An efficient algorithm for high-dimensional function optimization. - Yuanfang Ren; Yan Wu 011 (Soft Comput., 2013)

Convolutional deep belief networks for feature extraction of EEG signal. - Yuanfang Ren; Yan Wu 011 (IJCNN, 2014)

A co-training algorithm for EEG classification with biomimetic pattern recognition and sparse representation. - Yuanfang Ren; Yan Wu 011; Yanbin Ge (Neurocomputing, 2014)

Construction of signaling networks with incomplete RNAi data. - Qiyao Wang; Yuanfang Ren; Md Mahmudul Hasan; Ahmet Ay; Tamer Kahveci (BIBM, 2015)

Counting independent motifs in probabilistic networks. - Aisharjya Sarkar; Yuanfang Ren; Rasha Elhesha; Tamer Kahveci (BCB, 2016)

Identifying the topology of signaling networks from partial RNAi data. - Yuanfang Ren; Qiyao Wang; Md Mahmudul Hasan; Ahmet Ay; Tamer Kahveci (BMC Syst. Biol., 2016)

Shortest path counting in probabilistic biological networks. - Yuanfang Ren; Ahmet Ay; Tamer Kahveci (BMC Bioinform., 2018)

ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. - Yuanfang Ren; Aisharjya Sarkar; Tamer Kahveci (BMC Bioinform., 2018)

Identification of jointly correlated gene sets. - Yuanfang Ren; Ahmet Ay; Travis A. Gerke; Tamer Kahveci (J. Bioinform. Comput. Biol., 2018)

Finding Conserved Patterns in Multilayer Networks. - Yuanfang Ren; Aisharjya Sarkar; Ahmet Ay; Alin Dobra; Tamer Kahveci (BCB, 2019)

Characterizing building blocks of resource constrained biological networks. - Yuanfang Ren; Ahmet Ay; Alin Dobra; Tamer Kahveci (BMC Bioinform., 2019)

Added Value of Intraoperative Data for Predicting Postoperative Complications: Development and Validation of a MySurgeryRisk Extension. - Shounak Datta; Tyler J. Loftus; Matthew M. Ruppert; Chris Giordano; Lasith Adhikari; Ying-Chih Peng; Yuanfang Ren; Benjamin Shickel; Zheng Feng; Gloria Lipori; Gilbert R. Upchurch Jr.; Xiaolin Li 001; et al. (CoRR, 2019)

A New Algorithm for Counting Independent Motifs in Probabilistic Networks. - Aisharjya Sarkar; Yuanfang Ren; Rasha Elhesha; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Application of Deep Interpolation Network for Clustering of Physiologic Time Series. - Yanjun Li 005; Yuanfang Ren; Tyler J. Loftus; Shounak Datta; Matthew Ruppert; Ziyuan Guan; Dapeng Oliver Wu; Parisa Rashidi; Tezcan Ozrazgat-Baslanti; Azra Bihorac (CoRR, 2020)

Development of Computable Phenotype to Identify and Characterize Transitions in Acuity Status in Intensive Care Unit. - Yuanfang Ren; Tyler J. Loftus; Rahul Sai Kasula; Prudhvee Narasimha Sadha; Parisa Rashidi; Azra Bihorac; Tezcan Ozrazgat-Baslanti (CoRR, 2020)

Identification of co-existing embeddings of a motif in multilayer networks. - Yuanfang Ren; Aisharjya Sarkar; Aysegul Bumin; Kejun Huang; Pierangelo Veltri; Alin Dobra; Tamer Kahveci (BCB, 2022)

Multi-dimensional patient acuity estimation with longitudinal EHR tokenization and flexible transformer networks. - Benjamin Shickel; Brandon Silva; Tezcan Ozrazgat-Baslanti; Yuanfang Ren; Kia Khezeli; Ziyuan Guan; Patrick James Tighe; Azra Bihorac; Parisa Rashidi (Frontiers Digit. Health, 2022)

Phenotype clustering in health care: A narrative review for clinicians. - Tyler J. Loftus; Benjamin Shickel; Jeremy A. Balch; Patrick James Tighe; Kenneth L. Abbott; Brian Fazzone; Erik M. Anderson; Jared Rozowsky; Tezcan Ozrazgat-Baslanti; Yuanfang Ren; Scott A. Berceli; William R. Hogan; et al. (Frontiers Artif. Intell., 2022)

Pattern Discovery in Multilayer Networks. - Yuanfang Ren; Aisharjya Sarkar; Pierangelo Veltri; Ahmet Ay; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Dynamic Delirium Prediction in the Intensive Care Unit using Machine Learning on Electronic Health Records. - Miguel Contreras; Brandon Silva; Benjamin Shickel; Sabyasachi Bandyopadhyay; Ziyuan Guan; Yuanfang Ren; Tezcan Ozrazgat-Baslanti; Kia Khezeli; Azra Bihorac; Parisa Rashidi (BHI, 2023)

