scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics.

Single-cell RNA sequencing has achieved massive success in biological research fields. Discovering novel cell types from single-cell transcriptomics has been demonstrated to be essential in the field of biomedicine, yet is time-consuming and needs prior knowledge. With the unprecedented boom in cell atlases, auto-annotation tools have become more prevalent due to their speed, accuracy and user-friendly features. However, existing tools have mostly focused on general cell-type annotation and have not adequately addressed the challenge of discovering novel rare cell types. In this work, we introduce scNovel, a powerful deep learning-based neural network that specifically focuses on novel rare cell discovery. By testing our model on diverse datasets with different scales, protocols and degrees of imbalance, we demonstrate that scNovel significantly outperforms previous state-of-the-art novel cell detection models, reaching the most AUROC performance(the only one method whose averaged AUROC results are above 94%, up to 16.26% more comparing to the second-best method). We validate scNovel's performance on a million-scale dataset to illustrate the scalability of scNovel further. Applying scNovel on a clinical COVID-19 dataset, three potential novel subtypes of Macrophages are identified, where the COVID-related differential genes are also detected to have consistent expression patterns through deeper analysis. We believe that our proposed pipeline will be an important tool for high-throughput clinical data in a wide range of applications.

MECCH: Metapath Context Convolution-based Heterogeneous Graph Neural Networks.

Heterogeneous graph neural networks (HGNNs) were proposed for representation learning on structural data with multiple types of nodes and edges. To deal with the performance degradation issue when HGNNs become deep, researchers combine metapaths into HGNNs to associate nodes closely related in semantics but far apart in the graph. However, existing metapath-based models suffer from either information loss or high computation costs. To address these problems, we present a novel Metapath Context Convolution-based Heterogeneous Graph Neural Network (MECCH). MECCH leverages metapath contexts, a new kind of graph structure that facilitates lossless node information aggregation while avoiding any redundancy. Specifically, MECCH applies three novel components after feature preprocessing to extract comprehensive information from the input graph efficiently: (1) metapath context construction, (2) metapath context encoder, and (3) convolutional metapath fusion. Experiments on five real-world heterogeneous graph datasets for node classification and link prediction show that MECCH achieves superior prediction accuracy compared with state-of-the-art baselines with improved computational efficiency. The code is available at https://github.com/cynricfu/MECCH.

Graph-Based Semi-Supervised Learning: A Comprehensive Review.

Semi-supervised learning (SSL) has tremendous value in practice due to the utilization of both labeled and unlabelled data. An essential class of SSL methods, referred to as graph-based semi-supervised learning (GSSL) methods in the literature, is to first represent each sample as a node in an affinity graph, and then, the label information of unlabeled samples can be inferred based on the structure of the constructed graph. GSSL methods have demonstrated their advantages in various domains due to their uniqueness of structure, the universality of applications, and their scalability to large-scale data. Focusing on GSSL methods only, this work aims to provide both researchers and practitioners with a solid and systematic understanding of relevant advances as well as the underlying connections among them. The concentration on one class of SSL makes this article distinct from recent surveys that cover a more general and broader picture of SSL methods yet often neglect the fundamental understanding of GSSL methods. In particular, a significant contribution of this article lies in a newly generalized taxonomy for GSSL under the unified framework, with the most up-to-date references and valuable resources such as codes, datasets, and applications. Furthermore, we present several potential research directions as future work with our insights into this rapidly growing field.

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.

We present a novel self-supervised Contrastive LEArning framework for single-cell ribonucleic acid (RNA)-sequencing (CLEAR) data representation and the downstream analysis. Compared with current methods, CLEAR overcomes the heterogeneity of the experimental data with a specifically designed representation learning task and thus can handle batch effects and dropout events simultaneously. It achieves superior performance on a broad range of fundamental tasks, including clustering, visualization, dropout correction, batch effect removal, and pseudo-time inference. The proposed method successfully identifies and illustrates inflammatory-related mechanisms in a COVID-19 disease study with 43 695 single cells from peripheral blood mononuclear cells.

Single Cell Self-Paced Clustering with Transcriptome Sequencing Data.

