Biomedical Knowledge Graph Refinement with Embedding and Logic Rules

Currently, there is a rapidly increasing need for high-quality biomedical knowledge graphs (BioKG) that provide direct and precise biomedical knowledge. In the context of COVID-19, this issue is even more necessary to be highlighted. However, most BioKG construction inevitably includes numerous conflicts and noises deriving from incorrect knowledge descriptions in literature and defective information extraction techniques. Many studies have demonstrated that reasoning upon the knowledge graph is effective in eliminating such conflicts and noises. This paper proposes a method BioGRER to improve the BioKG's quality, which comprehensively combines the knowledge graph embedding and logic rules that support and negate triplets in the BioKG. In the proposed model, the BioKG refinement problem is formulated as the probability estimation for triplets in the BioKG. We employ the variational EM algorithm to optimize knowledge graph embedding and logic rule inference alternately. In this way, our model could combine efforts from both the knowledge graph embedding and logic rules, leading to better results than using them alone. We evaluate our model over a COVID-19 knowledge graph and obtain competitive results.

3D Registration for Self-Occluded Objects in Context

While much progress has been made on the task of 3D point cloud registration, there still exists no learning-based method able to estimate the 6D pose of an object observed by a 2.5D sensor in a scene. The challenges of this scenario include the fact that most measurements are outliers depicting the object's surrounding context, and the mismatch between the complete 3D object model and its self-occluded observations. We introduce the first deep learning framework capable of effectively handling this scenario. Our method consists of an instance segmentation module followed by a pose estimation one. It allows us to perform 3D registration in a one-shot manner, without requiring an expensive iterative procedure. We further develop an on-the-fly rendering-based training strategy that is both time- and memory-efficient. Our experiments evidence the superiority of our approach over the state-of-the-art traditional and learning-based 3D registration methods.

Explicitly Learning Topology for Differentiable Neural Architecture Search

Differentiable neural architecture search (DARTS) has gained much success in discovering more flexible and diverse cell types. Current methods couple the operations and topology during search, and simply derive optimal topology by a hand-craft rule. However, topology also matters for neural architectures since it controls the interactions between features of operations. In this paper, we highlight the topology learning in differentiable NAS, and propose an explicit topology modeling method, named TopoNAS, to directly decouple the operation selection and topology during search. Concretely, we introduce a set of topological variables and a combinatorial probabilistic distribution to explicitly indicate the target topology. Besides, we also leverage a passive-aggressive regularization to suppress invalid topology within supernet. Our introduced topological variables can be jointly learned with operation variables and supernet weights, and apply to various DARTS variants. Extensive experiments on CIFAR-10 and ImageNet validate the effectiveness of our proposed TopoNAS. The results show that TopoNAS does enable to search cells with more diverse and complex topology, and boost the performance significantly. For example, TopoNAS can improve DARTS by 0.16\% accuracy on CIFAR-10 dataset with 40\% parameters reduced or 0.35\% with similar parameters.

A Method to Generate High Precision Mesh Model and RGB-D Datasetfor 6D Pose Estimation Task

Recently, 3D version has been improved greatly due to the development of deep neural networks. A high quality dataset is important to the deep learning method. Existing datasets for 3D vision has been constructed, such as Bigbird and YCB. However, the depth sensors used to make these datasets are out of date, which made the resolution and accuracy of the datasets cannot full fill the higher standards of demand. Although the equipment and technology got better, but no one was trying to collect new and better dataset. Here we are trying to fill that gap. To this end, we propose a new method for object reconstruction, which takes into account the speed, accuracy and robustness. Our method could be used to produce large dataset with better and more accurate annotation. More importantly, our data is more close to the rendering data, which shrinking the gap between the real data and synthetic data further.

Data Agnostic Filter Gating for Efficient Deep Networks

To deploy a well-trained CNN model on low-end computation edge devices, it is usually supposed to compress or prune the model under certain computation budget (e.g., FLOPs). Current filter pruning methods mainly leverage feature maps to generate important scores for filters and prune those with smaller scores, which ignores the variance of input batches to the difference in sparse structure over filters. In this paper, we propose a data agnostic filter pruning method that uses an auxiliary network named Dagger module to induce pruning and takes pretrained weights as input to learn the importance of each filter. In addition, to help prune filters with certain FLOPs constraints, we leverage an explicit FLOPs-aware regularization to directly promote pruning filters toward target FLOPs. Extensive experimental results on CIFAR-10 and ImageNet datasets indicate our superiority to other state-of-the-art filter pruning methods. For example, our 50\% FLOPs ResNet-50 can achieve 76.1\% Top-1 accuracy on ImageNet dataset, surpassing many other filter pruning methods.

