Fangfang Xia

42 papers A* 1A 2B 1Journal 32Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
Continual learning in the presence of repetition.
Neural Networks
Hamed Hemati, Lorenzo Pellegrini, Xiaotian Duan, Zixuan Zhao, Fangfang Xia, Marc Masana, Benedikt Tscheschner, Eduardo E. Veas, Yuxiang Zheng, Shiji Zhao, Shao-Yuan Li, Sheng-Jun Huang, Vincenzo Lomonaco, Gido M. van de Ven
2025 J jnl
Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting.
Briefings Bioinform.
Oleksandr Narykov, Yitan Zhu, Thomas S. Brettin, Yvonne A. Evrard, Alexander Partin, Fangfang Xia, Maulik Shukla, Priyanka Vasanthakumari, James H. Doroshow, Rick L. Stevens
2025 J jnl
Scaling Large Vision-Language Models for Enhanced Multimodal Comprehension In Biomedical Image Analysis.
CoRR
Robinson Umeike, Neil Getty, Fangfang Xia, Rick Stevens
2025 — conf
Scaling Large Vision-Language Models for Enhanced Multimodal Comprehension in Biomedical Image Analysis.
ISBI
Robinson Umeike, Neil Getty, Fangfang Xia, Rick Stevens
2024 J jnl
Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches.
CoRR
Xuefeng Liu, Songhao Jiang, Xiaotian Duan, Archit Vasan, Chong Liu, Chih-chan Tien, Heng Ma, Thomas S. Brettin, Fangfang Xia, Ian T. Foster, Rick L. Stevens
2024 A* conf
Contextual Active Model Selection.
NeurIPS
Xuefeng Liu, Fangfang Xia, Rick Stevens, Yuxin Chen
2024 J jnl
Continual Learning in the Presence of Repetition.
CoRR
Hamed Hemati, Lorenzo Pellegrini, Xiaotian Duan, Zixuan Zhao, Fangfang Xia, Marc Masana, Benedikt Tscheschner, Eduardo E. Veas, Yuxiang Zheng, Shiji Zhao, Shao-Yuan Li, Sheng-Jun Huang, Vincenzo Lomonaco, Gido M. van de Ven
2023 J jnl
CholecTriplet2021: A benchmark challenge for surgical action triplet recognition.
Medical Image Anal.
Chinedu Innocent Nwoye, Deepak Alapatt, Tong Yu, Armine Vardazaryan, Fangfang Xia, Zixuan Zhao, Tong Xia, Fucang Jia, Yuxuan Yang, Hao Wang, Derong Yu, Guoyan Zheng, Xiaotian Duan, Neil Getty, Ricardo Sanchez-Matilla, Maria Robu, Li Zhang, Huabin Chen, Jiacheng Wang, Liansheng Wang, Bokai Zhang, Beerend G. A. Gerats, Sista Raviteja, Rachana Sathish, Rong Tao, Satoshi Kondo, Winnie Pang, Hongliang Ren, Julian Ronald Abbing, Mohammad Hasan Sarhan, Sebastian Bodenstedt, Nithya Bhasker, Bruno Oliveira, Helena R. Torres, Li Ling, Finn Gaida, Tobias Czempiel, João L. Vilaça, Pedro Morais, Jaime C. Fonseca, Ruby Mae Egging, Inge Nicole Wijma, Chen Qian, Guibin Bian, Zhen Li, Velmurugan Balasubramanian, Debdoot Sheet, Imanol Luengo, Yuanbo Zhu, Shuai Ding, Jakob-Anton Aschenbrenner, Nicolas Elini van der Kar, Mengya Xu, Mobarakol Islam, Lalithkumar Seenivasan, Alexander Jenke, Danail Stoyanov, Didier Mutter, Pietro Mascagni, Barbara Seeliger, Cristians Gonzalez, Nicolas Padoy
2023 — conf
Deep Fair Partition for Hyperspectral Image Classification.
WHISPERS
Miao Tony He, Fangfang Xia, Rick L. Stevens
2023 J jnl
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.
Nucleic Acids Res.
Robert D. Olson, Rida Assaf, Thomas S. Brettin, Neal Conrad, Clark Cucinell, James J. Davis, Donald M. Dempsey, Allan Dickerman, Emily M. Dietrich, Ronald W. Kenyon, Mehmet Kuscuoglu, Elliot J. Lefkowitz, Jian Lu, Dustin Machi, Catherine Macken, Chunhong Mao, Anna Maria Niewiadomska, Marcus Nguyen, Gary J. Olsen, Jamie C. Overbeek, Bruce D. Parrello, Victoria Parrello, Jacob s Porter, Gordon D. Pusch, Maulik Shukla, Indresh Singh, Lucy Stewart, Gene Tan, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Zachary S. Wallace, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann, Rick L. Stevens
2023 J jnl
Surgical tool classification and localization: results and methods from the MICCAI 2022 SurgToolLoc challenge.
