arXiv subjects

Xiaoning Qian

Publications and source records attributed to Xiaoning Qian.

At least 73 records · Page 4Linked to original sources

arXiv2020

NADS: Neural Architecture Distribution Search for Uncertainty Awareness

Machine learning (ML) systems often encounter Out-of-Distribution (OoD) errors when dealing with testing data coming from a distribution different from training data. It becomes important for ML systems in critical applications to accurately quantify its predictive uncertainty and screen out these anomalous inputs. However, existing OoD detection approaches are prone to errors and even sometimes assign higher likelihoods to OoD samples. Unlike standard learning tasks, there is currently no well established guiding principle for designing OoD detection architectures that can accurately quantify uncertainty. To address these problems, we first seek to identify guiding principles for designing uncertainty-aware architectures, by proposing Neural Architecture Distribution Search (NADS). NADS searches for a distribution of architectures that perform well on a given task, allowing us to identify common building blocks among all uncertainty-aware architectures. With this formulation, we are able to optimize a stochastic OoD detection objective and construct an ensemble of models to perform OoD detection. We perform multiple OoD detection experiments and observe that our NADS performs favorably, with up to 57% improvement in accuracy compared to state-of-the-art methods among 15 different testing configurations.

cs.LG↗

arXiv2020

Pairwise Supervised Hashing with Bernoulli Variational Auto-Encoder and Self-Control Gradient Estimator

Semantic hashing has become a crucial component of fast similarity search in many large-scale information retrieval systems, in particular, for text data. Variational auto-encoders (VAEs) with binary latent variables as hashing codes provide state-of-the-art performance in terms of precision for document retrieval. We propose a pairwise loss function with discrete latent VAE to reward within-class similarity and between-class dissimilarity for supervised hashing. Instead of solving the optimization relying on existing biased gradient estimators, an unbiased low-variance gradient estimator is adopted to optimize the hashing function by evaluating the non-differentiable loss function over two correlated sets of binary hashing codes to control the variance of gradient estimates. This new semantic hashing framework achieves superior performance compared to the state-of-the-arts, as demonstrated by our comprehensive experiments.

cs.LG↗

arXiv2020

Variational Graph Recurrent Neural Networks

Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph recurrent neural network (GRNN) to capture both topology and node attribute changes in dynamic graphs. We argue that the use of high-level latent random variables in this variational GRNN (VGRNN) can better capture potential variability observed in dynamic graphs as well as the uncertainty of node latent representation. With semi-implicit variational inference developed for this new VGRNN architecture (SI-VGRNN), we show that flexible non-Gaussian latent representations can further help dynamic graph analytic tasks. Our experiments with multiple real-world dynamic graph datasets demonstrate that SI-VGRNN and VGRNN consistently outperform the existing baseline and state-of-the-art methods by a significant margin in dynamic link prediction.

cs.LG↗

arXiv2020

Semi-Implicit Stochastic Recurrent Neural Networks

Stochastic recurrent neural networks with latent random variables of complex dependency structures have shown to be more successful in modeling sequential data than deterministic deep models. However, the majority of existing methods have limited expressive power due to the Gaussian assumption of latent variables. In this paper, we advocate learning implicit latent representations using semi-implicit variational inference to further increase model flexibility. Semi-implicit stochastic recurrent neural network(SIS-RNN) is developed to enrich inferred model posteriors that may have no analytic density functions, as long as independent random samples can be generated via reparameterization. Extensive experiments in different tasks on real-world datasets show that SIS-RNN outperforms the existing methods.

cs.LG↗

arXiv2020

Semi-Implicit Graph Variational Auto-Encoders

Semi-implicit graph variational auto-encoder (SIG-VAE) is proposed to expand the flexibility of variational graph auto-encoders (VGAE) to model graph data. SIG-VAE employs a hierarchical variational framework to enable neighboring node sharing for better generative modeling of graph dependency structure, together with a Bernoulli-Poisson link decoder. Not only does this hierarchical construction provide a more flexible generative graph model to better capture real-world graph properties, but also does SIG-VAE naturally lead to semi-implicit hierarchical variational inference that allows faithful modeling of implicit posteriors of given graph data, which may exhibit heavy tails, multiple modes, skewness, and rich dependency structures. Compared to VGAE, the derived graph latent representations by SIG-VAE are more interpretable, due to more expressive generative model and more faithful inference enabled by the flexible semi-implicit construction. Extensive experiments with a variety of graph data show that SIG-VAE significantly outperforms state-of-the-art methods on several different graph analytic tasks.

