Identification of important gene signatures in schizophrenia through feature fusion and genetic algorithm.

Schizophrenia is a debilitating psychiatric disorder that can significantly affect a patient's quality of life and lead to permanent brain damage. Although medical research has identified certain genetic risk factors, the specific pathogenesis of the disorder remains unclear. Despite the prevalence of research employing magnetic resonance imaging, few studies have focused on the gene level and gene expression profile involving a large number of screened genes. However, the high dimensionality of genetic data presents a great challenge to accurately modeling the data. To tackle the current challenges, this study presents a novel feature selection strategy that utilizes heuristic feature fusion and a multi-objective optimization genetic algorithm. The goal is to improve classification performance and identify the key gene subset for schizophrenia diagnostics. Traditional gene screening techniques are inadequate for accurately determining the precise number of key genes associated with schizophrenia. Our innovative approach integrates a filter-based feature selection method to reduce data dimensionality and a multi-objective optimization genetic algorithm for improved classification tasks. By combining the filtering and wrapper methods, our strategy leverages their respective strengths in a deliberate manner, leading to superior classification accuracy and a more efficient selection of relevant genes. This approach has demonstrated significant improvements in classification results across 11 out of 14 relevant datasets. The performance on the remaining three datasets is comparable to the existing methods. Furthermore, visual and enrichment analyses have confirmed the practicality of our proposed method as a promising tool for the early detection of schizophrenia.

Static Memory Deduplication for Performance Optimization in Cloud Computing.

In a cloud computing environment, the number of virtual machines (VMs) on a single physical server and the number of applications running on each VM are continuously growing. This has led to an enormous increase in the demand of memory capacity and subsequent increase in the energy consumption in the cloud. Lack of enough memory has become a major bottleneck for scalability and performance of virtualization interfaces in cloud computing. To address this problem, memory deduplication techniques which reduce memory demand through page sharing are being adopted. However, such techniques suffer from overheads in terms of number of online comparisons required for the memory deduplication. In this paper, we propose a static memory deduplication (SMD) technique which can reduce memory capacity requirement and provide performance optimization in cloud computing. The main innovation of SMD is that the process of page detection is performed offline, thus potentially reducing the performance cost, especially in terms of response time. In SMD, page comparisons are restricted to the code segment, which has the highest shared content. Our experimental results show that SMD efficiently reduces memory capacity requirement and improves performance. We demonstrate that, compared to other approaches, the cost in terms of the response time is negligible.

An Efficient Virtual Machine Consolidation Scheme for Multimedia Cloud Computing.

Cloud computing has innovated the IT industry in recent years, as it can delivery subscription-based services to users in the pay-as-you-go model. Meanwhile, multimedia cloud computing is emerging based on cloud computing to provide a variety of media services on the Internet. However, with the growing popularity of multimedia cloud computing, its large energy consumption cannot only contribute to greenhouse gas emissions, but also result in the rising of cloud users' costs. Therefore, the multimedia cloud providers should try to minimize its energy consumption as much as possible while satisfying the consumers' resource requirements and guaranteeing quality of service (QoS). In this paper, we have proposed a remaining utilization-aware (RUA) algorithm for virtual machine (VM) placement, and a power-aware algorithm (PA) is proposed to find proper hosts to shut down for energy saving. These two algorithms have been combined and applied to cloud data centers for completing the process of VM consolidation. Simulation results have shown that there exists a trade-off between the cloud data center's energy consumption and service-level agreement (SLA) violations. Besides, the RUA algorithm is able to deal with variable workload to prevent hosts from overloading after VM placement and to reduce the SLA violations dramatically.

HybAVPnet: a Novel Hybrid Network Architecture for Antiviral Peptides Prediction.

Viruses pose a great threat to human production and life, thus the research and development of antiviral drugs is urgently needed. Antiviral peptides play an important role in drug design and development. Compared with the time-consuming and laborious wet chemical experiment methods, it is critical to use computational methods to predict antiviral peptides accurately and rapidly. However, due to limited data, accurate prediction of antiviral peptides is still challenging and extracting effective feature representations from sequences is crucial for creating accurate models. This study introduces a novel two-step approach, named HybAVPnet, to predict antiviral peptides with a hybrid network architecture based on neural networks and traditional machine learning methods. We adopted a stacking-like structure to capture both the long-term dependencies and local evolution information to achieve a comprehensive and diverse prediction using the predicted labels and probabilities. Using an ensemble technique with the different kinds of features can reduce the variance without increasing the bias. The experimental result shows HybAVPnet can achieve better and more robust performance compared with the state-of-the-art methods, which makes it useful for the research and development of antiviral drugs. Meanwhile, it can also be extended to other peptide recognition problems because of its generalization ability.

