Nassour N, Acitores JM, Jang C, et al. Automated AI Detection Tool for Ankle Fractures Using X-Rays and Smart Devices. Foot & Ankle Orthopaedics. 2023;8(4). doi:10.1177/2473011423S00026