cs.LG↗

arXiv2020

Uncertainty Quantification for Deep Context-Aware Mobile Activity Recognition and Unknown Context Discovery

Activity recognition in wearable computing faces two key challenges: i) activity characteristics may be context-dependent and change under different contexts or situations; ii) unknown contexts and activities may occur from time to time, requiring flexibility and adaptability of the algorithm. We develop a context-aware mixture of deep models termed the α-\b{eta} network coupled with uncertainty quantification (UQ) based upon maximum entropy to enhance human activity recognition performance. We improve accuracy and F score by 10% by identifying high-level contexts in a data-driven way to guide model development. In order to ensure training stability, we have used a clustering-based pre-training in both public and in-house datasets, demonstrating improved accuracy through unknown context discovery.

cs.LG↗

arXiv2020

ARSM Gradient Estimator for Supervised Learning to Rank

We propose a new model for supervised learning to rank. In our model, the relevance labels are assumed to follow a categorical distribution whose probabilities are constructed based on a scoring function. We optimize the training objective with respect to the multivariate categorical variables with an unbiased and low-variance gradient estimator. Learning-to-rank methods can generally be categorized into pointwise, pairwise, and listwise approaches. Although our scoring function is pointwise, the proposed framework permits flexibility over the choice of the loss function. In our new model, the loss function need not be differentiable and can either be pointwise or listwise. Our proposed method achieves better or comparable results on two datasets compared with existing pairwise and listwise methods.

cs.LG↗

arXiv2020

Learnable Bernoulli Dropout for Bayesian Deep Learning

In this work, we propose learnable Bernoulli dropout (LBD), a new model-agnostic dropout scheme that considers the dropout rates as parameters jointly optimized with other model parameters. By probabilistic modeling of Bernoulli dropout, our method enables more robust prediction and uncertainty quantification in deep models. Especially, when combined with variational auto-encoders (VAEs), LBD enables flexible semi-implicit posterior representations, leading to new semi-implicit VAE~(SIVAE) models. We solve the optimization for training with respect to the dropout parameters using Augment-REINFORCE-Merge (ARM), an unbiased and low-variance gradient estimator. Our experiments on a range of tasks show the superior performance of our approach compared with other commonly used dropout schemes. Overall, LBD leads to improved accuracy and uncertainty estimates in image classification and semantic segmentation. Moreover, using SIVAE, we can achieve state-of-the-art performance on collaborative filtering for implicit feedback on several public datasets.

cs.LG↗

arXiv2019

Bayesian Gamma-Negative Binomial Modeling of Single-Cell RNA Sequencing Data

Background: Single-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the underlying cellular process to better understand development and disease mechanisms. The unique analytic challenge is to appropriately model highly over-dispersed scRNA-seq count data with prevalent dropouts (zero counts), making zero-inflated dimensionality reduction techniques popular for scRNA-seq data analyses. Employing zero-inflated distributions, however, may place extra emphasis on zero counts, leading to potential bias when identifying the latent structure of the data. Results: In this paper, we propose a fully generative hierarchical gamma-negative binomial (hGNB) model of scRNA-seq data, obviating the need for explicitly modeling zero inflation. At the same time, hGNB can naturally account for covariate effects at both the gene and cell levels to identify complex latent representations of scRNA-seq data, without the need for commonly adopted pre-processing steps such as normalization. Efficient Bayesian model inference is derived by exploiting conditional conjugacy via novel data augmentation techniques. Conclusion: Experimental results on both simulated data and several real-world scRNA-seq datasets suggest that hGNB is a powerful tool for cell cluster discovery as well as cell lineage inference.

stat.AP↗

arXiv2019

Optimal Clustering with Missing Values

Missing values frequently arise in modern biomedical studies due to various reasons, including missing tests or complex profiling technologies for different omics measurements. Missing values can complicate the application of clustering algorithms, whose goals are to group points based on some similarity criterion. A common practice for dealing with missing values in the context of clustering is to first impute the missing values, and then apply the clustering algorithm on the completed data. We consider missing values in the context of optimal clustering, which finds an optimal clustering operator with reference to an underlying random labeled point process (RLPP). We show how the missing-value problem fits neatly into the overall framework of optimal clustering by incorporating the missing value mechanism into the random labeled point process and then marginalizing out the missing-value process. In particular, we demonstrate the proposed framework for the Gaussian model with arbitrary covariance structures. Comprehensive experimental studies on both synthetic and real-world RNA-seq data show the superior performance of the proposed optimal clustering with missing values when compared to various clustering approaches. Optimal clustering with missing values obviates the need for imputation-based pre-processing of the data, while at the same time possessing smaller clustering errors.