Single cell RNA sequencing (scRNA-seq) allows researchers to explore tissue heterogeneity, distinguish unusual cell identities, and find novel cellular subtypes by providing transcriptome profiling for individual cells. Clustering analysis is usually used to predict cell class assignments and infer cell identities. However, the performance of existing single-cell clustering methods is extremely sensitive to the presence of noise data and outliers. Existing clustering algorithms can easily fall into local optimal solutions. There is still no consensus on the best performing method. To address this issue, we introduce a single cell self-paced clustering (scSPaC) method with F-norm based nonnegative matrix factorization (NMF) for scRNA-seq data and a sparse single cell self-paced clustering (sscSPaC) method with l21-norm based nonnegative matrix factorization for scRNA-seq data. We gradually add single cells from simple to complex to our model until all cells are selected. In this way, the influences of noisy data and outliers can be significantly reduced. The proposed method achieved the best performance on both simulation data and real scRNA-seq data. A case study about human clara cells and ependymal cells scRNA-seq data clustering shows that scSPaC is more advantageous near the clustering dividing line.

Learning by Distillation: A Self-Supervised Learning Framework for Optical Flow Estimation.

We present DistillFlow, a knowledge distillation approach to learning optical flow. DistillFlow trains multiple teacher models and a student model, where challenging transformations are applied to the input of the student model to generate hallucinated occlusions as well as less confident predictions. Then, a self-supervised learning framework is constructed: confident predictions from teacher models are served as annotations to guide the student model to learn optical flow for those less confident predictions. The self-supervised learning framework enables us to effectively learn optical flow from unlabeled data, not only for non-occluded pixels, but also for occluded pixels. DistillFlow achieves state-of-the-art unsupervised learning performance on both KITTI and Sintel datasets. Our self-supervised pre-trained model also provides an excellent initialization for supervised fine-tuning, suggesting an alternate training paradigm in contrast to current supervised learning methods that highly rely on pre-training on synthetic data. At the time of writing, our fine-tuned models ranked 1st among all monocular methods on the KITTI 2015 benchmark, and outperform all published methods on the Sintel Final benchmark. More importantly, we demonstrate the generalization capability of DistillFlow in three aspects: framework generalization, correspondence generalization and cross-dataset generalization. Our code and models will be available on https://github.com/ppliuboy/DistillFlow.

Characterising frailty, metrics of continuous glucose monitoring, and mortality hazards in older adults with type 2 diabetes on insulin therapy (HARE): a prospective, observational cohort study.

BACKGROUND: To our knowledge, no previous study has examined the inter-relationship between frailty, dysglycaemia, and mortality in frail older adults with type 2 diabetes who are on insulin therapy. We used continuous glucose monitors (CGMs) to profile this patient population and determine the prognostic value of CGM metrics. We hypothesised that incremental frailty was associated with increased hypoglycaemia or time below range (TBR). METHODS: HARE was a multicentre, prospective, observational cohort study with mortality hazard analysis carried out in four hospitals in Hong Kong. Eligible participants were community-living adults aged 70 years and older; had had type 2 diabetes for 5 years or more; were on insulin therapy; were frail; and were not hospitalised at the time of frailty assessment and CGM recording. Glucose control was characterised according to the Advanced Technologies and Treatments for Diabetes 2019 international consensus clinical targets. Frailty index was computed, and comprehensive frailty assessments and targeted serum metabolic profiling were performed. The Jonckheere-Terpstra test for trend was used to analyse frailty index tertiles and variables. Inter-relationships between CGM metrics and frailty, glycated haemoglobin A1c (HbA1c), and serum albumin were characterised using adjusted regression models. Survival analysis and Cox proportional hazard modelling were performed. FINDINGS: Between July 25, 2018, and Sept 27, 2019, 225 participants were recruited, 222 of whom had CGMs fitted and 215 of whom had analysable CGM data (190 were frail, 25 were not frail). Incremental frailty was associated with older age, greater HbA1c, worse renal function, and history of stroke. Eight of 11 CGM metrics were significantly associated with frailty. Decreased time in range (TIR; glucose concentration 3·9-10·0 mmol/L) and increased time above range (TAR) metrics were strongly correlated with increased frailty and hyperglycaemia, whereas TBR metrics were marginally or not different between frailty levels. Glucose-lowering agents did not significantly affect regression estimates. In patients with HbA1c of 7·5% or more, reduced serum albumin was associated with level 2 TAR (glucose concentration >13·9 mmol/L) and dysglycaemia. During a median follow-up of 28·0 months (IQR 25·3-30·4), increased level 2 TAR was predictive of mortality explainable by frailty in the absence of detectable interaction. Each 1% increment of level 2 TAR was associated with 1·9% increase in mortality hazard. INTERPRETATION: In older adults with type 2 diabetes who are on insulin therapy, incremental frailty was associated with increased dysglycaemia and hyperglycaemia rather than hypoglycaemia. Mortality hazard was increased with severe hyperglycaemia. Future clinical studies and trials targeting actionable CGM metrics highlighted in this study could translate into improved care and outcomes. FUNDING: Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region of China.

