no code implementations • 15 Mar 2024 • Pengcheng Jiang, Cao Xiao, Zifeng Wang, Parminder Bhatia, Jimeng Sun, Jiawei Han
To overcome this, we introduce TriSum, a framework for distilling LLMs' text summarization abilities into a compact, local model.
no code implementations • 2 Feb 2024 • Jiaqi Wang, Junyu Luo, Muchao Ye, Xiaochen Wang, Yuan Zhong, Aofei Chang, Guanjie Huang, Ziyi Yin, Cao Xiao, Jimeng Sun, Fenglong Ma
This survey systematically reviews recent advances in deep learning-based predictive models using EHR data.
no code implementations • 28 Jan 2024 • Lang Cao, Zifeng Wang, Cao Xiao, Jimeng Sun
We demonstrate the importance of accurately identifying precedent cases and mitigating the temporal shift when making predictions for case law, as our method shows a significant improvement over the prior methods that focus on civil law case outcome predictions.
no code implementations • 10 Dec 2023 • Brandon Theodorou, Shrusti Jain, Cao Xiao, Jimeng Sun
Generative models can produce synthetic patient records for analytical tasks when real data is unavailable or limited.
1 code implementation • 6 Sep 2023 • Junyu Luo, Cao Xiao, Fenglong Ma
Existing techniques for hallucination detection in language assistants rely on intricate fuzzy, specific free-language-based chain of thought (CoT) techniques or parameter-based methods that suffer from interpretability issues.
no code implementations • 19 Jul 2023 • Brandon Theodorou, Cao Xiao, Jimeng Sun
In recent years, machine learning models have been proposed for speeding up patient recruitment via automatically matching patients with clinical trials based on longitudinal patient electronic health records (EHR) data and eligibility criteria of clinical trials.
1 code implementation • 6 Jun 2023 • Zifeng Wang, Brandon Theodorou, Tianfan Fu, Cao Xiao, Jimeng Sun
The code is available at https://github. com/RyanWangZf/PyTrial.
no code implementations • 2 Jun 2023 • Pengcheng Jiang, Cao Xiao, Tianfan Fu, Jimeng Sun
In this paper, we propose a novel method called GODE, which takes into account the two-level structure of individual molecules.
no code implementations • 30 May 2023 • Brandon Theodorou, Lucas Glass, Cao Xiao, Jimeng Sun
This paper focuses on the trial site selection task and proposes FRAMM, a deep reinforcement learning framework for fair trial site selection.
no code implementations • 22 May 2023 • Pengcheng Jiang, Cao Xiao, Adam Cross, Jimeng Sun
This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data.
1 code implementation • 20 May 2023 • Zifeng Wang, Chufan Gao, Cao Xiao, Jimeng Sun
Tabular data prediction has been employed in medical applications such as patient health risk prediction.
no code implementations • 19 May 2023 • Zifeng Wang, Cao Xiao, Jimeng Sun
Clinical trials are critical for drug development.
no code implementations • 7 Apr 2023 • Zifeng Wang, Cao Xiao, Jimeng Sun
Accurate trial outcome prediction based on historical trial data promises better trial investment decisions and more trial success.
1 code implementation • 4 Apr 2023 • Brandon Theodorou, Cao Xiao, Jimeng Sun
In this paper, we propose Hierarchical Autoregressive Language mOdel (HALO) for generating longitudinal high-dimensional EHR, which preserve the statistical properties of real EHR and can be used to train accurate ML models without privacy concerns.
