arXiv subjects
Publications and source records attributed to Joyce C. Ho.
A collection of invited non-archival papers for the Conference on Health, Inference, and Learning (CHIL) 2022. This index is incomplete as some authors of invited non-archival presentations opted not to include their papers in this index.
Representation learning on static graph-structured data has shown a significant impact on many real-world applications. However, less attention has been paid to the evolving nature of temporal networks, in which the edges are often changing over time. The embeddings of such temporal networks should encode both graph-structured information and the temporally evolving pattern. Existing approaches in learning temporally evolving network representations fail to capture the temporal interdependence. In this paper, we propose Toffee, a novel approach for temporal network representation learning based on tensor decomposition. Our method exploits the tensor-tensor product operator to encode the cross-time information, so that the periodic changes in the evolving networks can be captured. Experimental results demonstrate that Toffee outperforms existing methods on multiple real-world temporal networks in generating effective embeddings for the link prediction tasks.
Samples with ground truth labels may not always be available in numerous domains. While learning from crowdsourcing labels has been explored, existing models can still fail in the presence of sparse, unreliable, or diverging annotations. Co-teaching methods have shown promising improvements for computer vision problems with noisy labels by employing two classifiers trained on each others' confident samples in each batch. Inspired by the idea of separating confident and uncertain samples during the training process, we extend it for the crowdsourcing problem. Our model, CrowdTeacher, uses the idea that perturbation in the input space model can improve the robustness of the classifier for noisy labels. Treating crowdsourcing annotations as a source of noisy labeling, we perturb samples based on the certainty from the aggregated annotations. The perturbed samples are fed to a Co-teaching algorithm tuned to also accommodate smaller tabular data. We showcase the boost in predictive power attained using CrowdTeacher for both synthetic and real datasets across various label density settings. Our experiments reveal that our proposed approach beats baselines modeling individual annotations and then combining them, methods simultaneously learning a classifier and inferring truth labels, and the Co-teaching algorithm with aggregated labels through common truth inference methods.
Existing tensor factorization methods assume that the input tensor follows some specific distribution (i.e. Poisson, Bernoulli, and Gaussian), and solve the factorization by minimizing some empirical loss functions defined based on the corresponding distribution. However, it suffers from several drawbacks: 1) In reality, the underlying distributions are complicated and unknown, making it infeasible to be approximated by a simple distribution. 2) The correlation across dimensions of the input tensor is not well utilized, leading to sub-optimal performance. Although heuristics were proposed to incorporate such correlation as side information under Gaussian distribution, they can not easily be generalized to other distributions. Thus, a more principled way of utilizing the correlation in tensor factorization models is still an open challenge. Without assuming any explicit distribution, we formulate the tensor factorization as an optimal transport problem with Wasserstein distance, which can handle non-negative inputs. We introduce SWIFT, which minimizes the Wasserstein distance that measures the distance between the input tensor and that of the reconstruction. In particular, we define the N-th order tensor Wasserstein loss for the widely used tensor CP factorization and derive the optimization algorithm that minimizes it. By leveraging sparsity structure and different equivalent formulations for optimizing computational efficiency, SWIFT is as scalable as other well-known CP algorithms. Using the factor matrices as features, SWIFT achieves up to 9.65% and 11.31% relative improvement over baselines for downstream prediction tasks. Under the noisy conditions, SWIFT achieves up to 15% and 17% relative improvements over the best competitors for the prediction tasks.
Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly. In addition, optimizing these multiple properties is a challenging task because the optimization of one property is prone to changing other properties. In this paper, we pose this multi-property optimization problem as a sequence translation process and propose a new optimized molecule generator model based on the Transformer with two constraint networks: property prediction and similarity prediction. We further improve the model by incorporating score predictions from these constraint networks in a modified beam search algorithm. The experiments demonstrate that our proposed model outperforms state-of-the-art models by a significant margin for optimizing multiple properties simultaneously.
Mining massive spatio-temporal data can help a variety of real-world applications such as city capacity planning, event management, and social network analysis. The tensor representation can be used to capture the correlation between space and time and simultaneously exploit the latent structure of the spatial and temporal patterns in an unsupervised fashion. However, the increasing volume of spatio-temporal data has made it prohibitively expensive to store and analyze using tensor factorization. In this paper, we propose SkeTenSmooth, a novel tensor factorization framework that uses adaptive sampling to compress the tensor in a temporally streaming fashion and preserves the underlying global structure. SkeTenSmooth adaptively samples incoming tensor slices according to the detected data dynamics. Thus, the sketches are more representative and informative of the tensor dynamic patterns. In addition, we propose a robust tensor factorization method that can deal with the sketched tensor and recover the original patterns. Experiments on the New York City Yellow Taxi data show that SkeTenSmooth greatly reduces the memory cost and outperforms random sampling and fixed rate sampling method in terms of retaining the underlying patterns.
Mining social media content for tasks such as detecting personal experiences or events, suffer from lexical sparsity, insufficient training data, and inventive lexicons. To reduce the burden of creating extensive labeled data and improve classification performance, we propose to perform these tasks in two steps: 1. Decomposing the task into domain-specific sub-tasks by identifying key concepts, thus utilizing human domain understanding; and 2. Combining the results of learners for each key concept using co-training to reduce the requirements for labeled training data. We empirically show the effectiveness and generality of our approach, Co-Decomp, using three representative social media mining tasks, namely Personal Health Mention detection, Crisis Report detection, and Adverse Drug Reaction monitoring. The experiments show that our model is able to outperform the state-of-the-art text classification models--including those using the recently introduced BERT model--when small amounts of training data are available.