Effective Data-Aware Covariance Estimator From Compressed Data.

Estimating covariance matrix from massive high-dimensional and distributed data is significant for various real-world applications. In this paper, we propose a data-aware weighted sampling-based covariance matrix estimator, namely DACE, which can provide an unbiased covariance matrix estimation and attain more accurate estimation under the same compression ratio. Moreover, we extend our proposed DACE to tackle multiclass classification problems with theoretical justification and conduct extensive experiments on both synthetic and real-world data sets to demonstrate the superior performance of our DACE.

Online Nonlinear AUC Maximization for Imbalanced Data Sets.

Classifying binary imbalanced streaming data is a significant task in both machine learning and data mining. Previously, online area under the receiver operating characteristic (ROC) curve (AUC) maximization has been proposed to seek a linear classifier. However, it is not well suited for handling nonlinearity and heterogeneity of the data. In this paper, we propose the kernelized online imbalanced learning (KOIL) algorithm, which produces a nonlinear classifier for the data by maximizing the AUC score while minimizing a functional regularizer. We address four major challenges that arise from our approach. First, to control the number of support vectors without sacrificing the model performance, we introduce two buffers with fixed budgets to capture the global information on the decision boundary by storing the corresponding learned support vectors. Second, to restrict the fluctuation of the learned decision function and achieve smooth updating, we confine the influence on a new support vector to its -nearest opposite support vectors. Third, to avoid information loss, we propose an effective compensation scheme after the replacement is conducted when either buffer is full. With such a compensation scheme, the performance of the learned model is comparable to the one learned with infinite budgets. Fourth, to determine good kernels for data similarity representation, we exploit the multiple kernel learning framework to automatically learn a set of kernels. Extensive experiments on both synthetic and real-world benchmark data sets demonstrate the efficacy of our proposed approach.

Budget constrained non-monotonic feature selection.

Feature selection is an important problem in machine learning and data mining. We consider the problem of selecting features under the budget constraint on the feature subset size. Traditional feature selection methods suffer from the "monotonic" property. That is, if a feature is selected when the number of specified features is set, it will always be chosen when the number of specified feature is larger than the previous setting. This sacrifices the effectiveness of the non-monotonic feature selection methods. Hence, in this paper, we develop an algorithm for non-monotonic feature selection that approximates the related combinatorial optimization problem by a Multiple Kernel Learning (MKL) problem. We justify the performance guarantee for the derived solution when compared to the global optimal solution for the related combinatorial optimization problem. Finally, we conduct a series of empirical evaluation on both synthetic and real-world benchmark datasets for the classification and regression tasks to demonstrate the promising performance of the proposed framework compared with the baseline feature selection approaches.

Maximum margin semi-supervised learning with irrelevant data.

