Surrogate variables in electronic health records (EHR) and biobank data play an important role in biomedical studies due to the scarcity or absence of chart-reviewed gold standard labels. We develop a novel approach named SASH for {\bf S}urrogate-{\bf A}ssisted and data-{\bf S}hielding {\bf H}igh-dimensional integrative regression. It is a semi-supervised approach that efficiently leverages sizable unlabeled samples with error-prone EHR surrogate outcomes from multiple local sites, to improve the learning accuracy of the small gold-labeled data. {To facilitate stable and efficient knowledge extraction from the surrogates, our method first obtains a preliminary supervised estimator, and then uses it to assist training a regularized single index model (SIM) for the surrogates. Interestingly, through a chain of convex and properly penalized sparse regressions that approximate the SIM loss with bias-correction, our method avoids the local minima issue of the SIM training, and fully eliminates the impact of the preliminary estimator's large error. In addition, it protects individual-level information through summary-statistics-based data aggregation across the local sites, leveraging a similar idea of bias-corrected approximation for SIM.} Through simulation studies, we demonstrate that our method outperforms existing approaches on finite samples. Finally, we apply our method to develop a high dimensional genetic risk model for type II diabetes using large-scale data sets from UK and Mass General Brigham biobanks, where only a small fraction of subjects in one site has been labeled via chart reviewing.
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ACM/IEEE第23屆模型驅動工程語言和系統國際會議，是模型驅動軟件和系統工程的首要會議系列，由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來，模型涵蓋了建模的各個方面，從語言和方法到工具和應用程序。模特的參加者來自不同的背景，包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇，參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會，并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。
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Semi-inductive link prediction (LP) in knowledge graphs (KG) is the task of predicting facts for new, previously unseen entities based on context information. Although new entities can be integrated by retraining the model from scratch in principle, such an approach is infeasible for large-scale KGs, where retraining is expensive and new entities may arise frequently. In this paper, we propose and describe a large-scale benchmark to evaluate semi-inductive LP models. The benchmark is based on and extends Wikidata5M: It provides transductive, k-shot, and 0-shot LP tasks, each varying the available information from (i) only KG structure, to (ii) including textual mentions, and (iii) detailed descriptions of the entities. We report on a small study of recent approaches and found that semi-inductive LP performance is far from transductive performance on long-tail entities throughout all experiments. The benchmark provides a test bed for further research into integrating context and textual information in semi-inductive LP models.
Medical image fusion combines the complementary information of multimodal medical images to assist medical professionals in the clinical diagnosis of patients' disorders and provide guidance during preoperative and intra-operative procedures. Deep learning (DL) models have achieved end-to-end image fusion with highly robust and accurate fusion performance. However, most DL-based fusion models perform down-sampling on the input images to minimize the number of learnable parameters and computations. During this process, salient features of the source images become irretrievable leading to the loss of crucial diagnostic edge details and contrast of various brain tissues. In this paper, we propose a new multimodal medical image fusion model is proposed that is based on integrated Laplacian-Gaussian concatenation with attention pooling (LGCA). We prove that our model preserves effectively complementary information and important tissue structures.
Atrial fibrillation (AF) is the most common arrhythmia, associated with significant burdens to patients and the healthcare system. The atrioventricular (AV) node plays a vital role in regulating heart rate during AF, but is often insufficient in regards to maintaining a healthy heart rate. Thus, the AV node properties are modified using rate-control drugs. Hence, quantifying individual differences in diurnal and short-term variability of AV-nodal function could aid in personalized treatment selection. This study presents a novel methodology for estimating the refractory period (RP) and conduction delay (CD) trends and their uncertainty in the two pathways of the AV node during 24 hours using non-invasive data. This was achieved using a network model together with a problem-specific genetic algorithm and an approximate Bayesian computation algorithm. Diurnal and short-term variability in the estimated RP and CD was quantified by the difference between the daytime and nighttime estimates and by the Kolmogorov-Smirnov distance between adjacent 10-minute segments in the 24-hour trends. Holter ECGs from 51 patients with permanent AF during baseline were analyzed, and the predictive power of variations in RP and CD on the resulting heart rate reduction after treatment with four rate control drugs was investigated. Diurnal variability yielded no correlation to treatment outcome, and no prediction of drug outcome was possible using the machine learning tools. However, a correlation between the short-term variability for the RP and CD in the fast pathway and resulting heart rate reduction during treatment with metoprolol ($\rho=0.48, p<0.005$ in RP, $\rho=0.35, p<0.05$ in CD) were found. The proposed methodology enables non-invasive estimation of the AV node properties during 24 hours, which may have the potential to assist in treatment selection.
