Search Results for author: Lucas M. Glass

Found 15 papers, 7 papers with code

Machine Learning Applications for Therapeutic Tasks with Genomics Data

no code implementations3 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.

HINT: Hierarchical Interaction Network for Trial Outcome Prediction Leveraging Web Data

1 code implementation8 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.

Imputation

STELAR: Spatio-temporal Tensor Factorization with Latent Epidemiological Regularization

no code implementations8 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.

FLANNEL: Focal Loss Based Neural Network Ensemble for COVID-19 Detection

no code implementations30 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.

UNITE: Uncertainty-based Health Risk Prediction Leveraging Multi-sourced Data

no code implementations22 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.

Variational Inference

MolDesigner: Interactive Design of Efficacious Drugs with Deep Learning

1 code implementation5 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.

MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization

1 code implementation5 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.

Drug Discovery Type prediction

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization

1 code implementation4 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.

Knowledge Graphs

COMPOSE: Cross-Modal Pseudo-Siamese Network for Patient Trial Matching

1 code implementation15 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.

CLARA: Clinical Report Auto-completion

no code implementations26 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.

EEG

StageNet: Stage-Aware Neural Networks for Health Risk Prediction

1 code implementation24 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.

DeepEnroll: Patient-Trial Matching with Deep Embedding and Entailment Prediction

no code implementations22 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.

Sentence Embedding Sentence-Embedding

CONAN: Complementary Pattern Augmentation for Rare Disease Detection

no code implementations26 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?

Doctor2Vec: Dynamic Doctor Representation Learning for Clinical Trial Recruitment

no code implementations23 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.

Representation Learning

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