Semi-supervised learning (SSL) is a typical learning paradigms training a model from both labeled and unlabeled data. The traditional SSL models usually assume unlabeled data are relevant to the labeled data, i.e., following the same distributions of the targeted labeled data. In this paper, we address a different, yet formidable scenario in semi-supervised classification, where the unlabeled data may contain irrelevant data to the labeled data. To tackle this problem, we develop a maximum margin model, named tri-class support vector machine (3C-SVM), to utilize the available training data, while seeking a hyperplane for separating the targeted data well. Our 3C-SVM exhibits several characteristics and advantages. First, it does not need any prior knowledge and explicit assumption on the data relatedness. On the contrary, it can relieve the effect of irrelevant unlabeled data based on the logistic principle and maximum entropy principle. That is, 3C-SVM approaches an ideal classifier. This classifier relies heavily on labeled data and is confident on the relevant data lying far away from the decision hyperplane, while maximally ignoring the irrelevant data, which are hardly distinguished. Second, theoretical analysis is provided to prove that in what condition, the irrelevant data can help to seek the hyperplane. Third, 3C-SVM is a generalized model that unifies several popular maximum margin models, including standard SVMs, Semi-supervised SVMs (S(3)VMs), and SVMs learned from the universum (U-SVMs) as its special cases. More importantly, we deploy a concave-convex produce to solve the proposed 3C-SVM, transforming the original mixed integer programming, to a semi-definite programming relaxation, and finally to a sequence of quadratic programming subproblems, which yields the same worst case time complexity as that of S(3)VMs. Finally, we demonstrate the effectiveness and efficiency of our proposed 3C-SVM through systematical experimental comparisons.

Enhanced models for expertise retrieval using community-aware strategies.

Expertise retrieval, whose task is to suggest people with relevant expertise on the topic of interest, has received increasing interest in recent years. One of the issues is that previous algorithms mainly consider the documents associated with the experts while ignoring the community information that is affiliated with the documents and the experts. Motivated by the observation that communities could provide valuable insight and distinctive information, we investigate and develop two community-aware strategies to enhance expertise retrieval. We first propose a new smoothing method using the community context for statistical language modeling, which is employed to identify the most relevant documents so as to boost the performance of expertise retrieval in the document-based model. Furthermore, we propose a query-sensitive AuthorRank to model the authors' authorities based on the community coauthorship networks and develop an adaptive ranking refinement method to enhance expertise retrieval. Experimental results demonstrate the effectiveness and robustness of both community-aware strategies. Moreover, the improvements made in the enhanced models are significant and consistent.

Efficient sparse generalized multiple kernel learning.

Kernel methods have been successfully applied in various applications. To succeed in these applications, it is crucial to learn a good kernel representation, whose objective is to reveal the data similarity precisely. In this paper, we address the problem of multiple kernel learning (MKL), searching for the optimal kernel combination weights through maximizing a generalized performance measure. Most MKL methods employ the L(1)-norm simplex constraints on the kernel combination weights, which therefore involve a sparse but non-smooth solution for the kernel weights. Despite the success of their efficiency, they tend to discard informative complementary or orthogonal base kernels and yield degenerated generalization performance. Alternatively, imposing the L(p)-norm (p > 1) constraint on the kernel weights will keep all the information in the base kernels. This leads to non-sparse solutions and brings the risk of being sensitive to noise and incorporating redundant information. To tackle these problems, we propose a generalized MKL (GMKL) model by introducing an elastic-net-type constraint on the kernel weights. More specifically, it is an MKL model with a constraint on a linear combination of the L(1)-norm and the squared L(2)-norm on the kernel weights to seek the optimal kernel combination weights. Therefore, previous MKL problems based on the L(1)-norm or the L(2)-norm constraints can be regarded as special cases. Furthermore, our GMKL enjoys the favorable sparsity property on the solution and also facilitates the grouping effect. Moreover, the optimization of our GMKL is a convex optimization problem, where a local solution is the global optimal solution. We further derive a level method to efficiently solve the optimization problem. A series of experiments on both synthetic and real-world datasets have been conducted to show the effectiveness and efficiency of our GMKL.

Discriminative semi-supervised feature selection via manifold regularization.

