arXiv subjects

Xiaoning Qian

Publications and source records attributed to Xiaoning Qian.

At least 55 records · Page 3Linked to original sources

arXiv2023

An Interpretable Boosting-based Predictive Model for Transformation Temperatures of Shape Memory Alloys

In this study, we demonstrate how the incorporation of appropriate feature engineering together with the selection of a Machine Learning (ML) algorithm that best suits the available dataset, leads to the development of a predictive model for transformation temperatures that can be applied to a wide range of shape memory alloys. We develop a gradient boosting ML surrogate model capable of predicting Martensite Start, Martensite Finish, Austenite Start, and Austenite Finish transformation temperatures with an average accuracy of more than 95% by explicitly taking care of potential distribution changes when modeling different alloy systems. We included heat treatment, rolling, extrusion processing parameters, and alloy system categorical features in the model input features to achieve more accurate and realistic results. In addition, using Shapley values, which are calculated based on the average marginal contribution of features to all possible coalitions, this study was able to gain insights into the governing features and their effect on predicted transformation temperatures, providing a unique opportunity to examine the critical parameters and features in martensite transformation temperatures.

cond-mat.mtrl-sci↗

arXiv2023

Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response

There are various sources of ionizing radiation exposure, where medical exposure for radiation therapy or diagnosis is the most common human-made source. Understanding how gene expression is modulated after ionizing radiation exposure and investigating the presence of any dose-dependent gene expression patterns have broad implications for health risks from radiotherapy, medical radiation diagnostic procedures, as well as other environmental exposure. In this paper, we perform a comprehensive pathway-based analysis of gene expression profiles in response to low-dose radiation exposure, in order to examine the potential mechanism of gene regulation underlying such responses. To accomplish this goal, we employ a statistical framework to determine whether a specific group of genes belonging to a known pathway display coordinated expression patterns that are modulated in a manner consistent with the radiation level. Findings in our study suggest that there exist complex yet consistent signatures that reflect the molecular response to radiation exposure, which differ between low-dose and high-dose radiation.

q-bio.GN↗

arXiv2022

Optimal Decision Making in High-Throughput Virtual Screening Pipelines

The need for efficient computational screening of molecular candidates that possess desired properties frequently arises in various scientific and engineering problems, including drug discovery and materials design. However, the large size of the search space containing the candidates and the substantial computational cost of high-fidelity property prediction models makes screening practically challenging. In this work, we propose a general framework for constructing and optimizing a virtual screening (HTVS) pipeline that consists of multi-fidelity models. The central idea is to optimally allocate the computational resources to models with varying costs and accuracy to optimize the return-on-computational-investment (ROCI). Based on both simulated as well as real data, we demonstrate that the proposed optimal HTVS framework can significantly accelerate screening virtually without any degradation in terms of accuracy. Furthermore, it enables an adaptive operational strategy for HTVS, where one can trade accuracy for efficiency.

math.OC↗

arXiv2022

DynImp: Dynamic Imputation for Wearable Sensing Data Through Sensory and Temporal Relatedness

In wearable sensing applications, data is inevitable to be irregularly sampled or partially missing, which pose challenges for any downstream application. An unique aspect of wearable data is that it is time-series data and each channel can be correlated to another one, such as x, y, z axis of accelerometer. We argue that traditional methods have rarely made use of both times-series dynamics of the data as well as the relatedness of the features from different sensors. We propose a model, termed as DynImp, to handle different time point's missingness with nearest neighbors along feature axis and then feeding the data into a LSTM-based denoising autoencoder which can reconstruct missingness along the time axis. We experiment the model on the extreme missingness scenario ($>50\%$ missing rate) which has not been widely tested in wearable data. Our experiments on activity recognition show that the method can exploit the multi-modality features from related sensors and also learn from history time-series dynamics to reconstruct the data under extreme missingness.

eess.SP↗

arXiv2022

Density-Aware Personalized Training for Risk Prediction in Imbalanced Medical Data

Medical events of interest, such as mortality, often happen at a low rate in electronic medical records, as most admitted patients survive. Training models with this imbalance rate (class density discrepancy) may lead to suboptimal prediction. Traditionally this problem is addressed through ad-hoc methods such as resampling or reweighting but performance in many cases is still limited. We propose a framework for training models for this imbalance issue: 1) we first decouple the feature extraction and classification process, adjusting training batches separately for each component to mitigate bias caused by class density discrepancy; 2) we train the network with both a density-aware loss and a learnable cost matrix for misclassifications. We demonstrate our model's improved performance in real-world medical datasets (TOPCAT and MIMIC-III) to show improved AUC-ROC, AUC-PRC, Brier Skill Score compared with the baselines in the domain.

