Siyu He

Weixin Liang, Yuhui Zhang, Hancheng Cao et al. · stanford

Expert feedback lays the foundation of rigorous research. However, the rapid growth of scholarly production and intricate knowledge specialization challenge the conventional scientific feedback mechanisms. High-quality peer reviews are increasingly difficult to obtain. Researchers who are more junior or from under-resourced settings have especially hard times getting timely feedback. With the breakthrough of large language models (LLM) such as GPT-4, there is growing interest in using LLMs to generate scientific feedback on research manuscripts. However, the utility of LLM-generated feedback has not been systematically studied. To address this gap, we created an automated pipeline using GPT-4 to provide comments on the full PDFs of scientific papers. We evaluated the quality of GPT-4's feedback through two large-scale studies. We first quantitatively compared GPT-4's generated feedback with human peer reviewer feedback in 15 Nature family journals (3,096 papers in total) and the ICLR machine learning conference (1,709 papers). The overlap in the points raised by GPT-4 and by human reviewers (average overlap 30.85% for Nature journals, 39.23% for ICLR) is comparable to the overlap between two human reviewers (average overlap 28.58% for Nature journals, 35.25% for ICLR). The overlap between GPT-4 and human reviewers is larger for the weaker papers. We then conducted a prospective user study with 308 researchers from 110 US institutions in the field of AI and computational biology to understand how researchers perceive feedback generated by our GPT-4 system on their own papers. Overall, more than half (57.4%) of the users found GPT-4 generated feedback helpful/very helpful and 82.4% found it more beneficial than feedback from at least some human reviewers. While our findings show that LLM-generated feedback can help researchers, we also identify several limitations.

Weixin Liang, Yaohui Zhang, Zhengxuan Wu et al. · berkeley, stanford

Scientific publishing lays the foundation of science by disseminating research findings, fostering collaboration, encouraging reproducibility, and ensuring that scientific knowledge is accessible, verifiable, and built upon over time. Recently, there has been immense speculation about how many people are using large language models (LLMs) like ChatGPT in their academic writing, and to what extent this tool might have an effect on global scientific practices. However, we lack a precise measure of the proportion of academic writing substantially modified or produced by LLMs. To address this gap, we conduct the first systematic, large-scale analysis across 950,965 papers published between January 2020 and February 2024 on the arXiv, bioRxiv, and Nature portfolio journals, using a population-level statistical framework to measure the prevalence of LLM-modified content over time. Our statistical estimation operates on the corpus level and is more robust than inference on individual instances. Our findings reveal a steady increase in LLM usage, with the largest and fastest growth observed in Computer Science papers (up to 17.5%). In comparison, Mathematics papers and the Nature portfolio showed the least LLM modification (up to 6.3%). Moreover, at an aggregate level, our analysis reveals that higher levels of LLM-modification are associated with papers whose first authors post preprints more frequently, papers in more crowded research areas, and papers of shorter lengths. Our findings suggests that LLMs are being broadly used in scientific writings.

Haojun Yu, Youcheng Li, Nan Zhang et al.

Foundational models have emerged as powerful tools for addressing various tasks in clinical settings. However, their potential development to breast ultrasound analysis remains untapped. In this paper, we present BUSGen, the first foundational generative model specifically designed for breast ultrasound image analysis. Pretrained on over 3.5 million breast ultrasound images, BUSGen has acquired extensive knowledge of breast structures, pathological features, and clinical variations. With few-shot adaptation, BUSGen can generate repositories of realistic and informative task-specific data, facilitating the development of models for a wide range of downstream tasks. Extensive experiments highlight BUSGen's exceptional adaptability, significantly exceeding real-data-trained foundational models in breast cancer screening, diagnosis, and prognosis. In breast cancer early diagnosis, our approach outperformed all board-certified radiologists (n=9), achieving an average sensitivity improvement of 16.5% (P-value<0.0001). Additionally, we characterized the scaling effect of using generated data which was as effective as the collected real-world data for training diagnostic models. Moreover, extensive experiments demonstrated that our approach improved the generalization ability of downstream models. Importantly, BUSGen protected patient privacy by enabling fully de-identified data sharing, making progress forward in secure medical data utilization. An online demo of BUSGen is available at https://aibus.bio.

Amrita Mathuriya, Deborah Bard, Peter Mendygral et al.

Deep learning is a promising tool to determine the physical model that describes our universe. To handle the considerable computational cost of this problem, we present CosmoFlow: a highly scalable deep learning application built on top of the TensorFlow framework. CosmoFlow uses efficient implementations of 3D convolution and pooling primitives, together with improvements in threading for many element-wise operations, to improve training performance on Intel(C) Xeon Phi(TM) processors. We also utilize the Cray PE Machine Learning Plugin for efficient scaling to multiple nodes. We demonstrate fully synchronous data-parallel training on 8192 nodes of Cori with 77% parallel efficiency, achieving 3.5 Pflop/s sustained performance. To our knowledge, this is the first large-scale science application of the TensorFlow framework at supercomputer scale with fully-synchronous training. These enhancements enable us to process large 3D dark matter distribution and predict the cosmological parameters $Ω_M$, $σ_8$ and n$_s$ with unprecedented accuracy.