Information on the number and category of cervical cells is crucial for the diagnosis of cervical cancer. However, existing classification methods capable of automatically measuring this information require the training dataset to be representative, which consumes an expensive or even unaffordable human cost. We herein propose active labeling that enables us to construct a representative training dataset using a much smaller human cost for data-efficient cervical cell classification. This cost-effective method efficiently leverages the classifier's uncertainty on the unlabeled cervical cell images to accurately select images that are most beneficial to label. With a fast estimation of the uncertainty, this new algorithm exhibits its validity and effectiveness in enhancing the representative ability of the constructed training dataset. The extensive empirical results confirm its efficacy again in navigating the usage of human cost, opening the avenue for data-efficient cervical cell classification.

MOTIVATION: Antiviral peptides (AVPs) are short chains of amino acids, showing great potential as antiviral drugs. The traditional wisdom (e.g. wet experiments) for identifying the AVPs is time-consuming and laborious, while cutting-edge computational methods are less accurate to predict them. RESULTS: In this article, we propose an AVPs prediction model via biological words representation, dubbed AVPpred-BWR. Based on the fact that the secondary structures of AVPs mainly consist of α-helix and loop, we explore the biological words of 1mer (corresponding to loops) and 4mer (4 continuous residues, corresponding to α-helix). That is, the peptides sequences are decomposed into biological words, and then the concealed sequential information is represented by training the Word2Vec models. Moreover, in order to extract multi-scale features, we leverage a CNN-Transformer framework to process the embeddings of 1mer and 4mer generated by Word2Vec models. To the best of our knowledge, this is the first time to realize the word segmentation of protein primary structure sequences based on the regularity of protein secondary structure. AVPpred-BWR illustrates clear improvements over its competitors on the independent test set (e.g. improvements of 4.6% and 11.0% for AUROC and MCC, respectively, compared to UniDL4BioPep). AVAILABILITY AND IMPLEMENTATION: AVPpred-BWR is publicly available at: https://github.com/zyweizm/AVPpred-BWR or https://zenodo.org/records/14880447 (doi: 10.5281/zenodo.14880447).

Data-driven machine learning is increasingly involved in human life and industrial development due to its large-scale testing and low time cost. However, existing learning algorithms are not suitable for real-world applications with data dilemmas, such as extremely high-dimension-low-sample-size problems, non-Gaussian noise, and uncertainty. In this article, we propose a novel fuzzy multikernel subspace learning (FMKSL) to address these problems, which provides a robust multikernel representation with a fuzzy constraint and sparse coding. We then develop an adaptive learner chain optimization method based on the iterative process of FMKSL to speed up learning and achieve the best performance. Different from previous methods, we also design a flexible data augmentation method, namely generalized correntropy-based adaptive data augmentation (GC-ADA), to effectively use the$\alpha$-order statistics between samples to transform the exact value prediction task into a simpler classification one. It is important that our general framework only needs an extremely small dataset to predict the related ranking of the sample since the exact label value measured by different institutions in reality varies largely. A typical scenario is the drug screening task, i.e., the inhibitory potency prediction of the nicotinamide phosphoribosyltransferase inhibitors. Extensive experiments on nine real-world datasets (four tasks) show that our framework outperforms state-of-the-art methods in prioritizing candidate samples and chemicals for experimental research and analysis via a data-driven computational approach.

We propose a novel and effective deep learning method, called deep pattern matching, for predicting the energy consumption of complex structures, which helps designers to develop ecological solutions with minimal fabrication energy for additive manufacturing. This new method does not necessitate the real energy consumption values of complex structures for training the prediction model, substantially reducing the cost of training data collection, which can be prohibitively expensive. This novel method exploits simple structures whose real energy consumption values are far cheaper to measure, by matching the similar infill pattern of complex structures from simple structures, and then approximating the energy value of the pattern in the complex structures by the matched one in training phase. This effective algorithm is designed dynamically for allowing us to match patterns with arbitrary shapes. We evaluate our deep pattern matching algorithm on various complex structures, where the highest total energy accuracy is up to 97.3%. The extensive empirical results confirm the effectiveness and robustness of the proposed method, exhibiting a great potential to advance the real usage of deep learning models for energy consumption prediction of complex structures in ecological additive manufacturing.