Feature selection has attracted a huge amount of interest in both research and application communities of data mining. We consider the problem of semi-supervised feature selection, where we are given a small amount of labeled examples and a large amount of unlabeled examples. Since a small number of labeled samples are usually insufficient for identifying the relevant features, the critical problem arising from semi-supervised feature selection is how to take advantage of the information underneath the unlabeled data. To address this problem, we propose a novel discriminative semi-supervised feature selection method based on the idea of manifold regularization. The proposed approach selects features through maximizing the classification margin between different classes and simultaneously exploiting the geometry of the probability distribution that generates both labeled and unlabeled data. In comparison with previous semi-supervised feature selection algorithms, our proposed semi-supervised feature selection method is an embedded feature selection method and is able to find more discriminative features. We formulate the proposed feature selection method into a convex-concave optimization problem, where the saddle point corresponds to the optimal solution. To find the optimal solution, the level method, a fairly recent optimization method, is employed. We also present a theoretic proof of the convergence rate for the application of the level method to our problem. Empirical evaluation on several benchmark data sets demonstrates the effectiveness of the proposed semi-supervised feature selection method.

Arbitrary norm support vector machines.

Support vector machines (SVM) are state-of-the-art classifiers. Typically L2-norm or L1-norm is adopted as a regularization term in SVMs, while other norm-based SVMs, for example, the L0-norm SVM or even the L(infinity)-norm SVM, are rarely seen in the literature. The major reason is that L0-norm describes a discontinuous and nonconvex term, leading to a combinatorially NP-hard optimization problem. In this letter, motivated by Bayesian learning, we propose a novel framework that can implement arbitrary norm-based SVMs in polynomial time. One significant feature of this framework is that only a sequence of sequential minimal optimization problems needs to be solved, thus making it practical in many real applications. The proposed framework is important in the sense that Bayesian priors can be efficiently plugged into most learning methods without knowing the explicit form. Hence, this builds a connection between Bayesian learning and the kernel machines. We derive the theoretical framework, demonstrate how our approach works on the L0-norm SVM as a typical example, and perform a series of experiments to validate its advantages. Experimental results on nine benchmark data sets are very encouraging. The implemented L0-norm is competitive with or even better than the standard L2-norm SVM in terms of accuracy but with a reduced number of support vectors, -9.46% of the number on average. When compared with another sparse model, the relevance vector machine, our proposed algorithm also demonstrates better sparse properties with a training speed over seven times faster.

A novel kernel-based maximum a posteriori classification method.

Kernel methods have been widely used in pattern recognition. Many kernel classifiers such as Support Vector Machines (SVM) assume that data can be separated by a hyperplane in the kernel-induced feature space. These methods do not consider the data distribution and are difficult to output the probabilities or confidences for classification. This paper proposes a novel Kernel-based Maximum A Posteriori (KMAP) classification method, which makes a Gaussian distribution assumption instead of a linear separable assumption in the feature space. Robust methods are further proposed to estimate the probability densities, and the kernel trick is utilized to calculate our model. The model is theoretically and empirically important in the sense that: (1) it presents a more generalized classification model than other kernel-based algorithms, e.g., Kernel Fisher Discriminant Analysis (KFDA); (2) it can output probability or confidence for classification, therefore providing potential for reasoning under uncertainty; and (3) multi-way classification is as straightforward as binary classification in this model, because only probability calculation is involved and no one-against-one or one-against-others voting is needed. Moreover, we conduct an extensive experimental comparison with state-of-the-art classification methods, such as SVM and KFDA, on both eight UCI benchmark data sets and three face data sets. The results demonstrate that KMAP achieves very promising performance against other models.

A volume-based heat-diffusion classifier.

Heat-diffusion models have been successfully applied to various domains such as classification and dimensionality-reduction tasks in manifold learning. One critical local approximation technique is employed to weigh the edges in the graph constructed from data points. This approximation technique is based on an implicit assumption that the data are distributed evenly. However, this assumption is not valid in most cases, so the approximation is not accurate in these cases. To solve this challenging problem, we propose a volume-based heat-diffusion model (VHDM). In VHDM, the volume is theoretically justified by handling the input data that are unevenly distributed on an unknown manifold. We also propose a novel volume-based heat-diffusion classifier (VHDC) based on VHDM. One of the advantages of VHDC is that the computational complexity is linear on the number of edges given a constructed graph. Moreover, we give an analysis on the stability of VHDC with respect to its three free parameters, and we demonstrate the connection between VHDC and some other classifiers. Experiments show that VHDC performs better than Parzen window approach, K nearest neighbor, and the HDC without volumes in prediction accuracy and outperforms some recently proposed transductive-learning algorithms. The enhanced performance of VHDC shows the validity of introducing the volume. The experiments also confirm the stability of VHDC with respect to its three free parameters.

