We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks. The code will be published at \url{https://github.com/ritaranx/RAM-EHR}.
Interactive search can provide a better experience by incorporating interaction feedback from the users. This can significantly improve search accuracy as it helps avoid irrelevant information and captures the users' search intents. Existing state-of-the-art (SOTA) systems use reinforcement learning (RL) models to incorporate the interactions but focus on item-level feedback, ignoring the fine-grained information found in sentence-level feedback. Yet such feedback requires extensive RL action space exploration and large amounts of annotated data. This work addresses these challenges by proposing a new deep Q-learning (DQ) approach, DQrank. DQrank adapts BERT-based models, the SOTA in natural language processing, to select crucial sentences based on users' engagement and rank the items to obtain more satisfactory responses. We also propose two mechanisms to better explore optimal actions. DQrank further utilizes the experience replay mechanism in DQ to store the feedback sentences to obtain a better initial ranking performance. We validate the effectiveness of DQrank on three search datasets. The results show that DQRank performs at least 12% better than the previous SOTA RL approaches. We also conduct detailed ablation studies. The ablation results demonstrate that each model component can efficiently extract and accumulate long-term engagement effects from the users' sentence-level feedback. This structure offers new technologies with promised performance to construct a search system with sentence-level interaction.
Scientific document classification is a critical task for a wide range of applications, but the cost of obtaining massive amounts of human-labeled data can be prohibitive. To address this challenge, we propose a weakly-supervised approach for scientific document classification using label names only. In scientific domains, label names often include domain-specific concepts that may not appear in the document corpus, making it difficult to match labels and documents precisely. To tackle this issue, we propose WANDER, which leverages dense retrieval to perform matching in the embedding space to capture the semantics of label names. We further design the label name expansion module to enrich the label name representations. Lastly, a self-training step is used to refine the predictions. The experiments on three datasets show that WANDER outperforms the best baseline by 11.9% on average. Our code will be published at https://github.com/ritaranx/wander.
Tensor factorization has been proved as an efficient unsupervised learning approach for health data analysis, especially for computational phenotyping, where the high-dimensional Electronic Health Records (EHRs) with patients history of medical procedures, medications, diagnosis, lab tests, etc., are converted to meaningful and interpretable medical concepts. Federated tensor factorization distributes the tensor computation to multiple workers under the coordination of a central server, which enables jointly learning the phenotypes across multiple hospitals while preserving the privacy of the patient information. However, existing federated tensor factorization algorithms encounter the single-point-failure issue with the involvement of the central server, which is not only easily exposed to external attacks, but also limits the number of clients sharing information with the server under restricted uplink bandwidth. In this paper, we propose CiderTF, a communication-efficient decentralized generalized tensor factorization, which reduces the uplink communication cost by leveraging a four-level communication reduction strategy designed for a generalized tensor factorization, which has the flexibility of modeling different tensor distribution with multiple kinds of loss functions. Experiments on two real-world EHR datasets demonstrate that CiderTF achieves comparable convergence with the communication reduction up to 99.99%.
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.
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.
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.
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.