1 code implementation • 2 Feb 2023 • Zhen Lin, Shubhendu Trivedi, Cao Xiao, Jimeng Sun
We focus on a typical scenario where such requirements, separately encoding $\textit{value}$ and $\textit{cost}$, compete with each other.
no code implementations • 13 Apr 2022 • Rakshith S Srinivasa, Cheng Qian, Brandon Theodorou, Jeffrey Spaeder, Cao Xiao, Lucas Glass, Jimeng Sun
More recently, the issue of diversity and inclusion in clinical trials is gaining importance.
no code implementations • 4 Mar 2022 • Zhenbang Wu, Cao Xiao, Lucas M Glass, David M Liebovitz, Jimeng Sun
To tackle this problem, we propose AutoMap to automatically map the medical codes across different EHR systems in a coarse-to-fine manner: (1) Ontology-level Alignment: We leverage the ontology structure to learn a coarse alignment between the source and target medical coding systems; (2) Code-level Refinement: We refine the alignment at a fine-grained code level for the downstream tasks using a teacher-student framework.
no code implementations • 11 Dec 2021 • Muchao Ye, Junyu Luo, Guanjie Zheng, Cao Xiao, Ting Wang, Fenglong Ma
Deep neural networks (DNNs) have been broadly adopted in health risk prediction to provide healthcare diagnoses and treatments.
no code implementations • ICLR 2022 • Tianfan Fu, Wenhao Gao, Cao Xiao, Jacob Yasonik, Connor W. Coley, Jimeng Sun
The structural design of functional molecules, also called molecular optimization, is an essential chemical science and engineering task with important applications, such as drug discovery.
no code implementations • 22 Sep 2021 • Tianfan Fu, Wenhao Gao, Cao Xiao, Jacob Yasonik, Connor W. Coley, Jimeng Sun
The structural design of functional molecules, also called molecular optimization, is an essential chemical science and engineering task with important applications, such as drug discovery.
1 code implementation • 15 Jun 2021 • Chaoqi Yang, Cheng Qian, Navjot Singh, Cao Xiao, M Brandon Westover, Edgar Solomonik, Jimeng Sun
This paper addresses the above challenges by proposing augmented tensor decomposition (ATD), which effectively incorporates data augmentations and self-supervised learning (SSL) to boost downstream classification.
1 code implementation • 14 Jun 2021 • Chaoqi Yang, Navjot Singh, Cao Xiao, Cheng Qian, Edgar Solomonik, Jimeng Sun
Our MTC model explores tensor mode properties and leverages the hierarchy of resolutions to recursively initialize an optimization setup, and optimizes on the coupled system using alternating least squares.
no code implementations • 11 May 2021 • Cheng Qian, Nikos Kargas, Cao Xiao, Lucas Glass, Nicholas Sidiropoulos, Jimeng Sun
Recovering such missing or noisy (under-reported) elements of the input tensor can be viewed as a generalized tensor completion problem.
no code implementations • 5 May 2021 • Chaoqi Yang, Cao Xiao, Fenglong Ma, Lucas Glass, Jimeng Sun
On a benchmark dataset, our SafeDrug is relatively shown to reduce DDI by 19. 43% and improves 2. 88% on Jaccard similarity between recommended and actually prescribed drug combinations over previous approaches.
no code implementations • 5 May 2021 • Chaoqi Yang, Cao Xiao, Lucas Glass, Jimeng Sun
Deep learning is revolutionizing predictive healthcare, including recommending medications to patients with complex health conditions.
no code implementations • 3 May 2021 • Kexin Huang, Cao Xiao, Lucas M. Glass, Cathy W. Critchlow, Greg Gibson, Jimeng Sun
Thanks to the increasing availability of genomics and other biomedical data, many machine learning approaches have been proposed for a wide range of therapeutic discovery and development tasks.
no code implementations • 5 Mar 2021 • Zhen Lin, Cao Xiao, Lucas Glass, M. Brandon Westover, Jimeng Sun
Despite deep learning (DL) success in classification problems, DL classifiers do not provide a sound mechanism to decide when to refrain from predicting.
2 code implementations • 18 Feb 2021 • Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik
Here, we introduce Therapeutics Data Commons (TDC), the first unifying platform to systematically access and evaluate machine learning across the entire range of therapeutics.
1 code implementation • 8 Feb 2021 • Tianfan Fu, Kexin Huang, Cao Xiao, Lucas M. Glass, Jimeng Sun
Next, these embeddings will be fed into the knowledge embedding module to generate knowledge embeddings that are pretrained using external knowledge on pharmaco-kinetic properties and trial risk from the web.
