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Computational challenges arising in algorithmic fairness and health equity with generative AI. 生成式人工智能在算法公平和健康公平方面产生的计算挑战。
IF 12
Nature computational science Pub Date : 2025-05-16 DOI: 10.1038/s43588-025-00806-9
Vinith M Suriyakumar, Anna Zink, Maia Hightower, Marzyeh Ghassemi, Brett Beaulieu-Jones
{"title":"Computational challenges arising in algorithmic fairness and health equity with generative AI.","authors":"Vinith M Suriyakumar, Anna Zink, Maia Hightower, Marzyeh Ghassemi, Brett Beaulieu-Jones","doi":"10.1038/s43588-025-00806-9","DOIUrl":"https://doi.org/10.1038/s43588-025-00806-9","url":null,"abstract":"","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toward fair AI-driven medical text generation. 朝着公平的人工智能驱动的医学文本生成。
IF 12
Nature computational science Pub Date : 2025-05-14 DOI: 10.1038/s43588-025-00807-8
Yumeng Zhang, Jiangning Song
{"title":"Toward fair AI-driven medical text generation.","authors":"Yumeng Zhang, Jiangning Song","doi":"10.1038/s43588-025-00807-8","DOIUrl":"https://doi.org/10.1038/s43588-025-00807-8","url":null,"abstract":"","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DNA data storage for biomedical images using HELIX. 利用HELIX存储生物医学图像的DNA数据。
IF 12
Nature computational science Pub Date : 2025-05-13 DOI: 10.1038/s43588-025-00793-x
Guanjin Qu, Zihui Yan, Xin Chen, Huaming Wu
{"title":"DNA data storage for biomedical images using HELIX.","authors":"Guanjin Qu, Zihui Yan, Xin Chen, Huaming Wu","doi":"10.1038/s43588-025-00793-x","DOIUrl":"https://doi.org/10.1038/s43588-025-00793-x","url":null,"abstract":"<p><p>Deoxyribonucleic acid (DNA) data storage is expected to become a key medium for large-scale data. Biomedical data images typically require substantial storage space over extended periods, making them ideal candidates for DNA data storage. However, existing DNA data storage models are primarily designed for generic files and lack a comprehensive retrieval system for biomedical images. Here, to address this, we propose HELIX, a DNA-based storage system for biomedical images. HELIX introduces an image-compression algorithm tailored to the characteristics of biomedical images, achieving high compression rates and robust error tolerance. In addition, HELIX incorporates an error-correcting encoding algorithm that eliminates the need for indexing, enhancing storage density and decoding speed. We utilize a deep learning-based image repair algorithm for the predictive restoration of partially missing image blocks. In our in vitro experiments, we successfully stored two spatiotemporal genomics images. This sequencing process achieved 97.20% image quality at a depth of 7× coverage.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Leveraging generative models with periodicity-aware, invertible and invariant representations for crystalline materials design. 利用具有周期性感知、可逆和不变表征的生成模型进行晶体材料设计。
IF 12
Nature computational science Pub Date : 2025-05-09 DOI: 10.1038/s43588-025-00797-7
Zhilong Wang, Fengqi You
{"title":"Leveraging generative models with periodicity-aware, invertible and invariant representations for crystalline materials design.","authors":"Zhilong Wang, Fengqi You","doi":"10.1038/s43588-025-00797-7","DOIUrl":"https://doi.org/10.1038/s43588-025-00797-7","url":null,"abstract":"<p><p>Designing periodicity-aware, invariant and invertible representations provides an opportunity for the inverse design of crystalline materials with desired properties by generative models. This objective requires optimizing representations and refining the architecture of generative models, yet its feasibility remains uncertain, given current progress in molecular inverse generation. In this Perspective, we highlight the progress of various methods for designing representations and generative schemes for crystalline materials, discuss the challenges in the field and propose a roadmap for future developments.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bi-level identification of governing equations for nonlinear physical systems. 非线性物理系统控制方程的双水平辨识。
IF 12
Nature computational science Pub Date : 2025-05-09 DOI: 10.1038/s43588-025-00804-x
Zeyu Li, Huining Yuan, Wang Han, Yimin Hou, Hongjue Li, Haidong Ding, Zhiguo Jiang, Lijun Yang
