BAWGNet: Boundary aware wavelet guided network for the nuclei segmentation in histopathology images.

Precise cell nucleus segmentation is very critical in many biologically related analyses and disease diagnoses. However, the variability in nuclei structure, color, and modalities of histopathology images make the automatic computer-aided nuclei segmentation task very difficult. Traditional encoder-decoder based deep learning schemes mainly utilize the spatial domain information that may limit the performance of recognizing small nuclei regions in subsequent downsampling operations. In this paper, a boundary aware wavelet guided network (BAWGNet) is proposed by incorporating a boundary aware unit along with an attention mechanism based on a wavelet domain guidance in each stage of the encoder-decoder output. Here the high-frequency 2 Dimensional discrete wavelet transform (2D-DWT) coefficients are utilized in the attention mechanism to guide the spatial information obtained from the encoder-decoder output stages to leverage the nuclei segmentation task. On the other hand, the boundary aware unit (BAU) captures the nuclei's boundary information, ensuring accurate prediction of the nuclei pixels in the edge region. Furthermore, the preprocessing steps used in our methodology confirm the data's uniformity by converting it to similar color statistics. Extensive experimentations conducted on three benchmark histopathology datasets (DSB, MoNuSeg and TNBC) exhibit the outstanding segmentation performance of the proposed method (with dice scores 90.82%, 85.74%, and 78.57%, respectively). Implementation of the proposed architecture is available at https://github.com/tamjidimtiaz/BAWGNet.

Automatic Metric Search for Few-Shot Learning.

Few-shot learning (FSL) aims to learn a model that can identify unseen classes using only a few training samples from each class. Most of the existing FSL methods adopt a manually predefined metric function to measure the relationship between a sample and a class, which usually require tremendous efforts and domain knowledge. In contrast, we propose a novel model called automatic metric search (Auto-MS), in which an Auto-MS space is designed for automatically searching task-specific metric functions. This allows us to further develop a new searching strategy to facilitate automated FSL. More specifically, by incorporating the episode-training mechanism into the bilevel search strategy, the proposed search strategy can effectively optimize the network weights and structural parameters of the few-shot model. Extensive experiments on the miniImageNet and tieredImageNet datasets demonstrate that the proposed Auto-MS achieves superior performance in FSL problems.

Privacy Enhancing Machine Learning via Removal of Unwanted Dependencies.

The rapid rise of IoT and Big Data has facilitated copious data-driven applications to enhance our quality of life. However, the omnipresent and all-encompassing nature of the data collection can generate privacy concerns. Hence, there is a strong need to develop techniques that ensure the data serve only the intended purposes, giving users control over the information they share. To this end, this article studies new variants of supervised and adversarial learning methods, which remove the sensitive information in the data before they are sent out for a particular application. The explored methods optimize privacy-preserving feature mappings and predictive models simultaneously in an end-to-end fashion. Additionally, the models are built with an emphasis on placing little computational burden on the user side so that the data can be desensitized on device in a cheap manner. Experimental results on mobile sensing and face datasets demonstrate that our models can successfully maintain the utility performances of predictive models while causing sensitive predictions to perform poorly.

Cross-Scale Residual Network: A General Framework for Image Super-Resolution, Denoising, and Deblocking.

In general, image restoration involves mapping from low-quality images to their high-quality counterparts. Such optimal mapping is usually nonlinear and learnable by machine learning. Recently, deep convolutional neural networks have proven promising for such learning processing. It is desirable for an image processing network to support well with three vital tasks, namely: 1) super-resolution; 2) denoising; and 3) deblocking. It is commonly recognized that these tasks have strong correlations, which enable us to design a general framework to support all tasks. In particular, the selection of feature scales is known to significantly impact the performance on these tasks. To this end, we propose the cross-scale residual network to exploit scale-related features among the three tasks. The proposed network can extract spatial features across different scales and establish cross-temporal feature reusage, so as to handle different tasks in a general framework. Our experiments show that the proposed approach outperforms state-of-the-art methods in both quantitative and qualitative evaluations for multiple image restoration tasks.

Exploiting Operation Importance for Differentiable Neural Architecture Search.