Computable Phenotypes to Characterize Changing Patient Brain Dysfunction in the Intensive Care Unit. - Yuanfang Ren; Tyler J. Loftus; Ziyuan Guan; Rayon Uddin; Benjamin Shickel; Carolina B. Maciel; Katharina Busl; Parisa Rashidi; Azra Bihorac; Tezcan Ozrazgat-Baslanti (CoRR, 2023)

Clinical Courses of Acute Kidney Injury in Hospitalized Patients: A Multistate Analysis. - Esra Adiyeke; Yuanfang Ren; Ziyuan Guan; Matthew M. Ruppert; Parisa Rashidi; Azra Bihorac; Tezcan Ozrazgat-Baslanti (CoRR, 2023)

Transformer Models for Acute Brain Dysfunction Prediction. - Brandon Silva; Miguel Contreras; Tezcan Ozrazgat-Baslanti; Yuanfang Ren; Ziyuan Guan; Kia Khezeli; Azra Bihorac; Parisa Rashidi (CoRR, 2023)

Identifying acute illness phenotypes via deep temporal interpolation and clustering network on physiologic signatures. - Yuanfang Ren; Yanjun Li 005; Tyler J. Loftus; Jeremy A. Balch; Kenneth L. Abbott; Shounak Datta; Matthew M. Ruppert; Ziyuan Guan; Benjamin Shickel; Parisa Rashidi; Tezcan Ozrazgat-Baslanti; Azra Bihorac (CoRR, 2023)

Detecting Visual Cues in the Intensive Care Unit and Association with Patient Clinical Status. - Subhash Nerella; Ziyuan Guan; Andrea Davidson; Yuanfang Ren; Tezcan Baslanti; Brooke Armfield; Patrick James Tighe; Azra Bihorac; Parisa Rashidi (CoRR, 2023)

APRICOT: Acuity Prediction in Intensive Care Unit (ICU): Predicting Stability, Transitions, and Life-Sustaining Therapies. - Miguel Contreras; Brandon Silva; Benjamin Shickel; Tezcan Ozrazgat-Baslanti; Yuanfang Ren; Ziyuan Guan; Sabyasachi Bandyopadhyay; Kia Khezeli; Azra Bihorac; Parisa Rashidi (CoRR, 2023)

The Potential of Wearable Sensors for Assessing Patient Acuity in Intensive Care Unit (ICU). - Jessica Sena; Mohammad Tahsin Mostafiz; Jiaqing Zhang; Andrea Davidson; Sabyasachi Bandyopadhyay; Yuanfang Ren; Tezcan Ozrazgat-Baslanti; Benjamin Shickel; Tyler J. Loftus; William Robson Schwartz; Azra Bihorac; Parisa Rashidi (CoRR, 2023)

Acute kidney injury prediction for non-critical care patients: a retrospective external and internal validation study. - Esra Adiyeke; Yuanfang Ren; Benjamin Shickel; Matthew M. Ruppert; Ziyuan Guan; Sandra L. Kane-Gill; Raghavan Murugan; Nabihah Amatullah; Britney A. Stottlemyer; Tiffany L. Tran; Dan Ricketts; Christopher M. Horvat; et al. (CoRR, 2024)

Temporal Cross-Attention for Dynamic Embedding and Tokenization of Multimodal Electronic Health Records. - Yingbo Ma; Suraj Kolla; Dhruv Kaliraman; Victoria Nolan; Zhenhong Hu; Ziyuan Guan; Yuanfang Ren; Brooke Armfield; Tezcan Ozrazgat-Baslanti; Tyler J. Loftus; Parisa Rashidi; Azra Bihorac; et al. (CoRR, 2024)

A multi-cohort study on prediction of acute brain dysfunction states using selective state space models. - Brandon Silva; Miguel Contreras; Sabyasachi Bandyopadhyay; Yuanfang Ren; Ziyuan Guan; Jeremy A. Balch; Kia Khezeli; Tezcan Ozrazgat-Baslanti; Benjamin Shickel; Azra Bihorac; Parisa Rashidi (CoRR, 2024)

Federated learning model for predicting major postoperative complications. - Yonggi Park; Yuanfang Ren; Benjamin Shickel; Ziyuan Guan; Ayush Patela; Yingbo Ma; Zhenhong Hu; Tyler J. Loftus; Parisa Rashidi; Tezcan Ozrazgat-Baslanti; Azra Bihorac (CoRR, 2024)