Robust BMPM training based on second-order cone programming and its application in medical diagnosis.

The Biased Minimax Probability Machine (BMPM) constructs a classifier which deals with the imbalanced learning tasks. It provides a worst-case bound on the probability of misclassification of future data points based on reliable estimates of means and covariance matrices of the classes from the training data samples, and achieves promising performance. In this paper, we develop a novel yet critical extension training algorithm for BMPM that is based on Second-Order Cone Programming (SOCP). Moreover, we apply the biased classification model to medical diagnosis problems to demonstrate its usefulness. By removing some crucial assumptions in the original solution to this model, we make the new method more accurate and robust. We outline the theoretical derivatives of the biased classification model, and reformulate it into an SOCP problem which could be efficiently solved with global optima guarantee. We evaluate our proposed SOCP-based BMPM (BMPMSOCP) scheme in comparison with traditional solutions on medical diagnosis tasks where the objectives are to focus on improving the sensitivity (the accuracy of the more important class, say "ill" samples) instead of the overall accuracy of the classification. Empirical results have shown that our method is more effective and robust to handle imbalanced classification problems than traditional classification approaches, and the original Fractional Programming-based BMPM (BMPMFP).

Imbalanced learning with a biased minimax probability machine.

Imbalanced learning is a challenged task in machine learning. In this context, the data associated with one class are far fewer than those associated with the other class. Traditional machine learning methods seeking classification accuracy over a full range of instances are not suitable to deal with this problem, since they tend to classify all the data into a majority class, usually the less important class. In this correspondence, the authors describe a new approach named the biased minimax probability machine (BMPM) to deal with the problem of imbalanced learning. This BMPM model is demonstrated to provide an elegant and systematic way for imbalanced learning. More specifically, by controlling the accuracy of the majority class under all possible choices of class-conditional densities with a given mean and covariance matrix, this model can quantitatively and systematically incorporate a bias for the minority class. By establishing an explicit connection between the classification accuracy and the bias, this approach distinguishes itself from the many current imbalanced-learning methods; these methods often impose a certain bias on the minority data by adapting intermediate factors via the trial-and-error procedure. The authors detail the theoretical foundation, prove its solvability, propose an efficient optimization algorithm, and perform a series of experiments to evaluate the novel model. The comparison with other competitive methods demonstrates the effectiveness of this new model.

Maximizing sensitivity in medical diagnosis using biased minimax probability machine.

The challenging task of medical diagnosis based on machine learning techniques requires an inherent bias, i.e., the diagnosis should favor the "ill" class over the "healthy" class, since misdiagnosing a patient as a healthy person may delay the therapy and aggravate the illness. Therefore, the objective in this task is not to improve the overall accuracy of the classification, but to focus on improving the sensitivity (the accuracy of the "ill" class) while maintaining an acceptable specificity (the accuracy of the "healthy" class). Some current methods adopt roundabout ways to impose a certain bias toward the important class, i.e., they try to utilize some intermediate factors to influence the classification. However, it remains uncertain whether these methods can improve the classification performance systematically. In this paper, by engaging a novel learning tool, the biased minimax probability machine (BMPM), we deal with the issue in a more elegant way and directly achieve the objective of appropriate medical diagnosis. More specifically, the BMPM directly controls the worst case accuracies to incorporate a bias toward the "ill" class. Moreover, in a distribution-free way, the BMPM derives the decision rule in such a way as to maximize the worst case sensitivity while maintaining an acceptable worst case specificity. By directly controlling the accuracies, the BMPM provides a more rigorous way to handle medical diagnosis; by deriving a distribution-free decision rule, the BMPM distinguishes itself from a large family of classifiers, namely, the generative classifiers, where an assumption on the data distribution is necessary. We evaluate the performance of the model and compare it with three traditional classifiers: the k-nearest neighbor, the naive Bayesian, and the C4.5. The test results on two medical datasets, the breast-cancer dataset and the heart disease dataset, show that the BMPM outperforms the other three models.