Recently, differentiable neural architecture search (NAS) methods have made significant progress in reducing the computational costs of NASs. Existing methods search for the best architecture by choosing candidate operations with higher architecture weights. However, architecture weights cannot accurately reflect the importance of each operation, that is, the operation with the highest weight might not be related to the best performance. To circumvent this deficiency, we propose a novel indicator that can fully represent the operation importance and, thus, serve as an effective metric to guide the model search. Based on this indicator, we further develop a NAS scheme for "exploiting operation importance for effective NAS" (EoiNAS). More precisely, we propose a high-order Markov chain-based strategy to slim the search space to further improve search efficiency and accuracy. To evaluate the effectiveness of the proposed EoiNAS, we applied our method to two tasks: image classification and semantic segmentation. Extensive experiments on both tasks provided strong evidence that our method is capable of discovering high-performance architectures while guaranteeing the requisite efficiency during searching.

Adversarial Learning for Multiscale Crowd Counting Under Complex Scenes.

In this article, a multiscale generative adversarial network (MS-GAN) is proposed for generating high-quality crowd density maps of arbitrary crowd density scenes. The task of crowd counting has many challenges, such as severe occlusions in extremely dense crowd scenes, perspective distortion, and high visual similarity between the pedestrians and background elements. To address these problems, the proposed MS-GAN combines a multiscale convolutional neural network (generator) and an adversarial network (discriminator) to generate a high-quality density map and accurately estimate the crowd count in complex crowd scenes. The multiscale generator utilizes the fusion features from multiple hierarchical layers to detect people with large-scale variation. The resulting density map produced by the multiscale generator is processed by a discriminator network trained to solve a binary classification task between a poor quality density map and real ground-truth ones. The additional adversarial loss can improve the quality of the density map, which is critical to accurately estimate the crowd counts. The experiments were conducted on multiple datasets with different crowd scenes and densities. The results showed that the proposed method provided better performance compared to current state-of-the-art methods.

CovSegNet: A Multi Encoder-Decoder Architecture for Improved Lesion Segmentation of COVID-19 Chest CT Scans.

Automatic lung lesion segmentation of chest computer tomography (CT) scans is considered a pivotal stage toward accurate diagnosis and severity measurement of COVID-19. Traditional U-shaped encoder-decoder architecture and its variants suffer from diminutions of contextual information in pooling/upsampling operations with increased semantic gaps among encoded and decoded feature maps as well as instigate vanishing gradient problems for its sequential gradient propagation that result in suboptimal performance. Moreover, operating with 3-D CT volume poses further limitations due to the exponential increase of computational complexity making the optimization difficult. In this article, an automated COVID-19 lesion segmentation scheme is proposed utilizing a highly efficient neural network architecture, namely CovSegNet, to overcome these limitations. Additionally, a two-phase training scheme is introduced where a deeper 2-D network is employed for generating region-of-interest (ROI)-enhanced CT volume followed by a shallower 3-D network for further enhancement with more contextual information without increasing computational burden. Along with the traditional vertical expansion of Unet, we have introduced horizontal expansion with multistage encoder-decoder modules for achieving optimum performance. Additionally, multiscale feature maps are integrated into the scale transition process to overcome the loss of contextual information. Moreover, a multiscale fusion module is introduced with a pyramid fusion scheme to reduce the semantic gaps between subsequent encoder/decoder modules while facilitating the parallel optimization for efficient gradient propagation. Outstanding performances have been achieved in three publicly available datasets that largely outperform other state-of-the-art approaches. The proposed scheme can be easily extended for achieving optimum segmentation performances in a wide variety of applications. Impact Statement-With lower sensitivity (60-70%), elongated testing time, and a dire shortage of testing kits, traditional RTPCR based COVID-19 diagnostic scheme heavily relies on postCT based manual inspection for further investigation. Hence, automating the process of infected lesions extraction from chestCT volumes will be major progress for faster accurate diagnosis of COVID-19. However, in challenging conditions with diffused, blurred, and varying shaped edges of COVID-19 lesions, conventional approaches fail to provide precise segmentation of lesions that can be deleterious for false estimation and loss of information. The proposed scheme incorporating an efficient neural network architecture (CovSegNet) overcomes the limitations of traditional approaches that provide significant improvement of performance (8.4% in averaged dice measurement scale) over two datasets. Therefore, this scheme can be an effective, economical tool for the physicians for faster infection analysis to greatly reduce the spread and massive death toll of this deadly virus through mass-screening.

Semi-Supervised Salient Object Detection Using a Linear Feedback Control System Model.

To overcome the challenging problems in saliency detection, we propose a novel semi-supervised classifier which makes good use of a linear feedback control system (LFCS) model by establishing a relationship between control states and salient object detection. First, we develop a boundary homogeneity model to estimate the initial saliency and background likelihoods, which are regarded as the labeled samples in our semi-supervised learning procedure. Then in order to allocate an optimized saliency value to each superpixel, we present an iterative semi-supervised learning framework which integrates multiple saliency cues and image features using an LFCS model. Via an innovative iteration method, the system gradually converges an optimized stable state, which is associating with an accurate saliency map. This paper also covers comprehensive simulation study based on public datasets, which demonstrates the superiority of the proposed approach.