{"title":"Bi-level identification of governing equations for nonlinear physical systems.","authors":"Zeyu Li, Huining Yuan, Wang Han, Yimin Hou, Hongjue Li, Haidong Ding, Zhiguo Jiang, Lijun Yang","doi":"10.1038/s43588-025-00804-x","DOIUrl":"https://doi.org/10.1038/s43588-025-00804-x","url":null,"abstract":"<p><p>Identifying governing equations from observational data is crucial for understanding nonlinear physical systems but remains challenging due to the risk of overfitting. Here we introduce the Bi-Level Identification of Equations (BILLIE) framework, which simultaneously discovers and validates equations using a hierarchical optimization strategy. The policy gradient algorithm of reinforcement learning is leveraged to achieve the bi-level optimization. We demonstrate BILLIE's superior performance through comparisons with baseline methods in canonical nonlinear systems such as turbulent flows and three-body systems. Furthermore, we apply the BILLIE framework to discover RNA and protein velocity equations directly from single-cell sequencing data. The equations identified by BILLIE outperform empirical models in predicting cellular differentiation states, underscoring BILLIE's potential to reveal fundamental physical laws across a wide range of scientific fields.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Everything everywhere all at once: a probability-based enhanced sampling approach to rare events. 所有地方的一切都同时发生：一种基于概率的增强采样方法来处理罕见事件。
IF 12
Nature computational science Pub Date : 2025-05-05 DOI: 10.1038/s43588-025-00799-5
Enrico Trizio, Peilin Kang, Michele Parrinello
{"title":"Everything everywhere all at once: a probability-based enhanced sampling approach to rare events.","authors":"Enrico Trizio, Peilin Kang, Michele Parrinello","doi":"10.1038/s43588-025-00799-5","DOIUrl":"https://doi.org/10.1038/s43588-025-00799-5","url":null,"abstract":"<p><p>The problem of studying rare events is central to many areas of computer simulations. We recently proposed an approach to solving this problem that involves computing the committor function, showing how it can be iteratively computed in a variational way while efficiently sampling the transition state ensemble. Here we greatly improve this procedure by combining it with a metadynamics-like enhanced sampling approach in which a logarithmic function of the committor is used as a collective variable. This procedure leads to an accurate sampling of the free energy surface in which transition states and metastable basins are studied with the same thoroughness. We show that our approach can be used in cases with the possibility of competing reactive paths and metastable intermediates. In addition, we demonstrate how physical insights can be obtained from the optimized committor model and the sampled data, thus providing a full characterization of the rare event under study.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A quest toward comprehensive benchmarking of quantum computing software. 对量子计算软件的全面基准测试的探索。
IF 12
Nature computational science Pub Date : 2025-04-29 DOI: 10.1038/s43588-025-00803-y
Chenghong Zhu, Lei Zhang, Xin Wang
{"title":"A quest toward comprehensive benchmarking of quantum computing software.","authors":"Chenghong Zhu, Lei Zhang, Xin Wang","doi":"10.1038/s43588-025-00803-y","DOIUrl":"https://doi.org/10.1038/s43588-025-00803-y","url":null,"abstract":"","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evaluating and mitigating bias in AI-based medical text generation. 评估和减轻基于人工智能的医学文本生成中的偏见。
IF 12
Nature computational science Pub Date : 2025-04-23 DOI: 10.1038/s43588-025-00789-7
Xiuying Chen, Tairan Wang, Juexiao Zhou, Zirui Song, Xin Gao, Xiangliang Zhang
{"title":"Evaluating and mitigating bias in AI-based medical text generation.","authors":"Xiuying Chen, Tairan Wang, Juexiao Zhou, Zirui Song, Xin Gao, Xiangliang Zhang","doi":"10.1038/s43588-025-00789-7","DOIUrl":"https://doi.org/10.1038/s43588-025-00789-7","url":null,"abstract":"<p><p>Artificial intelligence (AI) systems, particularly those based on deep learning models, have increasingly achieved expert-level performance in medical applications. However, there is growing concern that such AI systems may reflect and amplify human bias, reducing the quality of their performance in historically underserved populations. The fairness issue has attracted considerable research interest in the medical imaging classification field, yet it remains understudied in the text-generation domain. In this study, we investigate the fairness problem in text generation within the medical field and observe substantial performance discrepancies across different races, sexes and age groups, including intersectional groups, various model scales and different evaluation metrics. To mitigate this fairness issue, we propose an algorithm that selectively optimizes those underserved groups to reduce bias. Our evaluations across multiple backbones, datasets and modalities demonstrate that our proposed algorithm enhances fairness in text generation without compromising overall performance.