2 code implementations • 11 Jan 2021 • Yue Zhao, Zhi Qiao, Cao Xiao, Lucas Glass, Jimeng Sun
PyHealth consists of data preprocessing module, predictive modeling module, and evaluation module.
no code implementations • 8 Dec 2020 • Nikos Kargas, Cheng Qian, Nicholas D. Sidiropoulos, Cao Xiao, Lucas M. Glass, Jimeng Sun
Accurate prediction of the transmission of epidemic diseases such as COVID-19 is crucial for implementing effective mitigation measures.
1 code implementation • COLING 2022 • Junyu Luo, Zifei Zheng, Hanzhong Ye, Muchao Ye, Yaqing Wang, Quanzeng You, Cao Xiao, Fenglong Ma
To fairly evaluate the performance, we also propose three specific evaluation metrics.
no code implementations • 30 Oct 2020 • Zhi Qiao, Austin Bae, Lucas M. Glass, Cao Xiao, Jimeng Sun
To test the possibility of differentiating chest x-ray images of COVID-19 against other pneumonia and healthy patients using deep neural networks.
no code implementations • 28 Oct 2020 • Yanbo Xu, Cao Xiao, Jimeng Sun
How to model such time-varying effects from longitudinal observational data?
no code implementations • 22 Oct 2020 • Chacha Chen, Junjie Liang, Fenglong Ma, Lucas M. Glass, Jimeng Sun, Cao Xiao
However, existing uncertainty estimation approaches often failed in handling high-dimensional data, which are present in multi-sourced data.
1 code implementation • 5 Oct 2020 • Tianfan Fu, Cao Xiao, Xinhao Li, Lucas M. Glass, Jimeng Sun
Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule.
1 code implementation • 5 Oct 2020 • Kexin Huang, Tianfan Fu, Dawood Khan, Ali Abid, Ali Abdalla, Abubakar Abid, Lucas M. Glass, Marinka Zitnik, Cao Xiao, Jimeng Sun
The efficacy of a drug depends on its binding affinity to the therapeutic target and pharmacokinetics.
1 code implementation • 4 Oct 2020 • Yue Yu, Kexin Huang, Chao Zhang, Lucas M. Glass, Jimeng Sun, Cao Xiao
Furthermore, most previous works focus on binary DDI prediction whereas the multi-typed DDI pharmacological effect prediction is a more meaningful but harder task.
1 code implementation • 15 Jun 2020 • Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun
The other path processes EHR with multi-granularity memory network that encodes structured patient records into multiple levels based on medical ontology.
no code implementations • 15 Jun 2020 • Rakshith S Srinivasa, Cao Xiao, Lucas Glass, Justin Romberg, Jimeng Sun
The attention mechanism has demonstrated superior performance for inference over nodes in graph neural networks (GNNs), however, they result in a high computational burden during both training and inference.
no code implementations • 21 May 2020 • Cao Xiao, Trong Nghia Hoang, Shenda Hong, Tengfei Ma, Jimeng Sun
There is a growing interest in applying deep learning (DL) to healthcare, driven by the availability of data with multiple feature channels in rich-data environments (e. g., intensive care units).
1 code implementation • 30 Apr 2020 • Kexin Huang, Cao Xiao, Lucas Glass, Marinka Zitnik, Jimeng Sun
Here, we present SkipGNN, a graph neural network approach for the prediction of molecular interactions.
1 code implementation • 23 Apr 2020 • Kexin Huang, Cao Xiao, Lucas Glass, Jimeng Sun
Drug target interaction (DTI) prediction is a foundational task for in silico drug discovery, which is costly and time-consuming due to the need of experimental search over large drug compound space.
1 code implementation • 19 Apr 2020 • Kexin Huang, Tianfan Fu, Lucas Glass, Marinka Zitnik, Cao Xiao, Jimeng Sun
Accurate prediction of drug-target interactions (DTI) is crucial for drug discovery.