Semisupervised Learning Based on a Novel Iterative Optimization Model for Saliency Detection.

In this paper, we propose a novel iterative optimization model for bottom-up saliency detection. By exploring bottom-up saliency principles and semisupervised learning approaches, we design a high-performance saliency analysis method for wide ranging scenes. The proposed algorithm consists of two stages: 1) we develop a boundary homogeneity model to characterize the general position and the contour of the salient objects and 2) we propose a novel iterative optimization model, termed gradual saliency optimization, for further performance improvement. Our main contribution falls on the second stage, where we propose an iterative framework with self-repairing mechanisms for refining saliency maps. In this framework, we further develop a more comprehensive optimization function applying a novel semisupervised learning scheme to enhance the traditional saliency measure. More elaborately, the iterative method can gradually improve the output in each iteration and finally converge to high-quality saliency maps. Based on our experiments on four different public data sets, it can be demonstrated that our approach significantly outperforms the state-of-the-art methods.

CLAss-Specific Subspace Kernel Representations and Adaptive Margin Slack Minimization for Large Scale Classification.

In kernel-based classification models, given limited computational power and storage capacity, operations over the full kernel matrix becomes prohibitive. In this paper, we propose a new supervised learning framework using kernel models for sequential data processing. The framework is based on two components that both aim at enhancing the classification capability with a subset selection scheme. The first part is a subspace projection technique in the reproducing kernel Hilbert space using a CLAss-specific Subspace Kernel representation for kernel approximation. In the second part, we propose a novel structural risk minimization algorithm called the adaptive margin slack minimization to iteratively improve the classification accuracy by an adaptive data selection. We motivate each part separately, and then integrate them into learning frameworks for large scale data. We propose two such frameworks: the memory efficient sequential processing for sequential data processing and the parallelized sequential processing for distributed computing with sequential data acquisition. We test our methods on several benchmark data sets and compared with the state-of-the-art techniques to verify the validity of the proposed techniques.

Transductive Learning for Multi-Label Protein Subchloroplast Localization Prediction.

Predicting the localization of chloroplast proteins at the sub-subcellular level is an essential yet challenging step to elucidate their functions. Most of the existing subchloroplast localization predictors are limited to predicting single-location proteins and ignore the multi-location chloroplast proteins. While recent studies have led to some multi-location chloroplast predictors, they usually perform poorly. This paper proposes an ensemble transductive learning method to tackle this multi-label classification problem. Specifically, given a protein in a dataset, its composition-based sequence information and profile-based evolutionary information are respectively extracted. These two kinds of features are respectively compared with those of other proteins in the dataset. The comparisons lead to two similarity vectors which are weighted-combined to constitute an ensemble feature vector. A transductive learning model based on the least squares and nearest neighbor algorithms is proposed to process the ensemble features. We refer to the resulting predictor to as EnTrans-Chlo. Experimental results on a stringent benchmark dataset and a novel dataset demonstrate that EnTrans-Chlo significantly outperforms state-of-the-art predictors and particularly gains more than 4% (absolute) improvement on the overall actual accuracy. For readers' convenience, EnTrans-Chlo is freely available online at http://bioinfo.eie.polyu.edu.hk/EnTransChloServer/.

FUEL-mLoc: feature-unified prediction and explanation of multi-localization of cellular proteins in multiple organisms.

Although many web-servers for predicting protein subcellular localization have been developed, they often have the following drawbacks: (i) lack of interpretability or interpreting results with heterogenous information which may confuse users; (ii) ignoring multi-location proteins and (iii) only focusing on specific organism. To tackle these problems, we present an interpretable and efficient web-server, namely FUEL-mLoc, using eature- nified prediction and xplanation of m ulti- oc alization of cellular proteins in multiple organisms. Compared to conventional localization predictors, FUEL-mLoc has the following advantages: (i) using unified features (i.e. essential GO terms) to interpret why a prediction is made; (ii) being capable of predicting both single- and multi-location proteins and (iii) being able to handle proteins of multiple organisms, including Eukaryota, Homo sapiens, Viridiplantae, Gram-positive Bacteria, Gram-negative Bacteria and Virus . Experimental results demonstrate that FUEL-mLoc outperforms state-of-the-art subcellular-localization predictors. Availability and Implementation: http://bioinfo.eie.polyu.edu.hk/FUEL-mLoc/. Contacts: shibiao.wan@princeton.edu or enmwmak@polyu.edu.hk. Supplementary information: Supplementary data are available at Bioinformatics online.