Realistic virtual humans play a crucial role in numerous industries, such as metaverse, intelligent healthcare, and self-driving simulation. But creating them on a large scale with high levels of realism remains a challenge. The utilization of deep implicit function sparks a new era of image-based 3D clothed human reconstruction, enabling pixel-aligned shape recovery with fine details. Subsequently, the vast majority of works locate the surface by regressing the deterministic implicit value for each point. However, should all points be treated equally regardless of their proximity to the surface? In this paper, we propose replacing the implicit value with an adaptive uncertainty distribution, to differentiate between points based on their distance to the surface. This simple ``value to distribution'' transition yields significant improvements on nearly all the baselines. Furthermore, qualitative results demonstrate that the models trained using our uncertainty distribution loss, can capture more intricate wrinkles, and realistic limbs. Code and models are available for research purposes at //github.com/psyai-net/D-IF_release.
Biomedical named entity recognition is one of the core tasks in biomedical natural language processing (BioNLP). To tackle this task, numerous supervised/distantly supervised approaches have been proposed. Despite their remarkable success, these approaches inescapably demand laborious human effort. To alleviate the need of human effort, dictionary-based approaches have been proposed to extract named entities simply based on a given dictionary. However, one downside of existing dictionary-based approaches is that they are challenged to identify concept synonyms that are not listed in the given dictionary, which we refer as the synonym generalization problem. In this study, we propose a novel Synonym Generalization (SynGen) framework that recognizes the biomedical concepts contained in the input text using span-based predictions. In particular, SynGen introduces two regularization terms, namely, (1) a synonym distance regularizer; and (2) a noise perturbation regularizer, to minimize the synonym generalization error. To demonstrate the effectiveness of our approach, we provide a theoretical analysis of the bound of synonym generalization error. We extensively evaluate our approach on a wide range of benchmarks and the results verify that SynGen outperforms previous dictionary-based models by notable margins. Lastly, we provide a detailed analysis to further reveal the merits and inner-workings of our approach.
Dense embedding-based retrieval is now the industry standard for semantic search and ranking problems, like obtaining relevant web documents for a given query. Such techniques use a two-stage process: (a) contrastive learning to train a dual encoder to embed both the query and documents and (b) approximate nearest neighbor search (ANNS) for finding similar documents for a given query. These two stages are disjoint; the learned embeddings might be ill-suited for the ANNS method and vice-versa, leading to suboptimal performance. In this work, we propose End-to-end Hierarchical Indexing -- EHI -- that jointly learns both the embeddings and the ANNS structure to optimize retrieval performance. EHI uses a standard dual encoder model for embedding queries and documents while learning an inverted file index (IVF) style tree structure for efficient ANNS. To ensure stable and efficient learning of discrete tree-based ANNS structure, EHI introduces the notion of dense path embedding that captures the position of a query/document in the tree. We demonstrate the effectiveness of EHI on several benchmarks, including de-facto industry standard MS MARCO (Dev set and TREC DL19) datasets. For example, with the same compute budget, EHI outperforms state-of-the-art (SOTA) in by 0.6% (MRR@10) on MS MARCO dev set and by 4.2% (nDCG@10) on TREC DL19 benchmarks.
Tensor-valued data arise frequently from a wide variety of scientific applications, and many among them can be translated into an alteration detection problem of tensor dependence structures. In this article, we formulate the problem under the popularly adopted tensor-normal distributions and aim at two-sample correlation/partial correlation comparisons of tensor-valued observations. Through decorrelation and centralization, a separable covariance structure is employed to pool sample information from different tensor modes to enhance the power of the test. Additionally, we propose a novel Sparsity-Exploited Reranking Algorithm (SERA) to further improve the multiple testing efficiency. The algorithm is approached through reranking of the p-values derived from the primary test statistics, by incorporating a carefully constructed auxiliary tensor sequence. Besides the tensor framework, SERA is also generally applicable to a wide range of two-sample large-scale inference problems with sparsity structures, and is of independent interest. The asymptotic properties of the proposed test are derived and the algorithm is shown to control the false discovery at the pre-specified level. We demonstrate the efficacy of the proposed method through intensive simulations and two scientific applications.
Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.
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