cs.LG↗

arXiv2022

Probabilistic Best Subset Selection via Gradient-Based Optimization

In high-dimensional statistics, variable selection recovers the latent sparse patterns from all possible covariate combinations. This paper proposes a novel optimization method to solve the exact L0-regularized regression problem, which is also known as the best subset selection. We reformulate the optimization problem from a discrete space to a continuous one via probabilistic reparameterization. The new objective function is differentiable but its gradient often cannot be computed in a closed form. Then we propose a family of unbiased gradient estimators to optimize the best subset selection objectives by the stochastic gradient descent. Within this family, we identify the estimator with uniformly minimum variance. Theoretically, we study the general conditions under which the method is guaranteed to converge to the ground truth in expectation. The proposed method can find the true regression model from thousands of covariates in seconds. In a wide variety of synthetic and semi-synthetic data, the proposed method outperforms existing variable selection tools based on the relaxed penalties, coordinate descent, and mixed integer optimization in both sparse pattern recovery and out-of-sample prediction.

stat.ME↗

arXiv2022

VFDS: Variational Foresight Dynamic Selection in Bayesian Neural Networks for Efficient Human Activity Recognition

In many machine learning tasks, input features with varying degrees of predictive capability are acquired at varying costs. In order to optimize the performance-cost trade-off, one would select features to observe a priori. However, given the changing context with previous observations, the subset of predictive features to select may change dynamically. Therefore, we face the challenging new problem of foresight dynamic selection (FDS): finding a dynamic and light-weight policy to decide which features to observe next, before actually observing them, for overall performance-cost trade-offs. To tackle FDS, this paper proposes a Bayesian learning framework of Variational Foresight Dynamic Selection (VFDS). VFDS learns a policy that selects the next feature subset to observe, by optimizing a variational Bayesian objective that characterizes the trade-off between model performance and feature cost. At its core is an implicit variational distribution on binary gates that are dependent on previous observations, which will select the next subset of features to observe. We apply VFDS on the Human Activity Recognition (HAR) task where the performance-cost trade-off is critical in its practice. Extensive results demonstrate that VFDS selects different features under changing contexts, notably saving sensory costs while maintaining or improving the HAR accuracy. Moreover, the features that VFDS dynamically select are shown to be interpretable and associated with the different activity types. We will release the code.

cs.LG↗

arXiv2022

MoReL: Multi-omics Relational Learning

Multi-omics data analysis has the potential to discover hidden molecular interactions, revealing potential regulatory and/or signal transduction pathways for cellular processes of interest when studying life and disease systems. One of critical challenges when dealing with real-world multi-omics data is that they may manifest heterogeneous structures and data quality as often existing data may be collected from different subjects under different conditions for each type of omics data. We propose a novel deep Bayesian generative model to efficiently infer a multi-partite graph encoding molecular interactions across such heterogeneous views, using a fused Gromov-Wasserstein (FGW) regularization between latent representations of corresponding views for integrative analysis. With such an optimal transport regularization in the deep Bayesian generative model, it not only allows incorporating view-specific side information, either with graph-structured or unstructured data in different views, but also increases the model flexibility with the distribution-based regularization. This allows efficient alignment of heterogeneous latent variable distributions to derive reliable interaction predictions compared to the existing point-based graph embedding methods. Our experiments on several real-world datasets demonstrate enhanced performance of MoReL in inferring meaningful interactions compared to existing baselines.

q-bio.QM↗

arXiv2021

COVID-Datathon: Biomarker identification for COVID-19 severity based on BALF scRNA-seq data

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emergence began in late 2019 and has since spread rapidly worldwide. The characteristics of respiratory immune response to this emerging virus is not clear. Recently, Single-cell RNA sequencing (scRNA-seq) transcriptome profiling of Bronchoalveolar lavage fluid (BALF) cells has been done to elucidate the potential mechanisms underlying in COVID-19. With the aim of better utilizing this atlas of BALF cells in response to the virus, here we propose a bioinformatics pipeline to identify candidate biomarkers of COVID-19 severity, which may help characterize BALF cells to have better mechanistic understanding of SARS-CoV-2 infection. The proposed pipeline is implemented in R and is available at https://github.com/namini94/scBALF_Hackathon.