ISTA-NAS: Efficient and Consistent Neural Architecture Search by Sparse Coding

Neural architecture search (NAS) aims to produce the optimal sparse solution from a high-dimensional space spanned by all candidate connections. Current gradient-based NAS methods commonly ignore the constraint of sparsity in the search phase, but project the optimized solution onto a sparse one by post-processing. As a result, the dense super-net for search is inefficient to train and has a gap with the projected architecture for evaluation. In this paper, we formulate neural architecture search as a sparse coding problem. We perform the differentiable search on a compressed lower-dimensional space that has the same validation loss as the original sparse solution space, and recover an architecture by solving the sparse coding problem. The differentiable search and architecture recovery are optimized in an alternate manner. By doing so, our network for search at each update satisfies the sparsity constraint and is efficient to train. In order to also eliminate the depth and width gap between the network in search and the target-net in evaluation, we further propose a method to search and evaluate in one stage under the target-net settings. When training finishes, architecture variables are absorbed into network weights. Thus we get the searched architecture and optimized parameters in a single run. In experiments, our two-stage method on CIFAR-10 requires only 0.05 GPU-day for search. Our one-stage method produces state-of-the-art performances on both CIFAR-10 and ImageNet at the cost of only evaluation time.

Robust Finite Mixture Regression for Heterogeneous Targets

Finite Mixture Regression (FMR) refers to the mixture modeling scheme which learns multiple regression models from the training data set. Each of them is in charge of a subset. FMR is an effective scheme for handling sample heterogeneity, where a single regression model is not enough for capturing the complexities of the conditional distribution of the observed samples given the features. In this paper, we propose an FMR model that 1) finds sample clusters and jointly models multiple incomplete mixed-type targets simultaneously, 2) achieves shared feature selection among tasks and cluster components, and 3) detects anomaly tasks or clustered structure among tasks, and accommodates outlier samples. We provide non-asymptotic oracle performance bounds for our model under a high-dimensional learning framework. The proposed model is evaluated on both synthetic and real-world data sets. The results show that our model can achieve state-of-the-art performance.

Domain Agnostic Learning for Unbiased Authentication

Authentication is the task of confirming the matching relationship between a data instance and a given identity. Typical examples of authentication problems include face recognition and person re-identification. Data-driven authentication could be affected by undesired biases, i.e., the models are often trained in one domain (e.g., for people wearing spring outfits) while applied in other domains (e.g., they change the clothes to summer outfits). Previous works have made efforts to eliminate domain-difference. They typically assume domain annotations are provided, and all the domains share classes. However, for authentication, there could be a large number of domains shared by different identities/classes, and it is impossible to annotate these domains exhaustively. It could make domain-difference challenging to model and eliminate. In this paper, we propose a domain-agnostic method that eliminates domain-difference without domain labels. We alternately perform latent domain discovery and domain-difference elimination until our model no longer detects domain-difference. In our approach, the latent domains are discovered by learning the heterogeneous predictive relationships between inputs and outputs. Then domain-difference is eliminated in both class-dependent and class-independent components. Comprehensive empirical evaluation results are provided to demonstrate the effectiveness and superiority of our proposed method.

Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review

Patient representation learning refers to learning a dense mathematical representation of a patient that encodes meaningful information from Electronic Health Records (EHRs). This is generally performed using advanced deep learning methods. This study presents a systematic review of this field and provides both qualitative and quantitative analyses from a methodological perspective. We identified studies developing patient representations from EHRs with deep learning methods from MEDLINE, EMBASE, Scopus, the Association for Computing Machinery (ACM) Digital Library, and Institute of Electrical and Electronics Engineers (IEEE) Xplore Digital Library. After screening 362 articles, 48 papers were included for a comprehensive data collection. We noticed a typical workflow starting with feeding raw data, applying deep learning models, and ending with clinical outcome predictions as evaluations of the learned representations. Specifically, learning representations from structured EHR data was dominant (36 out of 48 studies). Recurrent Neural Networks were widely applied as the deep learning architecture (LSTM: 13 studies, GRU: 11 studies). Disease prediction was the most common application and evaluation (30 studies). Benchmark datasets were mostly unavailable (28 studies) due to privacy concerns of EHR data, and code availability was assured in 20 studies. We show the importance and feasibility of learning comprehensive representations of patient EHR data through a systematic review. Advances in patient representation learning techniques will be essential for powering patient-level EHR analyses. Future work will still be devoted to leveraging the richness and potential of available EHR data. Knowledge distillation and advanced learning techniques will be exploited to assist the capability of learning patient representation further.

Suicide Risk Modeling with Uncertain Diagnostic Records

Motivated by the pressing need for suicide prevention through improving behavioral healthcare, we use medical claims data to study the risk of subsequent suicide attempts for patients who were hospitalized due to suicide attempts and later discharged. Understanding the risk behaviors of such patients at elevated suicide risk is an important step towards the goal of "Zero Suicide". An immediate and unconventional challenge is that the identification of suicide attempts from medical claims contains substantial uncertainty: almost 20\% of "suspected" suicide attempts are identified from diagnostic codes indicating external causes of injury and poisoning with undermined intent. It is thus of great interest to learn which of these undetermined events are more likely actual suicide attempts and how to properly utilize them in survival analysis with severe censoring. To tackle these interrelated problems, we develop an integrative Cox cure model with regularization to perform survival regression with uncertain events and a latent cure fraction. We apply the proposed approach to study the risk of subsequent suicide attempt after suicide-related hospitalization for adolescent and young adult population, using medical claims data from Connecticut. The identified risk factors are highly interpretable; more intriguingly, our method distinguishes the risk factors that are most helpful in assessing either susceptibility or timing of subsequent attempt. The predicted statuses of the uncertain attempts are further investigated, leading to several new insights on suicide event identification.