Advanced Biomedical AIWeeksSyllabusReading listPaper sessionsTerm projectRepository ↗

Reading list

Every paper is linked to its publisher or arXiv page. PDFs are not stored in this repository; use the links (UF Libraries access may be needed for some journals).

Week Date Slot Paper Venue
1 Jan 14 Period 8 Moor et al., Foundation models for generalist medical artificial intelligence Nature, 2023
2 Jan 21 Period 7 Devlin et al., BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding NAACL, 2019
2 Jan 21 Period 8 Yang et al., A large language model for electronic health records (GatorTron) npj Digital Medicine, 2022
3 Jan 28 Period 7 Luo et al., BioGPT: generative pre-trained transformer for biomedical text generation and mining Briefings in Bioinformatics, 2022
3 Jan 28 Period 8 Dosovitskiy et al., An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale ICLR, 2021
4 Feb 4 Period 7 DeepSeek-AI, DeepSeek-V3 Technical Report arXiv, 2024
4 Feb 4 Period 8 Sellergren et al., MedGemma Technical Report arXiv, 2025
5 Feb 11 Period 7 Guo et al., DeepSeek-R1 incentivizes reasoning in LLMs through reinforcement learning Nature, 2025
5 Feb 11 Period 8 Singhal et al., Toward expert-level medical question answering with large language models (Med-PaLM 2) Nature Medicine, 2025
6 Feb 18 Period 7 He et al., Masked Autoencoders Are Scalable Vision Learners CVPR, 2022
6 Feb 18 Period 8 Chen et al., Towards a general-purpose foundation model for computational pathology (UNI) Nature Medicine, 2024
7 Feb 25 Period 7 Radford et al., Learning Transferable Visual Models From Natural Language Supervision (CLIP) ICML, 2021
7 Feb 25 Period 8 Tu et al., Towards Generalist Biomedical AI (Med-PaLM M) NEJM AI, 2024
8 Mar 4 Period 7 Wornow et al., The shaky foundations of large language models and foundation models for electronic health records npj Digital Medicine, 2023
8 Mar 4 Period 8 Renc et al., Zero shot health trajectory prediction using transformer (ETHOS) npj Digital Medicine, 2024
9 Mar 11 Period 7 Yao et al., ReAct: Synergizing Reasoning and Acting in Language Models ICLR, 2023
9 Mar 11 Period 8 Zakka et al., Almanac: Retrieval-Augmented Language Models for Clinical Medicine NEJM AI, 2024
11 Mar 25 Period 7 Watson et al., De novo design of protein structure and function with RFdiffusion Nature, 2023
11 Mar 25 Period 8 Abramson et al., Accurate structure prediction of biomolecular interactions with AlphaFold 3 Nature, 2024
12 Apr 1 Period 7 Goh et al., Large Language Model Influence on Diagnostic Reasoning: A Randomized Clinical Trial JAMA Network Open, 2024
12 Apr 1 Period 8 DeGrave et al., AI for radiographic COVID-19 detection selects shortcuts over signal Nature Machine Intelligence, 2021
13 Apr 8 Period 7 Wong et al., External Validation of a Widely Implemented Proprietary Sepsis Prediction Model in Hospitalized Patients JAMA Internal Medicine, 2021
13 Apr 8 Period 8 Haque et al., Illuminating the dark spaces of healthcare with ambient intelligence Nature, 2020

Week 1 is an instructor-led model session. All other sessions are student-led; the instructor assigns papers and groups, posted on Canvas by Friday, January 15.

Further reading (not assigned)

LLM architectures (Weeks 4 and 5)