CoRR
Aneeq Zia, Kiran Bhattacharyya, Xi Liu, Max Berniker, Ziheng Wang, Rogerio Nespolo, Satoshi Kondo, Satoshi Kasai, Kousuke Hirasawa, Bo Liu, David Austin, Yiheng Wang, Michal Futrega, Jean-Francois Puget, Zhenqiang Li, Yoichi Sato, Ryo Fujii, Ryo Hachiuma, Mana Masuda, Hideo Saito, An Wang, Mengya Xu, Mobarakol Islam, Long Bai, Winnie Pang, Hongliang Ren, Chinedu Innocent Nwoye, Luca Sestini, Nicolas Padoy, Maximilian Nielsen, Samuel Schüttler, Thilo Sentker, Hümeyra Husseini, Ivo M. Baltruschat, Rüdiger Schmitz, René Werner, Aleksandr Matsun, Mugariya Farooq, Numan Saeed, Jose Renato Restom Viera, Mohammad Yaqub, Neil Getty, Fangfang Xia, Zixuan Zhao, Xiaotian Duan, Xing Yao, Ange Lou, Hao Yang, Jintong Han, Jack H. Noble, Jie Ying Wu, Tamer Abdulbaki Alshirbaji, Nour Aldeen Jalal, Herag Arabian, Ning Ding, Knut Moeller, Weiliang Chen, Quan He, Lena Maier-Hein, Danail Stoyanov, Stefanie Speidel, Anthony M. Jarc
2022 J jnl
A cross-study analysis of drug response prediction in cancer cell lines.
Briefings Bioinform.
Fangfang Xia, Jonathan E. Allen, Prasanna Balaprakash, Thomas S. Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith D. Cohn, James H. Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne A. Evrard, Ya Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric A. Stahlberg, Justin M. Wozniak, Hyun Seung Yoo, George F. Zaki, Yitan Zhu, Rick Stevens
2022 J jnl
CholecTriplet2021: A benchmark challenge for surgical action triplet recognition.
CoRR
Chinedu Innocent Nwoye, Deepak Alapatt, Tong Yu, Armine Vardazaryan, Fangfang Xia, Zixuan Zhao, Tong Xia, Fucang Jia, Yuxuan Yang, Hao Wang, Derong Yu, Guoyan Zheng, Xiaotian Duan, Neil Getty, Ricardo Sanchez-Matilla, Maria Robu, Li Zhang, Huabin Chen, Jiacheng Wang, Liansheng Wang, Bokai Zhang, Beerend G. A. Gerats, Sista Raviteja, Rachana Sathish, Rong Tao, Satoshi Kondo, Winnie Pang, Hongliang Ren, Julian Ronald Abbing, Mohammad Hasan Sarhan, Sebastian Bodenstedt, Nithya Bhasker, Bruno Oliveira, Helena R. Torres, Li Ling, Finn Gaida, Tobias Czempiel, João L. Vilaça, Pedro Morais, Jaime C. Fonseca, Ruby Mae Egging, Inge Nicole Wijma, Chen Qian, Guibin Bian, Zhen Li, Velmurugan Balasubramanian, Debdoot Sheet, Imanol Luengo, Yuanbo Zhu, Shuai Ding, Jakob-Anton Aschenbrenner, Nicolas Elini van der Kar, Mengya Xu, Mobarakol Islam, Lalithkumar Seenivasan, Alexander Jenke, Danail Stoyanov, Didier Mutter, Pietro Mascagni, Barbara Seeliger, Cristians Gonzalez, Nicolas Padoy
2022 J jnl
Cost-Effective Online Contextual Model Selection.
CoRR
Xuefeng Liu, Fangfang Xia, Rick L. Stevens, Yuxin Chen
2021 A conf
AgEBO-tabular: joint neural architecture and hyperparameter search with autotuned data-parallel training for tabular data.
SC
Romain Égelé, Prasanna Balaprakash, Isabelle Guyon, Venkatram Vishwanath, Fangfang Xia, Rick Stevens, Zhengying Liu
2021 J jnl
Learning curves for drug response prediction in cancer cell lines.
BMC Bioinform.
Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick L. Stevens
2021 — conf
Neko: a Library for Exploring Neuromorphic Learning Rules.
ICONS
Zixuan Zhao, Nathan Wycoff, Neil Getty, Rick Stevens, Fangfang Xia
2021 J jnl
Neko: a Library for Exploring Neuromorphic Learning Rules.
CoRR
Zixuan Zhao, Nathan Wycoff, Neil Getty, Rick Stevens, Fangfang Xia
2021 J jnl
Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers.
CoRR
Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, André Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaotan Duan, Rick Stevens, Peter V. Coveney
2020 J jnl
A Systematic Approach to Featurization for Cancer Drug Sensitivity Predictions with Deep Learning.
CoRR
Austin Clyde, Tom Brettin, Alexander Partin, Maulik Shaulik, Hyun Seung Yoo, Yvonne A. Evrard, Yitan Zhu, Fangfang Xia, Rick Stevens
2020 J jnl
Deep Medical Image Analysis with Representation Learning and Neuromorphic Computing.