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Benchmarking the performance of quantum computing software for quantum circuit creation, manipulation and compilation. 对量子电路创建、操作和编译的量子计算软件的性能进行基准测试。
IF 12
Nature computational science Pub Date : 2025-04-18 DOI: 10.1038/s43588-025-00792-y
Paul D Nation, Abdullah Ash Saki, Sebastian Brandhofer, Luciano Bello, Shelly Garion, Matthew Treinish, Ali Javadi-Abhari
{"title":"Benchmarking the performance of quantum computing software for quantum circuit creation, manipulation and compilation.","authors":"Paul D Nation, Abdullah Ash Saki, Sebastian Brandhofer, Luciano Bello, Shelly Garion, Matthew Treinish, Ali Javadi-Abhari","doi":"10.1038/s43588-025-00792-y","DOIUrl":"https://doi.org/10.1038/s43588-025-00792-y","url":null,"abstract":"<p><p>We present Benchpress, a benchmarking suite for evaluating the performance and range of functionality of multiple quantum computing software development kits. This suite consists of a collection of over 1,000 tests measuring key performance metrics for a wide variety of operations on quantum circuits composed of up to 930 qubits and <math><mrow><mi>O</mi> <mrow><mo>(</mo> <mrow><mn>1</mn> <msup><mrow><mn>0</mn></mrow> <mrow><mn>6</mn></mrow> </msup> </mrow> <mo>)</mo></mrow> </mrow> </math> two-qubit gates, as well as an execution framework for running the tests over multiple quantum software packages in a unified manner. Here we give a detailed overview of the benchmark suite and its methodology and generate representative results over seven different quantum software packages. The flexibility of the Benchpress framework enables benchmarking that not only keeps pace with quantum hardware improvements but also can preemptively gauge the quantum circuit processing costs of future device architectures.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gender and racial diversity socialization in science. 科学中的性别和种族多样性社会化。
IF 12
Nature computational science Pub Date : 2025-04-17 DOI: 10.1038/s43588-025-00795-9
Weihua Li, Hongwei Zheng, Jennie E Brand, Aaron Clauset
{"title":"Gender and racial diversity socialization in science.","authors":"Weihua Li, Hongwei Zheng, Jennie E Brand, Aaron Clauset","doi":"10.1038/s43588-025-00795-9","DOIUrl":"https://doi.org/10.1038/s43588-025-00795-9","url":null,"abstract":"<p><p>Scientific collaboration networks are a form of unequally distributed social capital that shapes both researcher job placement and long-term research productivity and prominence. However, the role of collaboration networks in shaping the gender and racial diversity of the scientific workforce remains unclear. Here we propose a computational null model to investigate the degree to which early-career scientific collaborators with representationally diverse cohorts of scholars are associated with forming or participating in more diverse research groups as established researchers. When testing this hypothesis using two large-scale, longitudinal datasets on scientific collaborations, we find that the gender and racial diversity in a researcher's early-career collaboration environment is strongly associated with the diversity of their collaborators in their established period. This diversity-association effect is particularly prominent for men. Coupled with gender and racial homophily between advisors and advisees, collaborator diversity represents a generational effect that partly explains why changes in representation within the scientific workforce tend to happen very slowly.</p>","PeriodicalId":74246,"journal":{"name":"Nature computational science","volume":" ","pages":""},"PeriodicalIF":12.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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