Ranked #2 on Drug Discovery on KIBA
1 code implementation • 11 Mar 2020 • Yue Zhao, Xiyang Hu, Cheng Cheng, Cong Wang, Changlin Wan, Wen Wang, Jianing Yang, Haoping Bai, Zheng Li, Cao Xiao, Yunlong Wang, Zhi Qiao, Jimeng Sun, Leman Akoglu
Outlier detection (OD) is a key machine learning (ML) task for identifying abnormal objects from general samples with numerous high-stake applications including fraud detection and intrusion detection.
no code implementations • 26 Feb 2020 • Siddharth Biswal, Cao Xiao, Lucas M. Glass, M. Brandon Westover, Jimeng Sun
Most existing methods try to generate the whole reports from the raw input with limited success because 1) generated reports often contain errors that need manual review and correction, 2) it does not save time when doctors want to write additional information into the report, and 3) the generated reports are not customized based on individual doctors' preference.
1 code implementation • 29 Jan 2020 • Rahul Duggal, Scott Freitas, Cao Xiao, Duen Horng Chau, Jimeng Sun
By deploying these models to an Android application on a smartphone, we quantitatively observe that REST allows models to achieve up to 17x energy reduction and 9x faster inference.
1 code implementation • 24 Jan 2020 • Junyi Gao, Cao Xiao, Yasha Wang, Wen Tang, Lucas M. Glass, Jimeng Sun
Compared to the best baseline model, StageNet achieves up to 12% higher AUPRC for risk prediction task on two real-world patient datasets.
no code implementations • 22 Jan 2020 • Xingyao Zhang, Cao Xiao, Lucas M. Glass, Jimeng Sun
To address these challenges, we proposed DeepEnroll, a cross-modal inference learning model to jointly encode enrollment criteria (text) and patients records (tabular data) into a shared latent space for matching inference.
1 code implementation • 28 Dec 2019 • Shenda Hong, Yuxi Zhou, Junyuan Shang, Cao Xiao, Jimeng Sun
Methods:We extracted papers that applied deep learning (deep neural network) models to ECG data that were published between Jan. 1st of 2010 and Feb. 29th of 2020 from Google Scholar, PubMed, and the DBLP.
no code implementations • 26 Nov 2019 • Limeng Cui, Siddharth Biswal, Lucas M. Glass, Greg Lever, Jimeng Sun, Cao Xiao
How to further leverage patients with possibly uncertain diagnosis to improve detection?
no code implementations • 23 Nov 2019 • Siddharth Biswal, Cao Xiao, Lucas M. Glass, Elizabeth Milkovits, Jimeng Sun
We propose doctor2vec which simultaneously learns 1) doctor representations from EHR data and 2) trial representations from the description and categorical information about the trials.
1 code implementation • 23 Nov 2019 • Tianfan Fu, Cao Xiao, Jimeng Sun
The state-of-the-art approaches partition the molecules into a large set of substructures $S$ and grow the new molecule structure by iteratively predicting which substructure from $S$ to add.
1 code implementation • 19 Nov 2019 • Rahul Duggal, Cao Xiao, Richard Vuduc, Jimeng Sun
With CUP, we overcome two limitations of prior work-(1) non-uniform pruning: CUP can efficiently determine the ideal number of filters to prune in each layer of a neural network.
2 code implementations • 15 Nov 2019 • Kexin Huang, Cao Xiao, Trong Nghia Hoang, Lucas M. Glass, Jimeng Sun
Adverse drug-drug interactions (DDIs) remain a leading cause of morbidity and mortality.
no code implementations • 14 Oct 2019 • Irfan Al-Hussaini, Cao Xiao, M. Brandon Westover, Jimeng Sun
In this study, we propose Sleep staging via Prototypes from Expert Rules (SLEEPER), which combines deep learning models with expert defined rules using a prototype learning framework to generate simple interpretable models.