Cost-Effective Kernel Ridge Regression Implementation for Keystroke-Based Active Authentication System.

In this paper, a fast kernel ridge regression (KRR) learning algorithm is adopted with ( ) training cost for large-scale active authentication system. A truncated Gaussian radial basis function (TRBF) kernel is also implemented to provide better cost-performance tradeoff. The fast-KRR algorithm along with the TRBF kernel offers computational advantages over the traditional support vector machine (SVM) with Gaussian-RBF kernel while preserving the error rate performance. Experimental results validate the cost-effectiveness of the developed authentication system. In numbers, the fast-KRR learning model achieves an equal error rate (EER) of 1.39% with ( ) training time, while SVM with the RBF kernel shows an EER of 1.41% with ( ) training time.

Ensemble Linear Neighborhood Propagation for Predicting Subchloroplast Localization of Multi-Location Proteins.

In the postgenomic era, the number of unreviewed protein sequences is remarkably larger and grows tremendously faster than that of reviewed ones. However, existing methods for protein subchloroplast localization often ignore the information from these unlabeled proteins. This paper proposes a multi-label predictor based on ensemble linear neighborhood propagation (LNP), namely, LNP-Chlo, which leverages hybrid sequence-based feature information from both labeled and unlabeled proteins for predicting localization of both single- and multi-label chloroplast proteins. Experimental results on a stringent benchmark dataset and a novel independent dataset suggest that LNP-Chlo performs at least 6% (absolute) better than state-of-the-art predictors. This paper also demonstrates that ensemble LNP significantly outperforms LNP based on individual features. For readers' convenience, the online Web server LNP-Chlo is freely available at http://bioinfo.eie.polyu.edu.hk/LNPChloServer/ .

Benchmark data for identifying multi-functional types of membrane proteins.

Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. In this article, we provide data that are used for training and testing Mem-ADSVM (Wan et al., 2016. "Mem-ADSVM: a two-layer multi-label predictor for identifying multi-functional types of membrane proteins" [1]), a two-layer multi-label predictor for predicting multi-functional types of membrane proteins.

Mem-ADSVM: A two-layer multi-label predictor for identifying multi-functional types of membrane proteins.

Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. However, most of the existing membrane-protein predictors have the following problems: (1) they do not predict whether a given protein is a membrane protein or not; (2) they are limited to predicting membrane proteins with single-label functional types but ignore those with multi-functional types; and (3) there is still much room for improvement for their performance. To address these problems, this paper proposes a two-layer multi-label predictor, namely Mem-ADSVM, which can identify membrane proteins (Layer I) and their multi-functional types (Layer II). Specifically, given a query protein, its associated gene ontology (GO) information is retrieved by searching a compact GO-term database with its homologous accession number. Subsequently, the GO information is classified by a binary support vector machine (SVM) classifier to determine whether it is a membrane protein or not. If yes, it will be further classified by a multi-label multi-class SVM classifier equipped with an adaptive-decision (AD) scheme to determine to which functional type(s) it belongs. Experimental results show that Mem-ADSVM significantly outperforms state-of-the-art predictors in terms of identifying both membrane proteins and their multi-functional types. This paper also suggests that the two-layer prediction architecture is better than the one-layer for prediction performance. For reader׳s convenience, the Mem-ADSVM server is available online at http://bioinfo.eie.polyu.edu.hk/MemADSVMServer/.

Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins.

BACKGROUND: Predicting protein subcellular localization is indispensable for inferring protein functions. Recent studies have been focusing on predicting not only single-location proteins, but also multi-location proteins. Almost all of the high performing predictors proposed recently use gene ontology (GO) terms to construct feature vectors for classification. Despite their high performance, their prediction decisions are difficult to interpret because of the large number of GO terms involved. RESULTS: This paper proposes using sparse regressions to exploit GO information for both predicting and interpreting subcellular localization of single- and multi-location proteins. Specifically, we compared two multi-label sparse regression algorithms, namely multi-label LASSO (mLASSO) and multi-label elastic net (mEN), for large-scale predictions of protein subcellular localization. Both algorithms can yield sparse and interpretable solutions. By using the one-vs-rest strategy, mLASSO and mEN identified 87 and 429 out of more than 8,000 GO terms, respectively, which play essential roles in determining subcellular localization. More interestingly, many of the GO terms selected by mEN are from the biological process and molecular function categories, suggesting that the GO terms of these categories also play vital roles in the prediction. With these essential GO terms, not only where a protein locates can be decided, but also why it resides there can be revealed. CONCLUSIONS: Experimental results show that the output of both mEN and mLASSO are interpretable and they perform significantly better than existing state-of-the-art predictors. Moreover, mEN selects more features and performs better than mLASSO on a stringent human benchmark dataset. For readers' convenience, an online server called SpaPredictor for both mLASSO and mEN is available at http://bioinfo.eie.polyu.edu.hk/SpaPredictorServer/.