Tensor factorization has been demonstrated as an efficient approach for computational phenotyping, where massive electronic health records (EHRs) are converted to concise and meaningful clinical concepts. While distributing the tensor factorization tasks to local sites can avoid direct data sharing, it still requires the exchange of intermediary results which could reveal sensitive patient information. Therefore, the challenge is how to jointly decompose the tensor under rigorous and principled privacy constraints, while still support the model's interpretability. We propose DPFact, a privacy-preserving collaborative tensor factorization method for computational phenotyping using EHR. It embeds advanced privacy-preserving mechanisms with collaborative learning. Hospitals can keep their EHR database private but also collaboratively learn meaningful clinical concepts by sharing differentially private intermediary results. Moreover, DPFact solves the heterogeneous patient population using a structured sparsity term. In our framework, each hospital decomposes its local tensors, and sends the updated intermediary results with output perturbation every several iterations to a semi-trusted server which generates the phenotypes. The evaluation on both real-world and synthetic datasets demonstrated that under strict privacy constraints, our method is more accurate and communication-efficient than state-of-the-art baseline methods.
Predicting drug-target interactions (DTI) is an essential part of the drug discovery process, which is an expensive process in terms of time and cost. Therefore, reducing DTI cost could lead to reduced healthcare costs for a patient. In addition, a precisely learned molecule representation in a DTI model could contribute to developing personalized medicine, which will help many patient cohorts. In this paper, we propose a new molecule representation based on the self-attention mechanism, and a new DTI model using our molecule representation. The experiments show that our DTI model outperforms the state of the art by up to 4.9% points in terms of area under the precision-recall curve. Moreover, a study using the DrugBank database proves that our model effectively lists all known drugs targeting a specific cancer biomarker in the top-30 candidate list.
It has been recently shown that sparse, nonnegative tensor factorization of multi-modal electronic health record data is a promising approach to high-throughput computational phenotyping. However, such approaches typically do not leverage available domain knowledge while extracting the phenotypes; hence, some of the suggested phenotypes may not map well to clinical concepts or may be very similar to other suggested phenotypes. To address these issues, we present a novel, automatic approach called PIVETed-Granite that mines existing biomedical literature (PubMed) to obtain cannot-link constraints that are then used as side-information during a tensor-factorization based computational phenotyping process. The resulting improvements are clearly observed in experiments using a large dataset from VUMC to identify phenotypes for hypertensive patients.
Stochastic Gradient TreeBoost is often found in many winning solutions in public data science challenges. Unfortunately, the best performance requires extensive parameter tuning and can be prone to overfitting. We propose PaloBoost, a Stochastic Gradient TreeBoost model that uses novel regularization techniques to guard against overfitting and is robust to parameter settings. PaloBoost uses the under-utilized out-of-bag samples to perform gradient-aware pruning and estimate adaptive learning rates. Unlike other Stochastic Gradient TreeBoost models that use the out-of-bag samples to estimate test errors, PaloBoost treats the samples as a second batch of training samples to prune the trees and adjust the learning rates. As a result, PaloBoost can dynamically adjust tree depths and learning rates to achieve faster learning at the start and slower learning as the algorithm converges. We illustrate how these regularization techniques can be efficiently implemented and propose a new formula for calculating feature importance to reflect the node coverages and learning rates. Extensive experimental results on seven datasets demonstrate that PaloBoost is robust to overfitting, is less sensitivity to the parameters, and can also effectively identify meaningful features.
The increased availability of electronic health records (EHRs) have spearheaded the initiative for precision medicine using data driven approaches. Essential to this effort is the ability to identify patients with certain medical conditions of interest from simple queries on EHRs, or EHR-based phenotypes. Existing rule--based phenotyping approaches are extremely labor intensive. Instead, dimensionality reduction and latent factor estimation techniques from machine learning can be adapted for phenotype extraction with no (or minimal) human supervision. We propose to identify an easily interpretable latent space shared across various sources of EHR data as potential candidates for phenotypes. By incorporating multiple EHR data sources (e.g., diagnosis, medications, and lab reports) available in heterogeneous datatypes in a generalized \textit{Collective Matrix Factorization (CMF)}, our methods can generate rich phenotypes. Further, easy interpretability in phenotyping application requires sparse representations of the candidate phenotypes, for example each phenotype derived from patients' medication and diagnosis data should preferably be represented by handful of diagnosis and medications, ($5$--$10$ active components). We propose a constrained formulation of CMF for estimating sparse phenotypes. We demonstrate the efficacy of our model through an extensive empirical study on EHR data from Vanderbilt University Medical Center.
Multiple sclerosis (MS) is a chronic autoimmune disease that affects the central nervous system. The progression and severity of MS varies by individual, but it is generally a disabling disease. Although medications have been developed to slow the disease progression and help manage symptoms, MS research has yet to result in a cure. Early diagnosis and treatment of the disease have been shown to be effective at slowing the development of disabilities. However, early MS diagnosis is difficult because symptoms are intermittent and shared with other diseases. Thus most previous works have focused on uncovering the risk factors associated with MS and predicting the progression of disease after a diagnosis rather than disease prediction. This paper investigates the use of data available in electronic medical records (EMRs) to create a risk prediction model; thereby helping clinicians perform the difficult task of diagnosing an MS patient. Our results demonstrate that even given a limited time window of patient data, one can achieve reasonable classification with an area under the receiver operating characteristic curve of 0.724. By restricting our features to common EMR components, the developed models also generalize to other healthcare systems.