Ranked #1 on Automatic Sleep Stage Classification on ISRUC-Sleep
no code implementations • 4 Oct 2019 • Tengfei Ma, Junyuan Shang, Cao Xiao, Jimeng Sun
We propose the graph energy neural network (GENN) to explicitly model link type correlations.
no code implementations • 1 Jul 2019 • Kezi Yu, Yunlong Wang, Yong Cai, Cao Xiao, Emily Zhao, Lucas Glass, Jimeng Sun
Rare diseases affecting 350 million individuals are commonly associated with delay in diagnosis or misdiagnosis.
no code implementations • 1 Jul 2019 • Fan Zhang, Tong Wu, Yunlong Wang, Yong Cai, Cao Xiao, Emily Zhao, Lucas Glass, Jimeng Sun
Many computational models were proposed to extract temporal patterns from clinical time series for each patient and among patient group for predictive healthcare.
1 code implementation • 2 Jun 2019 • Junyuan Shang, Tengfei Ma, Cao Xiao, Jimeng Sun
G-BERT is the first to bring the language model pre-training schema into the healthcare domain and it achieved state-of-the-art performance on the medication recommendation task.
1 code implementation • 27 May 2019 • Shenda Hong, Cao Xiao, Tengfei Ma, Hongyan Li, Jimeng Sun
Electrocardiography (ECG) signals are commonly used to diagnose various cardiac abnormalities.
no code implementations • ICLR 2019 • Tengfei Ma, Cao Xiao, Junyuan Shang, Jimeng Sun
By integrating the conditional random fields (CRF) in the graph convolutional networks, we explicitly model a joint probability of the entire set of node labels, thus taking advantage of neighborhood label information in the node label prediction task.
1 code implementation • NeurIPS 2018 • Edward Choi, Cao Xiao, Walter F. Stewart, Jimeng Sun
Deep learning models exhibit state-of-the-art performance for many predictive healthcare tasks using electronic health records (EHR) data, but these models typically require training data volume that exceeds the capacity of most healthcare systems.
no code implementations • 11 Sep 2018 • Tengfei Ma, Chiamin Wu, Cao Xiao, Jimeng Sun
It refers to the directional relation between text fragments such that the "premise" can infer "hypothesis".
1 code implementation • NeurIPS 2018 • Tengfei Ma, Jie Chen, Cao Xiao
We focus on the matrix representation of graphs and formulate penalty terms that regularize the output distribution of the decoder to encourage the satisfaction of validity constraints.
1 code implementation • 6 Sep 2018 • Shenda Hong, Cao Xiao, Trong Nghia Hoang, Tengfei Ma, Hongyan Li, Jimeng Sun
In many situations, we need to build and deploy separate models in related environments with different data qualities.
1 code implementation • 6 Sep 2018 • Junyuan Shang, Cao Xiao, Tengfei Ma, Hongyan Li, Jimeng Sun
Recent progress in deep learning is revolutionizing the healthcare domain including providing solutions to medication recommendations, especially recommending medication combination for patients with complex health conditions.
1 code implementation • 28 Apr 2018 • Tengfei Ma, Cao Xiao, Jiayu Zhou, Fei Wang
In this paper, we propose to learn accurate and interpretable similarity measures from multiple types of drug features.
3 code implementations • ICLR 2018 • Jie Chen, Tengfei Ma, Cao Xiao
The graph convolutional networks (GCN) recently proposed by Kipf and Welling are an effective graph model for semi-supervised learning.
Ranked #3 on Node Classification on Citeseer Full-supervised
1 code implementation • KDD '17 Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 2017 • Inci M. Baytas, Cao Xiao, Xi Zhang, Fei Wang, Anil K. Jain, Jiayu Zhou
We propose a patient subtyping model that leverages the proposed T-LSTM in an auto-encoder to learn a powerful single representation for sequential records of patients, which are then used to cluster patients into clinical subtypes.
Ranked #4 on Multivariate Time Series Forecasting on USHCN-Daily