Mem-mEN: Predicting Multi-Functional Types of Membrane Proteins by Interpretable Elastic Nets.

Membrane proteins play important roles in various biological processes within organisms. Predicting the functional types of membrane proteins is indispensable to the characterization of membrane proteins. Recent studies have extended to predicting single- and multi-type membrane proteins. However, existing predictors perform poorly and more importantly, they are often lack of interpretability. To address these problems, this paper proposes an efficient predictor, namely Mem-mEN, which can produce sparse and interpretable solutions for predicting membrane proteins with single- and multi-label functional types. Given a query membrane protein, its associated gene ontology (GO) information is retrieved by searching a compact GO-term database with its homologous accession number, which is subsequently classified by a multi-label elastic net (EN) classifier. Experimental results show that Mem-mEN significantly outperforms existing state-of-the-art membrane-protein predictors. Moreover, by using Mem-mEN, 338 out of more than 7,900 GO terms are found to play more essential roles in determining the functional types. Based on these 338 essential GO terms, Mem-mEN can not only predict the functional type of a membrane protein, but also explain why it belongs to that type. For the reader's convenience, the Mem-mEN server is available online at http://bioinfo.eie.polyu.edu.hk/MemmENServer/.

mLASSO-Hum: A LASSO-based interpretable human-protein subcellular localization predictor.

Knowing the subcellular compartments of human proteins is essential to shed light on the mechanisms of a broad range of human diseases. In computational methods for protein subcellular localization, knowledge-based methods (especially gene ontology (GO) based methods) are known to perform better than sequence-based methods. However, existing GO-based predictors often lack interpretability and suffer from overfitting due to the high dimensionality of feature vectors. To address these problems, this paper proposes an interpretable multi-label predictor, namely mLASSO-Hum, which can yield sparse and interpretable solutions for large-scale prediction of human protein subcellular localization. By using the one-vs-rest LASSO-based classifiers, 87 out of more than 8000 GO terms are found to play more significant roles in determining the subcellular localization. Based on these 87 essential GO terms, we can decide not only where a protein resides within a cell, but also why it is located there. To further exploit information from the remaining GO terms, a method based on the GO hierarchical information derived from the depth distance of GO terms is proposed. Experimental results show that mLASSO-Hum performs significantly better than state-of-the-art predictors. We also found that in addition to the GO terms from the cellular component category, GO terms from the other two categories also play important roles in the final classification decisions. For readers' convenience, the mLASSO-Hum server is available online at http://bioinfo.eie.polyu.edu.hk/mLASSOHumServer/.

mPLR-Loc: an adaptive decision multi-label classifier based on penalized logistic regression for protein subcellular localization prediction.

Proteins located in appropriate cellular compartments are of paramount importance to exert their biological functions. Prediction of protein subcellular localization by computational methods is required in the post-genomic era. Recent studies have been focusing on predicting not only single-location proteins but also multi-location proteins. However, most of the existing predictors are far from effective for tackling the challenges of multi-label proteins. This article proposes an efficient multi-label predictor, namely mPLR-Loc, based on penalized logistic regression and adaptive decisions for predicting both single- and multi-location proteins. Specifically, for each query protein, mPLR-Loc exploits the information from the Gene Ontology (GO) database by using its accession number (AC) or the ACs of its homologs obtained via BLAST. The frequencies of GO occurrences are used to construct feature vectors, which are then classified by an adaptive decision-based multi-label penalized logistic regression classifier. Experimental results based on two recent stringent benchmark datasets (virus and plant) show that mPLR-Loc remarkably outperforms existing state-of-the-art multi-label predictors. In addition to being able to rapidly and accurately predict subcellular localization of single- and multi-label proteins, mPLR-Loc can also provide probabilistic confidence scores for the prediction decisions. For readers' convenience, the mPLR-Loc server is available online (http://bioinfo.eie.polyu.edu.hk/mPLRLocServer).