q-bio.QM↗

arXiv2021

Adaptive Group Testing with Mismatched Models

Accurate detection of infected individuals is one of the critical steps in stopping any pandemic. When the underlying infection rate of the disease is low, testing people in groups, instead of testing each individual in the population, can be more efficient. In this work, we consider noisy adaptive group testing design with specific test sensitivity and specificity that select the optimal group given previous test results based on pre-selected utility function. As in prior studies on group testing, we model this problem as a sequential Bayesian Optimal Experimental Design (BOED) to adaptively design the groups for each test. We analyze the required number of group tests when using the updated posterior on the infection status and the corresponding Mutual Information (MI) as our utility function for selecting new groups. More importantly, we study how the potential bias on the ground-truth noise of group tests may affect the group testing sample complexity.

stat.ME↗

arXiv2021

Robust Importance Sampling for Error Estimation in the Context of Optimal Bayesian Transfer Learning

Classification has been a major task for building intelligent systems as it enables decision-making under uncertainty. Classifier design aims at building models from training data for representing feature-label distributions--either explicitly or implicitly. In many scientific or clinical settings, training data are typically limited, which makes designing accurate classifiers and evaluating their classification error extremely challenging. While transfer learning (TL) can alleviate this issue by incorporating data from relevant source domains to improve learning in a different target domain, it has received little attention for performance assessment, notably in error estimation. In this paper, we fill this gap by investigating knowledge transferability in the context of classification error estimation within a Bayesian paradigm. We introduce a novel class of Bayesian minimum mean-square error (MMSE) estimators for optimal Bayesian transfer learning (OBTL), which enables rigorous evaluation of classification error under uncertainty in a small-sample setting. Using Monte Carlo importance sampling, we employ the proposed estimator to evaluate the classification accuracy of a broad family of classifiers that span diverse learning capabilities. Experimental results based on both synthetic data as well as real-world RNA sequencing (RNA-seq) data show that our proposed OBTL error estimation scheme clearly outperforms standard error estimators, especially in a small-sample setting, by tapping into the data from other relevant domains.

stat.ML↗

arXiv2021

Quantifying the multi-objective cost of uncertainty

Various real-world applications involve modeling complex systems with immense uncertainty and optimizing multiple objectives based on the uncertain model. Quantifying the impact of the model uncertainty on the given operational objectives is critical for designing optimal experiments that can most effectively reduce the uncertainty that affect the objectives pertinent to the application at hand. In this paper, we propose the concept of mean multi-objective cost of uncertainty (multi-objective MOCU) that can be used for objective-based quantification of uncertainty for complex uncertain systems considering multiple operational objectives. We provide several illustrative examples that demonstrate the concept and strengths of the proposed multi-objective MOCU. Furthermore, we present a real-world example based on the mammalian cell cycle network to demonstrate how the multi-objective MOCU can be used for quantifying the operational impact of model uncertainty when there are multiple, possibly competing, objectives.

math.OC↗

arXiv2021

SimCD: Simultaneous Clustering and Differential expression analysis for single-cell transcriptomic data

Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better understand molecular mechanisms of different development processes. Several scRNA-seq analysis methods have been proposed to first identify cell sub-populations by clustering and then separately perform differential expression analysis to understand gene expression changes. Their corresponding statistical models and inference algorithms are often designed disjointly. We develop a new method -- SimCD -- that explicitly models cell heterogeneity and dynamic differential changes in one unified hierarchical gamma-negative binomial (hGNB) model, allowing simultaneous cell clustering and differential expression analysis for scRNA-seq data. Our method naturally defines cell heterogeneity by dynamic expression changes, which is expected to help achieve better performances on the two tasks compared to the existing methods that perform them separately. In addition, SimCD better models dropout (zero inflation) in scRNA-seq data by both cell- and gene-level factors and obviates the need for sophisticated pre-processing steps such as normalization, thanks to the direct modeling of scRNA-seq count data by the rigorous hGNB model with an efficient Gibbs sampling inference algorithm. Extensive comparisons with the state-of-the-art methods on both simulated and real-world scRNA-seq count data demonstrate the capability of SimCD to discover cell clusters and capture dynamic expression changes. Furthermore, SimCD helps identify several known genes affected by food deprivation in hypothalamic neuron cell subtypes as well as some new potential markers, suggesting the capability of SimCD for bio-marker discovery.

q-bio.GN↗

arXiv2021

Geometric Affinity Propagation for Clustering with Network Knowledge

Clustering data into meaningful subsets is a major task in scientific data analysis. To date, various strategies ranging from model-based approaches to data-driven schemes, have been devised for efficient and accurate clustering. One important class of clustering methods that is of a particular interest is the class of exemplar-based approaches. This interest primarily stems from the amount of compressed information encoded in these exemplars that effectively reflect the major characteristics of the respective clusters. Affinity propagation (AP) has proven to be a powerful exemplar-based approach that refines the set of optimal exemplars by iterative pairwise message updates. However, a critical limitation is its inability to capitalize on known networked relations between data points often available for various scientific datasets. To mitigate this shortcoming, we propose geometric-AP, a novel clustering algorithm that effectively extends AP to take advantage of the network topology. Geometric-AP obeys network constraints and uses max-sum belief propagation to leverage the available network topology for generating smooth clusters over the network. Extensive performance assessment reveals a significant enhancement in the quality of the clustering results when compared to benchmark clustering schemes. Especially, we demonstrate that geometric-AP performs extremely well even in cases where the original AP fails drastically.