CoRR
Neil Getty, Thomas S. Brettin, Dong Jin, Rick Stevens, Fangfang Xia
2020 J jnl
Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug Response.
CoRR
Yitan Zhu, Thomas S. Brettin, Yvonne A. Evrard, Alexander Partin, Fangfang Xia, Maulik Shukla, Hyun Seung Yoo, James H. Doroshow, Rick Stevens
2020 J jnl
Learning Curves for Drug Response Prediction in Cancer Cell Lines.
CoRR
Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick Stevens
2020 — conf
Recurrent and Spiking Modeling of Sparse Surgical Kinematics.
ICONS
Neil Getty, Zixuan Zhao, Stephan Gruessner, Liaohai Chen, Fangfang Xia
2020 J jnl
Recurrent and Spiking Modeling of Sparse Surgical Kinematics.
CoRR
Neil Getty, Zixuan Zhou, Stephan Gruessner, Liaohai Chen, Fangfang Xia
2020 J jnl
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.
Nucleic Acids Res.
James J. Davis, Alice R. Wattam, Ramy K. Aziz, Thomas S. Brettin, Ralph Butler, Rory Butler, Philippe Chlenski, Neal Conrad, Allan Dickerman, Emily M. Dietrich, Joseph L. Gabbard, Svetlana Gerdes, Andrew Guard, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Marcus Nguyen, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Jamie C. Overbeek, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Dawen Xie, Hyun Seung Yoo, Rick Stevens
2020 J jnl
Towards On-Chip Bayesian Neuromorphic Learning.
CoRR
Nathan Wycoff, Prasanna Balaprakash, Fangfang Xia
2019 — conf
Neuromorphic Acceleration for Approximate Bayesian Inference on Neural Networks via Permanent Dropout.
ICONS
Nathan Wycoff, Prasanna Balaprakash, Fangfang Xia
2019 J jnl
Neuromorphic Acceleration for Approximate Bayesian Inference on Neural Networks via Permanent Dropout.
CoRR
Nathan Wycoff, Prasanna Balaprakash, Fangfang Xia
2019 J jnl
PATRIC as a unique resource for studying antimicrobial resistance.
Briefings Bioinform.
Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas S. Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, John Santerre, Maulik Shukla, Rick L. Stevens, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo
2019 B conf
Performance, Energy, and Scalability Analysis and Improvement of Parallel Cancer Deep Learning CANDLE Benchmarks.
ICPP
Xingfu Wu, Valerie E. Taylor, Justin M. Wozniak, Rick Stevens, Thomas S. Brettin, Fangfang Xia
2019 J jnl
Scalable Reinforcement-Learning-Based Neural Architecture Search for Cancer Deep Learning Research.
CoRR
Prasanna Balaprakash, Romain Egele, Misha Salim, Stefan M. Wild, Venkatram Vishwanath, Fangfang Xia, Tom Brettin, Rick Stevens
2019 A conf
Scalable reinforcement-learning-based neural architecture search for cancer deep learning research.
SC
Prasanna Balaprakash, Romain Egele, Misha Salim, Stefan M. Wild, Venkatram Vishwanath, Fangfang Xia, Tom Brettin, Rick Stevens
2018 J jnl
CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research.
BMC Bioinform.
Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas S. Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia-Cardona, Brian Van Essen, Matthew Baughman
2018 J jnl
Predicting tumor cell line response to drug pairs with deep learning.
BMC Bioinform.
Fangfang Xia, Maulik Shukla, Thomas S. Brettin, Cristina Garcia-Cardona, Judith D. Cohn, Jonathan E. Allen, Sergei Maslov, Susan L. Holbeck, James H. Doroshow, Yvonne A. Evrard, Eric A. Stahlberg, Rick L. Stevens
2017 J jnl
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
Nucleic Acids Res.
Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens
2016 J jnl
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in
PLoS Comput. Biol.
Matthew A. Oberhardt, Raphy Zarecki, Leah Reshef, Fangfang Xia, Miquel Duran-Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben-Tal, Daniel J. Dwyer, Uri Gophna, Eytan Ruppin
2014 J jnl
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Briefings Bioinform.
José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
2014 J jnl
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).
Nucleic Acids Res.
Ross A. Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce D. Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Fangfang Xia, Rick Stevens
2013 J jnl
Human Analysts at Superhuman Scales: What Has Friendly Software To Do?
Big Data
Élénie Godzaridis, Sébastien Boisvert, Fangfang Xia, Mikhail Kandel, Steve Behling, Bill Long, Carlos P. Sosa, François Laviolette, Jacques Corbeil
2009 — conf
Inferring a Species Tree from Gene Trees in the Presence of HGT.
BIOCOMP
Fangfang Xia, Rick Stevens
2007 J jnl
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.
Nucleic Acids Res.
Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens