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Med-Flamingo: a Multimodal Medical Few-shot Learner - Discussion, Acknowledgments, and References

by The FewShot Prompting Publication June 19th, 2024

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This is an early proof-of-concept for a medical multimodal few-shot learner. We expect to see significant improvements with increased model and data scale, more thoroughly cleaned data, as well as with alignment to human preference via instruction tuning. In all VLMs we analyzed, hallucinations were observed. It is possible that the model occasionally outputs low-quality generations.

featured image - Med-Flamingo: a Multimodal Medical Few-shot Learner - Discussion, Acknowledgments, and References

Authors:

(1) Michael Moor, Department of Computer Science, Stanford University, Stanford, USA and these authors contributed equally to this work;

(2) Qian Huang, Department of Computer Science, Stanford University, Stanford, USA and these authors contributed equally to this work;

(3) Shirley Wu, Department of Computer Science, Stanford University, Stanford, USA;

(4) Michihiro Yasunaga, Department of Computer Science, Stanford University, Stanford, USA;

(5) Cyril Zakka, Department of Cardiothoracic Surgery, Stanford Medicine, Stanford, USA;

(6) Yash Dalmia, Department of Computer Science, Stanford University, Stanford, USA;

(7) Eduardo Pontes Reis, Hospital Israelita Albert Einstein, Sao Paulo, Brazil;

(8) Pranav Rajpurkar, Department of Biomedical Informatics, Harvard Medical School, Boston, USA;

(9) Jure Leskovec, Department of Computer Science, Stanford University, Stanford, USA.

Table of Links

Abstract and 1 Introduction

6 Discussion, Acknowledgments, and References

A Appendix

6 DISCUSSION

In this paper, we presented Med-Flamingo, the first medically adapted multimodal few-shot learner. While this is an early proof-of-concept for a medical multimodal few-shot learner, we expect to see significant improvements with increased model and data scale, more thoroughly cleaned data, as well as with alignment to human preference via instruction tuning or explicit optimization for preferences.

We expect that the rise of multimodal medical few-shot learners will lead to exciting opportunities with regard to model explainability (via rationale generation) as well as grounding the model in verified sources (via multimodal retrieval to augment the few-shot prompt). Thereby, our work serves as a first step towards more generalist medical AI models Moor et al. (2023).

Limitations This work demonstrates a proof-of-concept. As such, Med-Flamingo is not intended nor safe for clinical use. In all VLMs we analyzed, hallucinations were observed. Furthermore, as Med-Flamingo is a pre-trained model without further instruction or preference tuning, it is possible that the model occasionally outputs low-quality generations.

Future work It will be an exciting route for future work to further train Med-Flamingo on clinical data, high-resolution medical image datasets as well as 3D volumes and medical videos. While current general-purpose medical VLMs are pre-trained on the broad medical literature (i.e., they are only “book-smart”), also learning from diverse patient data directly will become crucial for down-stream applications.

ACKNOWLEDGMENTS

We thank Rok Sosic for his technical support in the data preprocessing.

REFERENCES

Armen Aghajanyan, Bernie Huang, Candace Ross, Vladimir Karpukhin, Hu Xu, Naman Goyal, Dmytro Okhonko, Mandar Joshi, Gargi Ghosh, Mike Lewis, and Luke Zettlemoyer. CM3: A causal masked multimodal model of the internet.

Jean-Baptiste Alayrac, Jeff Donahue, Pauline Luc, Antoine Miech, Iain Barr, Yana Hasson, Karel Lenc, Arthur Mensch, Katherine Millican, Malcolm Reynolds, Roman Ring, Eliza Rutherford, Serkan Cabi, Tengda Han, Zhitao Gong, Sina Samangooei, Marianne Monteiro, Jacob Menick, Sebastian Borgeaud, Andrew Brock, Aida Nematzadeh, Sahand Sharifzadeh, Mikolaj Binkowski, Ricardo Barreira, Oriol Vinyals, Andrew Zisserman, and Karen Simonyan. Flamingo: a visual language model for few-shot learning. In Advances in Neural Information Processing Systems.

Jean-Baptiste Alayrac, Jeff Donahue, Pauline Luc, Antoine Miech, Iain Barr, Yana Hasson, Karel Lenc, Arthur Mensch, Katherine Millican, Malcolm Reynolds, et al. Flamingo: a visual language model for few-shot learning. Advances in Neural Information Processing Systems, 35:23716– 23736, 2022.

Anas Awadalla, Irena Gao, Joshua Gardner, Jack Hessel, Yusuf Hanafy, Wanrong Zhu, Kalyani Marathe, Yonatan Bitton, Samir Gadre, Jenia Jitsev, Simon Kornblith, Pang Wei Koh, Gabriel Ilharco, Mitchell Wortsman, and Ludwig Schmidt. Openflamingo, March 2023.

Elliot Bolton, David Hall, Michihiro Yasunaga, Tony Lee, Chris Manning, and Percy Liang. BioMedLM: a domain-specific large language model for biomedical text.

Rishi Bommasani, Drew A Hudson, Ehsan Adeli, Russ Altman, Simran Arora, Sydney von Arx, Michael S Bernstein, Jeannette Bohg, Antoine Bosselut, Emma Brunskill, et al. On the opportunities and risks of foundation models. arXiv preprint arXiv:2108.07258, 2021.

Tom Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared D Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, Sandhini Agarwal, Ariel Herbert-Voss, Gretchen Krueger, Tom Henighan, Rewon Child, Aditya Ramesh, Daniel Ziegler, Jeffrey Wu, Clemens Winter, Chris Hesse, Mark Chen, Eric Sigler, Mateusz Litwin, Scott Gray, Benjamin Chess, Jack Clark, Christopher Berner, Sam McCandlish, Alec Radford, Ilya Sutskever, and Dario Amodei. Language models are few-shot learners. In Advances in Neural Information Processing Systems, volume 33, pp. 1877–1901.

Tom B. Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, Sandhini Agarwal, Ariel Herbert-Voss, Gretchen Krueger, Tom Henighan, Rewon Child, Aditya Ramesh, Daniel M. Ziegler, Jeffrey Wu, Clemens Winter, Christopher Hesse, Mark Chen, Eric Sigler, Mateusz Litwin, Scott Gray, Benjamin Chess, Jack Clark, Christopher Berner, Sam McCandlish, Alec Radford, Ilya Sutskever, and Dario Amodei. Language models are few-shot learners. In Hugo Larochelle, Marc’Aurelio Ranzato, Raia Hadsell, Maria-Florina Balcan, and Hsuan-Tien Lin (eds.), Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, NeurIPS 2020, December 6-12, 2020, virtual, 2020.

Alexey Dosovitskiy, Lucas Beyer, Alexander Kolesnikov, Dirk Weissenborn, Xiaohua Zhai, Thomas Unterthiner, Mostafa Dehghani, Matthias Minderer, Georg Heigold, Sylvain Gelly, Jakob Uszkoreit, and Neil Houlsby. An image is worth 16x16 words: Transformers for image recognition at scale. ICLR, 2021.

Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, and Hoifung Poon. Domain-specific language model pretraining for biomedical natural language processing. ACM Transactions on Computing for Healthcare (HEALTH), 3(1): 1–23, 2021.

Kexin Huang, Jaan Altosaar, and Rajesh Ranganath. Clinicalbert: Modeling clinical notes and predicting hospital readmission. arXiv preprint arXiv:1904.05342, 2019.

Jeff Johnson, Matthijs Douze, and Herve J ´ egou. Billion-scale similarity search with GPUs. ´ IEEE Transactions on Big Data, 7(3):535–547, 2019.

Dani Kiyasseh, Runzhuo Ma, Taseen F Haque, Brian J Miles, Christian Wagner, Daniel A Donoho, Animashree Anandkumar, and Andrew J Hung. A vision transformer for decoding surgeon activity from surgical videos. Nature Biomedical Engineering, pp. 1–17, 2023.

Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, and Jaewoo Kang. Biobert: a pre-trained biomedical language representation model for biomedical text mining. Bioinformatics, 36(4):1234–1240, 2020.

Chunyuan Li, Cliff Wong, Sheng Zhang, Naoto Usuyama, Haotian Liu, Jianwei Yang, Tristan Naumann, Hoifung Poon, and Jianfeng Gao. Llava-med: Training a large language-and-vision assistant for biomedicine in one day. arXiv preprint arXiv:2306.00890, 2023.

Percy Liang, Rishi Bommasani, Tony Lee, Dimitris Tsipras, Dilara Soylu, Michihiro Yasunaga, Yian Zhang, Deepak Narayanan, Yuhuai Wu, Ananya Kumar, et al. Holistic evaluation of language models. arXiv preprint arXiv:2211.09110, 2022.

Weixiong Lin, Ziheng Zhao, Xiaoman Zhang, Chaoyi Wu, Ya Zhang, Yanfeng Wang, and Weidi Xie. Pmc-clip: Contrastive language-image pre-training using biomedical documents. arXiv preprint arXiv:2303.07240, 2023.

Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, and Tie-Yan Liu. Biogpt: generative pre-trained transformer for biomedical text generation and mining. Briefings in Bioinformatics, 23(6):bbac409, 2022.

Michael Moor, Oishi Banerjee, Zahra Shakeri Hossein Abad, Harlan M Krumholz, Jure Leskovec, Eric J Topol, and Pranav Rajpurkar. Foundation models for generalist medical artificial intelligence. Nature, 616(7956):259–265, 2023.