Recently, federated learning has become a powerful technique for medical image classification due to its ability to utilize datasets from multiple clinical clients while satisfying privacy constraints. However, there are still some obstacles in federated learning. Firstly, most existing methods directly average the model parameters collected by medical clients on the server, ignoring the specificities of the local models. Secondly, class imbalance is a common issue in medical datasets. In this article, to handle these two challenges, we propose a novel specificity-aware federated learning framework that benefits from an Adaptive Aggregation Mechanism (AdapAM) and a Dynamic Feature Fusion Strategy (DFFS). Considering the specificity of each local model, we set the AdapAM on the server. The AdapAM utilizes reinforcement learning to adaptively weight and aggregate the parameters of local models based on their data distribution and performance feedback for obtaining the global model parameters. For the class imbalance in local datasets, we propose the DFFS to dynamically fuse the features of majority classes based on the imbalance ratio in the min-batch and collaborate the rest of features. We conduct extensive experiments on a dermoscopic dataset and a fundus image dataset. Experimental results show that our method can achieve state-of-the-art results in these two real-world medical applications.

Deep neural networks often suffer from performance inconsistency for multiorgan segmentation in medical images; some organs are segmented far worse than others. The main reason might be organs with different levels of learning difficulty for segmentation mapping, due to variations such as size, texture complexity, shape irregularity, and imaging quality. In this article, we propose a principled class-reweighting algorithm, termed dynamic loss weighting, which dynamically assigns a larger loss weight to organs if they are discriminated as more difficult to learn according to the data and network's status, for forcing the network to learn from them more to maximally promote the performance consistency. This new algorithm uses an extra autoencoder to measure the discrepancy between the segmentation network's output and the ground truth and dynamically estimates the loss weight of organs per the contribution of the organ to the new updated discrepancy. It can capture the variation in organs' learning difficult during training, and it is neither sensitive to data's property nor dependent on human priors. We evaluate this algorithm in two multiorgan segmentation tasks: abdominal organs and head-neck structures, on publicly available datasets, with positive results obtained from extensive experiments which confirm the validity and effectiveness. Source codes are available at: https://github.com/YouyiSong/Dynamic-Loss-Weighting.

Abstract Corona Virus disease 2019 (COVID‐19) has shattered people's daily lives and is spreading rapidly across the globe. Existing non‐pharmaceutical intervention solutions often require timely and precise selection of small areas of people for containment or even isolation. Although such containment has been successful in stopping or mitigating the spread of COVID‐19 in some countries, it has been criticized as inefficient or ineffective, because of the time‐delayed and sophisticated nature of the statistics on determining cases. To address these concerns, we propose a GSA‐ELM model based on a gravitational search algorithm to forecast the global number of active cases of COVID‐19. The model employs the gravitational search algorithm, which utilises the gravitational law between two particles to guide the motion of each particle to optimise the search for the global optimal solution, and utilises an extreme learning machine to address the effects of nonlinearity in the number of active cases. Extensive experiments are conducted on the statistical COVID‐19 dataset from Johns Hopkins University, the MAPE of the authors’ model is 7.79%, which corroborates the superiority of the model to state‐of‐the‐art methods.

Collecting sufficient high-quality training data for deep neural networks is often expensive or even unaffordable in medical image segmentation tasks. We thus propose to train the network by using external data that can be collected in a cheaper way, e.g., crowd-sourcing. We show that by data discernment, the network is able to mine valuable knowledge from external data, even though the data distribution is very different from that of the original (internal) data. We discern the external data by learning an importance weight for each of them, with the goal to enhance the contribution of informative external data to network updating, while suppressing the data that are 'useless' or even 'harmful'. An iterative algorithm that alternatively estimates the importance weight and updates the network is developed by formulating the data discernment as a constrained nonlinear programming problem. It estimates the importance weight according to the distribution discrepancy between the external data and the internal dataset, and imposes a constraint to drive the network to learn more effectively, compared with the network without using the external data. We evaluate the proposed algorithm on two tasks: abdominal CT image and cervical smear image segmentation, using totally 6 publicly available datasets. The effectiveness of the algorithm is demonstrated by extensive experiments. Source codes are available at: https://github.com/YouyiSong/Data-Discernment.

Detecting cells in blood smear images is of great significance for automatic diagnosis of blood diseases. However, this task is rather challenging, mainly because there are dense cells that are often overlapping, making some of the occluded boundary parts invisible. In this paper, we propose a generic and effective detection framework that exploits non-overlapping regions (NOR) for providing discriminative and confident information to compensate the intensity deficiency. In particular, we propose a feature masking (FM) to exploit the NOR mask generated from the original annotation information, which can guide the network to extract NOR features as supplementary information. Furthermore, we exploit NOR features to directly predict the NOR bounding boxes (NOR BBoxes). NOR BBoxes are combined with the original BBoxes for generating one-to-one corresponding BBox-pairs that are used for further improving the detection performance. Different from the non-maximum suppression (NMS), our proposed non-overlapping regions NMS (NOR-NMS) uses the NOR BBoxes in the BBox-pairs to calculate intersection over union (IoU) for suppressing redundant BBoxes, and consequently retains the corresponding original BBoxes, circumventing the dilemma of NMS. We conducted extensive experiments on two publicly available datasets, with positive results demonstrating the effectiveness of the proposed method against existing methods.