stat.ML↗

arXiv2019

Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty

Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. The goal of this paper is to develop optimal classification of single-cell trajectories accounting for potential model uncertainty. Partially-observed Boolean dynamical systems (POBDS) are used for modeling gene regulatory networks observed through noisy gene-expression data. We derive the exact optimal Bayesian classifier (OBC) for binary classification of single-cell trajectories. The application of the OBC becomes impractical for large GRNs, due to computational and memory requirements. To address this, we introduce a particle-based single-cell classification method that is highly scalable for large GRNs with much lower complexity than the optimal solution. The performance of the proposed particle-based method is demonstrated through numerical experiments using a POBDS model of the well-known T-cell large granular lymphocyte (T-LGL) leukemia network with noisy time-series gene-expression data.

q-bio.GN↗

arXiv2019

Fast Exact Computation of Expected HyperVolume Improvement

In multi-objective Bayesian optimization and surrogate-based evolutionary algorithms, Expected HyperVolume Improvement (EHVI) is widely used as the acquisition function to guide the search approaching the Pareto front. This paper focuses on the exact calculation of EHVI given a nondominated set, for which the existing exact algorithms are complex and can be inefficient for problems with more than three objectives. Integrating with different decomposition algorithms, we propose a new method for calculating the integral in each decomposed high-dimensional box in constant time. We develop three new exact EHVI calculation algorithms based on three region decomposition methods. The first grid-based algorithm has a complexity of $O(m\cdot n^m)$ with $n$ denoting the size of the nondominated set and $m$ the number of objectives. The Walking Fish Group (WFG)-based algorithm has a worst-case complexity of $O(m\cdot 2^n)$ but has a better average performance. These two can be applied for problems with any $m$. The third CLM-based algorithm is only for $m=3$ and asymptotically optimal with complexity $Θ(n\log{n})$. Performance comparison results show that all our three algorithms are at least twice faster than the state-of-the-art algorithms with the same decomposition methods. When $m>3$, our WFG-based algorithm can be over $10^2$ faster than the corresponding existing algorithms. Our algorithm is demonstrated in an example involving efficient multi-objective material design with Bayesian optimization.

stat.ML↗

arXiv2019

Adaptive Activity Monitoring with Uncertainty Quantification in Switching Gaussian Process Models

Emerging wearable sensors have enabled the unprecedented ability to continuously monitor human activities for healthcare purposes. However, with so many ambient sensors collecting different measurements, it becomes important not only to maintain good monitoring accuracy, but also low power consumption to ensure sustainable monitoring. This power-efficient sensing scheme can be achieved by deciding which group of sensors to use at a given time, requiring an accurate characterization of the trade-off between sensor energy usage and the uncertainty in ignoring certain sensor signals while monitoring. To address this challenge in the context of activity monitoring, we have designed an adaptive activity monitoring framework. We first propose a switching Gaussian process to model the observed sensor signals emitting from the underlying activity states. To efficiently compute the Gaussian process model likelihood and quantify the context prediction uncertainty, we propose a block circulant embedding technique and use Fast Fourier Transforms (FFT) for inference. By computing the Bayesian loss function tailored to switching Gaussian processes, an adaptive monitoring procedure is developed to select features from available sensors that optimize the trade-off between sensor power consumption and the prediction performance quantified by state prediction entropy. We demonstrate the effectiveness of our framework on the popular benchmark of UCI Human Activity Recognition using Smartphones.

cs.LG↗

arXiv2018

Autonomous Efficient Experiment Design for Materials Discovery with Bayesian Model Averaging

The accelerated exploration of the materials space in order to identify configurations with optimal properties is an ongoing challenge. Current paradigms are typically centered around the idea of performing this exploration through high-throughput experimentation/computation. Such approaches, however, do not account fo the always present constraints in resources available. Recently, this problem has been addressed by framing materials discovery as an optimal experiment design. This work augments earlier efforts by putting forward a framework that efficiently explores the materials design space not only accounting for resource constraints but also incorporating the notion of model uncertainty. The resulting approach combines Bayesian Model Averaging within Bayesian Optimization in order to realize a system capable of autonomously and adaptively learning not only the most promising regions in the materials space but also the models that most efficiently guide such exploration. The framework is demonstrated by efficiently exploring the MAX ternary carbide/nitride space through Density Functional Theory (DFT) calculations.