Global Contrastive Training for Multimodal Electronic Health Records with Language Supervision. - Yingbo Ma; Suraj Kolla; Zhenhong Hu; Dhruv Kaliraman; Victoria Nolan; Ziyuan Guan; Yuanfang Ren; Brooke Armfield; Tezcan Ozrazgat-Baslanti; Jeremy A. Balch; Tyler J. Loftus; Parisa Rashidi; et al. (CoRR, 2024)

Transparent AI: Developing an Explainable Interface for Predicting Postoperative Complications. - Yuanfang Ren; Chirayu Tripathi; Ziyuan Guan; Ruilin Zhu; Victoria Hougha; Yingbo Ma; Zhenhong Hu; Jeremy A. Balch; Tyler J. Loftus; Parisa Rashidi; Benjamin Shickel; Tezcan Ozrazgat-Baslanti; et al. (CoRR, 2024)

Promoting AI Competencies for Medical Students: A Scoping Review on Frameworks, Programs, and Tools. - Yingbo Ma; Yukyeong Song; Jeremy A. Balch; Yuanfang Ren; Divya Vellanki; Zhenhong Hu; Meghan Brennan; Suraj Kolla; Ziyuan Guan; Brooke Armfield; Tezcan Ozrazgat-Baslanti; Parisa Rashidi; et al. (CoRR, 2024)

DeLLiriuM: A large language model for delirium prediction in the ICU using structured EHR. - Miguel Contreras; Sumit Kapoor; Jiaqing Zhang; Andrea Davidson; Yuanfang Ren; Ziyuan Guan; Tezcan Ozrazgat-Baslanti; Subhash Nerella; Azra Bihorac; Parisa Rashidi (CoRR, 2024)

MANGO: Multimodal Acuity traNsformer for intelliGent ICU Outcomes. - Jiaqing Zhang; Miguel Contreras; Sabyasachi Bandyopadhyay; Andrea Davidson; Jessica Sena; Yuanfang Ren; Ziyuan Guan; Tezcan Ozrazgat-Baslanti; Tyler J. Loftus; Subhash Nerella; Azra Bihorac; Parisa Rashidi (CoRR, 2024)

MANDARIN: Mixture-of-Experts Framework for Dynamic Delirium and Coma Prediction in ICU Patients: Development and Validation of an Acute Brain Dysfunction Prediction Model. - Miguel Contreras; Jessica Sena; Andrea Davidson; Jiaqing Zhang; Tezcan Ozrazgat-Baslanti; Yuanfang Ren; Ziyuan Guan; Jeremy A. Balch; Tyler J. Loftus; Subhash Nerella; Azra Bihorac; Parisa Rashidi (CoRR, 2025)

Quantifying Circadian Desynchrony in ICU Patients and Its Association with Delirium. - Yuanfang Ren; Andrea Davidson; Jiaqing Zhang; Miguel Contreras; Ayush Patela; Michelle Gumz; Tezcan Ozrazgat-Baslanti; Parisa Rashidi; Azra Bihorac (CoRR, 2025)

MELON: Multimodal Mixture-of-Experts with Spectral-Temporal Fusion for Long-Term Mobility Estimation in Critical Care. - Jiaqing Zhang; Miguel Contreras; Jessica Sena; Andrea Davidson; Yuanfang Ren; Ziyuan Guan; Tezcan Ozrazgat-Baslanti; Tyler J. Loftus; Subhash Nerella; Azra Bihorac; Parisa Rashidi (CoRR, 2025)

Unlocking Health Insights with SDoH Data: A Comprehensive Open-Access Database and SDoH-EHR Linkage Tool. - Zhenhong Hu; Esra Adiyeke; Ziyuan Guan; Divya Vellanki; Jiahang Yu; Ruilin Zhu; Yuanfang Ren; Yingbo Ma; Annanya Sai Vedala; Tezcan Ozrazgat-Baslanti; Azra Bihorac (CoRR, 2025)

Learning optimal treatment strategies for intraoperative hypotension using deep reinforcement learning. - Esra Adiyeke; Tianqi Liu; Venkata Sai Dheeraj Naganaboina; Han Li; Tyler J. Loftus; Yuanfang Ren; Benjamin Shickel; Matthew M. Ruppert; Karandeep Singh; Ruogu Fang; Parisa Rashidi; Azra Bihorac; et al. (CoRR, 2025)

Validation of the MySurgeryRisk Algorithm for Predicting Complications and Death after Major Surgery: A Retrospective Multicenter Study Using OneFlorida Data Trust. - Yuanfang Ren; Esra Adiyeke; Ziyuan Guan; Zhenhong Hu; Mackenzie J. Meni; Benjamin Shickel; Parisa Rashidi; Tezcan Ozrazgat-Baslanti; Azra Bihorac (CoRR, 2025)