We study the semi-supervised learning problem, using a few labeled data and a large amount of unlabeled data to train the network, by developing a cross-patch dense contrastive learning framework, to segment cellular nuclei in histopathologic images. This task is motivated by the expensive burden on collecting labeled data for histopathologic image segmentation tasks. The key idea of our method is to align features of teacher and student networks, sampled from cross-image in both patch- and pixel-levels, for enforcing the intra-class compactness and inter-class separability of features that as we shown is helpful for extracting valuable knowledge from unlabeled data. We also design a novel optimization framework that combines consistency regularization and entropy minimization techniques, showing good property in eviction of gradient vanishing. We assess the proposed method on two publicly available datasets, and obtain positive results on extensive experiments, outperforming the state-of-the-art methods. Codes are available at https://github.com/zzw-szu/CDCL.

In this paper, we propose a cross-channel, cross-scale, and cross-stage network (C3Net) for single image super-resolution, which effectively shares the features learned from multiple channels, multiple scales, and multiple stages. Multi-scale spatial features are extracted in each stage in an encoder-decoder fashion. The channel attention is performed after each encoder to exploit the inter-channel dependencies. After that, we design a cross-stage and cross-scale feature sharing module to accelerate the feature sharing across different scales and different stages. The whole network is optimized by multiple similar stages to reduce the number of parameters. Finally, super-resolution images of multiple resolutions are reconstructed simultaneously. We evaluate the proposed network on four benchmark datasets by comparing it with eleven state-of-the-art methods. Comprehensive experiments show the proposed network outperforms state-of-the-art methods by fewer parameters. The source code is available at https://github.com/thinkerww/SR_Version.

Early diagnosis is currently the most effective way of saving the life of patients with neuropsychiatric systemic lupus erythematosus (NPSLE). However, it is rather difficult to detect this terrible disease at the early stage, due to the subtle and elusive symptomatic signals. Recent studies show that the$^{1}$H-MRS (proton magnetic resonance spectroscopy) imaging technique can capture more information reflecting the early appearance of this disease than conventional magnetic resonance imaging techniques.$^{1}$H-MRS data, however, also presents more noises that can bring serious diagnosis bias. We hence proposed a noise-immune extreme ensemble learning technique for effectively leveraging$^{1}$H-MRS data for advancing the early diagnosis of NPSLE. Our main results are that 1) by developing generalized maximum correntropy criterion in the kernel extreme learning setting, many types of non-Gaussian noises can be distinguished, and 2) weighted recursive feature elimination, using maximal information coefficient to weight feature’s importance, helps to further alleviate the bad impact of noises on the diagnosis performance. The proposed method is assessed on a publicly available dataset with 97.5% accuracy, 95.8% sensitivity and 99.9% specificity, which well demonstrates its efficacy.

We investigate vehicle density detection from traffic surveillance. This task is rather challenging, mainly due to the low-resolution of data and large-scale variance of vehicles. The main result is that by learning cross-scale features, high-quality vehicle density maps can be attainable. Our main technical contribution is a learning model, called Adaptive Cross-Scale Network (ACSNet), that can learn cross-scale features from traffic surveillance data with low-resolution and large scale variance of vehicles. ACSNet consists of 1) a series of cross-scale feature extraction blocks with dense bypassing paths for harvesting spatial information, 2) an attention block for learning from appropriate scales, and 3) a structural similarity index for learning from occlusion scenes. We assess our ACSNet on two benchmark datasets, and extensive empirical evidence shows that our ACSNet performs favor-ably against the state-of-the-art methods.

In this paper, we present a novel and effective technique for short-term traffic flow forecasting. Our main contribution is an extension of Kalman filter, such that it becomes to be able to identify the noise and then filter out it; we hence named the present technique as noise-identified Kalman filter. Our epistemological perspective is that the classic Kalman filter filters out not only the noise but also useful signals. We hence develop the Kalman filter for de-noising while preserving the useful signals by devising a cost function. By conducting extensive experiments on four benchmark data sets, the proposed technique is firmly verified to be effective for short-term traffic flow forecasting, outperforming not only the classic Kalman filter but also other frequently-used parametric and non-parametric techniques.

In [1], Baiying Lei was indicated as the corresponding author. Tianfu Wang and Baiying Lei should have been indicated as the corresponding authors.