Chengwei Qin, Aston Zhang, Zhuosheng Zhang, Jiaao Chen, Michihiro Yasunaga, and Diyi Yang. Is chatgpt a general-purpose natural language processing task solver? arXiv preprint arXiv:2302.06476, 2023.

Alec Radford, Jong Wook Kim, Chris Hallacy, Aditya Ramesh, Gabriel Goh, Sandhini Agarwal, Girish Sastry, Amanda Askell, Pamela Mishkin, Jack Clark, Gretchen Krueger, and Ilya Sutskever. Learning transferable visual models from natural language supervision. In Proceedings of the 38th International Conference on Machine Learning, pp. 8748–8763. ISSN: 2640-3498.

Aditya Ramesh, Mikhail Pavlov, Gabriel Goh, Scott Gray, Chelsea Voss, Alec Radford, Mark Chen, and Ilya Sutskever. Zero-shot text-to-image generation. In Proceedings of the 38th International Conference on Machine Learning, pp. 8821–8831. ISSN: 2640-3498.

Karan Singhal, Shekoofeh Azizi, Tao Tu, S. Sara Mahdavi, Jason Wei, Hyung Won Chung, Nathan Scales, Ajay Tanwani, Heather Cole-Lewis, Stephen Pfohl, Perry Payne, Martin Seneviratne, Paul Gamble, Chris Kelly, Nathaneal Scharli, Aakanksha Chowdhery, Philip Mansfield, Blaise Aguera y Arcas, Dale Webster, Greg S. Corrado, Yossi Matias, Katherine Chou, Juraj Gottweis, Nenad Tomasev, Yun Liu, Alvin Rajkomar, Joelle Barral, Christopher Semturs, Alan Karthikesalingam, and Vivek Natarajan. Large language models encode clinical knowledge.

Ethan Steinberg, Ken Jung, Jason A Fries, Conor K Corbin, Stephen R Pfohl, and Nigam H Shah. Language models are an effective representation learning technique for electronic health record data. Journal of biomedical informatics, 113:103637, 2021.

Weijie Su, Xizhou Zhu, Yue Cao, Bin Li, Lewei Lu, Furu Wei, and Jifeng Dai. Vl-bert: Pre-training of generic visual-linguistic representations. arXiv preprint arXiv:1908.08530, 2019.

Ekin Tiu, Ellie Talius, Pujan Patel, Curtis P Langlotz, Andrew Y Ng, and Pranav Rajpurkar. Expertlevel detection of pathologies from unannotated chest x-ray images via self-supervised learning. Nature Biomedical Engineering, 6(12):1399–1406, 2022.

Hugo Touvron, Thibaut Lavril, Gautier Izacard, Xavier Martinet, Marie-Anne Lachaux, Timothee´ Lacroix, Baptiste Roziere, Naman Goyal, Eric Hambro, Faisal Azhar, et al. Llama: Open and ` efficient foundation language models. arXiv preprint arXiv:2302.13971, 2023.

Michihiro Yasunaga, Antoine Bosselut, Hongyu Ren, Xikun Zhang, Christopher D. Manning, Percy Liang, and Jure Leskovec. Deep bidirectional language-knowledge graph pretraining. In Advances in Neural Information Processing Systems, a.

Michihiro Yasunaga, Jure Leskovec, and Percy Liang. LinkBERT: Pretraining language models with document links. In Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), pp. 8003–8016. Association for Computational Linguistics, b. doi: 10.18653/v1/2022.acl-long.551.

Michihiro Yasunaga, Armen Aghajanyan, Weijia Shi, Rich James, Jure Leskovec, Percy Liang, Mike Lewis, Luke Zettlemoyer, and Wen-tau Yih. Retrieval-augmented multimodal language modeling. 2023.

Sheng Zhang, Yanbo Xu, Naoto Usuyama, Jaspreet Bagga, Robert Tinn, Sam Preston, Rajesh Rao, Mu Wei, Naveen Valluri, Cliff Wong, et al. Large-scale domain-specific pretraining for biomedical vision-language processing. arXiv preprint arXiv:2303.00915, 2023a.

Tianyi Zhang, Varsha Kishore*, Felix Wu, Kilian Q. Weinberger, and Yoav Artzi. Bertscore: Evaluating text generation with bert. In International Conference on Learning Representations, 2020.

Xiaoman Zhang, Chaoyi Wu, Ziheng Zhao, Weixiong Lin, Ya Zhang, Yanfeng Wang, and Weidi Xie. Pmc-vqa: Visual instruction tuning for medical visual question answering. arXiv preprint arXiv:2305.10415, 2023b.