physics.comp-ph↗

arXiv2018

Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data

Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Second, compared to the number of involved molecules and system complexity, the number of available samples for studying complex disease, such as cancer, is often limited, especially considering disease heterogeneity. The key question is whether we may integrate available data from all different sources or domains to achieve reproducible disease prognosis based on NGS count data. In this paper, we develop a Bayesian Multi-Domain Learning (BMDL) model that derives domain-dependent latent representations of overdispersed count data based on hierarchical negative binomial factorization for accurate cancer subtyping even if the number of samples for a specific cancer type is small. Experimental results from both our simulated and NGS datasets from The Cancer Genome Atlas (TCGA) demonstrate the promising potential of BMDL for effective multi-domain learning without "negative transfer" effects often seen in existing multi-task learning and transfer learning methods.

stat.ML↗

arXiv2018

Multi-Objective Bayesian Materials Discovery: Application on the Discovery of Precipitation Strengthened NiTi Shape Memory Alloys through Micromechanical Modeling

In this study, a framework for the multi-objective materials discovery based on Bayesian approaches is developed. The capabilities of the framework are demonstrated on an example case related to the discovery of precipitation strengthened NiTi shape memory alloys with up to three desired properties. In the presented case the framework is used to carry out an efficient search of the shape memory alloys with desired properties while minimizing the required number of computational experiments. The developed scheme features a Bayesian optimal experimental design process that operates in a closed loop. A Gaussian process regression model is utilized in the framework to emulate the response and uncertainty of the physical/computational data while the sequential exploration of the materials design space is carried out by using an optimal policy based on the expected hyper-volume improvement acquisition function. This scalar metric provides a measure of the utility of querying the materials design space at different locations, irrespective of the number of objectives in the performed task. The framework is deployed for the determination of the composition and microstructure of precipitation-strengthened NiTi shape memory alloys with desired properties, while the materials response as a function of microstructure is determined through a thermodynamically-consistent micromechanical model.

cond-mat.mtrl-sci↗

arXiv2018

Safe Active Feature Selection for Sparse Learning

We present safe active incremental feature selection~(SAIF) to scale up the computation of LASSO solutions. SAIF does not require a solution from a heavier penalty parameter as in sequential screening or updating the full model for each iteration as in dynamic screening. Different from these existing screening methods, SAIF starts from a small number of features and incrementally recruits active features and updates the significantly reduced model. Hence, it is much more computationally efficient and scalable with the number of features. More critically, SAIF has the safe guarantee as it has the convergence guarantee to the optimal solution to the original full LASSO problem. Such an incremental procedure and theoretical convergence guarantee can be extended to fused LASSO problems. Compared with state-of-the-art screening methods as well as working set and homotopy methods, which may not always guarantee the optimal solution, SAIF can achieve superior or comparable efficiency and high scalability with the safe guarantee when facing extremely high dimensional data sets. Experiments with both synthetic and real-world data sets show that SAIF can be up to 50 times faster than dynamic screening, and hundreds of times faster than computing LASSO or fused LASSO solutions without screening.

cs.LG↗

arXiv2018

Optimal Bayesian Transfer Learning

Transfer learning has recently attracted significant research attention, as it simultaneously learns from different source domains, which have plenty of labeled data, and transfers the relevant knowledge to the target domain with limited labeled data to improve the prediction performance. We propose a Bayesian transfer learning framework where the source and target domains are related through the joint prior density of the model parameters. The modeling of joint prior densities enables better understanding of the "transferability" between domains. We define a joint Wishart density for the precision matrices of the Gaussian feature-label distributions in the source and target domains to act like a bridge that transfers the useful information of the source domain to help classification in the target domain by improving the target posteriors. Using several theorems in multivariate statistics, the posteriors and posterior predictive densities are derived in closed forms with hypergeometric functions of matrix argument, leading to our novel closed-form and fast Optimal Bayesian Transfer Learning (OBTL) classifier. Experimental results on both synthetic and real-world benchmark data confirm the superb performance of the OBTL compared to the other state-of-the-art transfer learning and domain adaptation methods.

stat.ML↗