cs.LG↗

arXiv2021

Contextual Dropout: An Efficient Sample-Dependent Dropout Module

Dropout has been demonstrated as a simple and effective module to not only regularize the training process of deep neural networks, but also provide the uncertainty estimation for prediction. However, the quality of uncertainty estimation is highly dependent on the dropout probabilities. Most current models use the same dropout distributions across all data samples due to its simplicity. Despite the potential gains in the flexibility of modeling uncertainty, sample-dependent dropout, on the other hand, is less explored as it often encounters scalability issues or involves non-trivial model changes. In this paper, we propose contextual dropout with an efficient structural design as a simple and scalable sample-dependent dropout module, which can be applied to a wide range of models at the expense of only slightly increased memory and computational cost. We learn the dropout probabilities with a variational objective, compatible with both Bernoulli dropout and Gaussian dropout. We apply the contextual dropout module to various models with applications to image classification and visual question answering and demonstrate the scalability of the method with large-scale datasets, such as ImageNet and VQA 2.0. Our experimental results show that the proposed method outperforms baseline methods in terms of both accuracy and quality of uncertainty estimation.

cs.LG↗

arXiv2021

Collaborative Global-Local Networks for Memory-Efficient Segmentation of Ultra-High Resolution Images

Segmentation of ultra-high resolution images is increasingly demanded, yet poses significant challenges for algorithm efficiency, in particular considering the (GPU) memory limits. Current approaches either downsample an ultra-high resolution image or crop it into small patches for separate processing. In either way, the loss of local fine details or global contextual information results in limited segmentation accuracy. We propose collaborative Global-Local Networks (GLNet) to effectively preserve both global and local information in a highly memory-efficient manner. GLNet is composed of a global branch and a local branch, taking the downsampled entire image and its cropped local patches as respective inputs. For segmentation, GLNet deeply fuses feature maps from two branches, capturing both the high-resolution fine structures from zoomed-in local patches and the contextual dependency from the downsampled input. To further resolve the potential class imbalance problem between background and foreground regions, we present a coarse-to-fine variant of GLNet, also being memory-efficient. Extensive experiments and analyses have been performed on three real-world ultra-high aerial and medical image datasets (resolution up to 30 million pixels). With only one single 1080Ti GPU and less than 2GB memory used, our GLNet yields high-quality segmentation results and achieves much more competitive accuracy-memory usage trade-offs compared to state-of-the-arts.

cs.CV↗

arXiv2020

BayReL: Bayesian Relational Learning for Multi-omics Data Integration

High-throughput molecular profiling technologies have produced high-dimensional multi-omics data, enabling systematic understanding of living systems at the genome scale. Studying molecular interactions across different data types helps reveal signal transduction mechanisms across different classes of molecules. In this paper, we develop a novel Bayesian representation learning method that infers the relational interactions across multi-omics data types. Our method, Bayesian Relational Learning (BayReL) for multi-omics data integration, takes advantage of a priori known relationships among the same class of molecules, modeled as a graph at each corresponding view, to learn view-specific latent variables as well as a multi-partite graph that encodes the interactions across views. Our experiments on several real-world datasets demonstrate enhanced performance of BayReL in inferring meaningful interactions compared to existing baselines.

cs.LG↗

arXiv2020

Bayesian Graph Neural Networks with Adaptive Connection Sampling

We propose a unified framework for adaptive connection sampling in graph neural networks (GNNs) that generalizes existing stochastic regularization methods for training GNNs. The proposed framework not only alleviates over-smoothing and over-fitting tendencies of deep GNNs, but also enables learning with uncertainty in graph analytic tasks with GNNs. Instead of using fixed sampling rates or hand-tuning them as model hyperparameters in existing stochastic regularization methods, our adaptive connection sampling can be trained jointly with GNN model parameters in both global and local fashions. GNN training with adaptive connection sampling is shown to be mathematically equivalent to an efficient approximation of training Bayesian GNNs. Experimental results with ablation studies on benchmark datasets validate that adaptively learning the sampling rate given graph training data is the key to boost the performance of GNNs in semi-supervised node classification, less prone to over-smoothing and over-fitting with more robust prediction.

cs.LG↗