We present a novel approach for segmenting overlapping cytoplasm of cells in cervical smear images by leveraging the adaptive shape priors extracted from cytoplasm's contour fragments and shape statistics. The main challenge of this task is that many occluded boundaries in cytoplasm clumps are extremely difficult to be identified and, sometimes, even visually indistinguishable. Given a clump where multiple cytoplasms overlap, our method starts by cutting its contour into a set of contour fragments. We then locate the corresponding contour fragments of each cytoplasm by a grouping process. For each cytoplasm, according to the grouped fragments and a set of known shape references, we construct its shape and, then, connect the fragments to form a closed contour as the segmentation result, which is explicitly constrained by the constructed shape. We further integrate the intensity and curvature information, which is complementary to the shape priors extracted from contour fragments, into our framework to improve the segmentation accuracy. We propose to iteratively conduct fragments grouping, shape constructing, and fragments connecting for progressively refining the shape priors and improving the segmentation results. We extensively evaluate the effectiveness of our method on two typical cervical smear datasets. The experimental results demonstrate that our approach is highly effective and consistently outperforms the state-of-the-art approaches. The proposed method is general enough to be applied to other similar microscopic image segmentation tasks, where heavily overlapped objects exist.

We present a novel method for automated segmentation of overlapping cytoplasm in cervical smear images based on contour fragments. We formulate the segmentation problem as a graphical model, and employ the contour fragments generated from cytoplasm clump to construct the graph. Compared with traditional methods that are based on pixels, our contour fragment-based solution can take more geometric information into account and hence generate more accurate prediction of the overlapping boundaries. We further design a novel energy function for the graph, and by minimizing the energy function, fragments that come from the same cytoplasm are selected into the same set. To construct the energy function, our fragments-based data term and pairwise term are measured from the spatial relation and shape prior, which offer more geometric information for the occluded boundary inference. Afterwards, occluded boundaries are inferred using the minimal path model, in which shape of each individual cytoplasm is reconstructed on the selected fragments set. Constructed shape is used as a constraint to locate the searching area, and curvature regulation is enforced to promote the smoothness of inference result. The inference result, in turn, is used as the shape prior to construct a high-level shape regulation energy term of the built graph, and then graph energy is updated. In other words, fragments selection and occluded boundary inference are iterative processed; this interaction makes more potential shape information accessible. Using two cervical smear datasets, the performance of our method is extensively evaluated and compared with that of the state-of-the-art approaches; the results show the superiority of the proposed method.

Quantitative analysis of bacterial morphotypes in the microscope images plays a vital role in diagnosis of bacterial vaginosis (BV) based on the Nugent score criterion. However, there are two main challenges for this task: 1) It is quite difficult to identify the bacterial regions due to various appearance, faint boundaries, heterogeneous shapes, low contrast with the background, and small bacteria sizes with regards to the image. 2) There are numerous bacteria overlapping each other, which hinder us to conduct accurate analysis on individual bacterium. To overcome these challenges, we propose an automatic method in this paper to diagnose BV by quantitative analysis of bacterial morphotypes, which consists of a three-step approach, i.e., bacteria regions segmentation, overlapping bacteria splitting, and bacterial morphotypes classification. Specifically, we first segment the bacteria regions via saliency cut, which simultaneously evaluates the global contrast and spatial weighted coherence. And then Markov random field model is applied for high-quality unsupervised segmentation of small object. We then decompose overlapping bacteria clumps into markers, and associate a pixel with markers to identify evidence for eventual individual bacterium splitting. Next, we extract morphotype features from each bacterium to learn the descriptors and to characterize the types of bacteria using an Adaptive Boosting machine learning framework. Finally, BV diagnosis is implemented based on the Nugent score criterion. Experiments demonstrate that our proposed method achieves high accuracy and efficiency in computation for BV diagnosis.

Accurate segmentation of cervical cells in Pap smear images is an important step in automatic pre-cancer identification in the uterine cervix. One of the major segmentation challenges is overlapping of cytoplasm, which has not been well-addressed in previous studies. To tackle the overlapping issue, this paper proposes a learning-based method with robust shape priors to segment individual cell in Pap smear images to support automatic monitoring of changes in cells, which is a vital prerequisite of early detection of cervical cancer. We define this splitting problem as a discrete labeling task for multiple cells with a suitable cost function. The labeling results are then fed into our dynamic multi-template deformation model for further boundary refinement. Multi-scale deep convolutional networks are adopted to learn the diverse cell appearance features. We also incorporated high-level shape information to guide segmentation where cell boundary might be weak or lost due to cell overlapping. An evaluation carried out using two different datasets demonstrates the superiority of our proposed method over the state-of-the-art methods in terms of segmentation accuracy.