An AS-OCT image dataset for deep learning-enabled segmentation and 3D reconstruction for keratitis.

Infectious keratitis is among the major causes of global blindness. Anterior segment optical coherence tomography (AS-OCT) images allow the characterizing of cross-sectional structures in the cornea with keratitis thus revealing the severity of inflammation, and can also provide 360-degree information on anterior chambers. The development of image analysis methods for such cases, particularly deep learning methods, requires a large number of annotated images, but to date, there is no such open-access AS-OCT image repository. For this reason, this work provides a dataset containing a total of 1168 AS-OCT images of patients with keratitis, including 768 full-frame images (6 patients). Each image has associated segmentation labels for lesions and cornea, and also labels of iris for full-frame images. This study provides a great opportunity to advance the field of image analysis on AS-OCT images in both two-dimensional (2D) and three-dimensional (3D) and would aid in the development of artificial intelligence-based keratitis management.

PGKD-Net: Prior-guided and Knowledge Diffusive Network for Choroid Segmentation.

The thickness of the choroid is considered to be an important indicator of clinical diagnosis. Therefore, accurate choroid segmentation in retinal OCT images is crucial for monitoring various ophthalmic diseases. However, this is still challenging due to the blurry boundaries and interference from other lesions. To address these issues, we propose a novel prior-guided and knowledge diffusive network (PGKD-Net) to fully utilize retinal structural information to highlight choroidal region features and boost segmentation performance. Specifically, it is composed of two parts: a Prior-mask Guided Network (PG-Net) for coarse segmentation and a Knowledge Diffusive Network (KD-Net) for fine segmentation. In addition, we design two novel feature enhancement modules, Multi-Scale Context Aggregation (MSCA) and Multi-Level Feature Fusion (MLFF). The MSCA module captures the long-distance dependencies between features from different receptive fields and improves the model's ability to learn global context. The MLFF module integrates the cascaded context knowledge learned from PG-Net to benefit fine-level segmentation. Comprehensive experiments are conducted to evaluate the performance of the proposed PGKD-Net. Experimental results show that our proposed method achieves superior segmentation accuracy over other state-of-the-art methods. Our code is made up publicly available at: https://github.com/yzh-hdu/choroid-segmentation.

CDNet: Contrastive Disentangled Network for Fine-Grained Image Categorization of Ocular B-Scan Ultrasound.

Precise and rapid categorization of images in the B-scan ultrasound modality is vital for diagnosing ocular diseases. Nevertheless, distinguishing various diseases in ultrasound still challenges experienced ophthalmologists. Thus a novel contrastive disentangled network (CDNet) is developed in this work, aiming to tackle the fine-grained image categorization (FGIC) challenges of ocular abnormalities in ultrasound images, including intraocular tumor (IOT), retinal detachment (RD), posterior scleral staphyloma (PSS), and vitreous hemorrhage (VH). Three essential components of CDNet are the weakly-supervised lesion localization module (WSLL), contrastive multi-zoom (CMZ) strategy, and hyperspherical contrastive disentangled loss (HCD-Loss), respectively. These components facilitate feature disentanglement for fine-grained recognition in both the input and output aspects. The proposed CDNet is validated on our ZJU Ocular Ultrasound Dataset (ZJUOUSD), consisting of 5213 samples. Furthermore, the generalization ability of CDNet is validated on two public and widely-used chest X-ray FGIC benchmarks. Quantitative and qualitative results demonstrate the efficacy of our proposed CDNet, which achieves state-of-the-art performance in the FGIC task.

SuccSPred2.0: A Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm.

Protein succinylation is a novel type of post-translational modification in recent decade years. It played an important role in biological structure and functions verified by experiments. However, it is time consuming and laborious for the wet experimental identification of succinylation sites. Traditional technology cannot adapt to the rapid growth of the biological sequence data sets. In this study, a new computational method named SuccSPred2.0 was proposed to identify succinylation sites in the protein sequences based on multifeature fusion and maximal information coefficient (MIC) method. SuccSPred2.0 was implemented based on a two-step strategy. At first, high-dimension features were reduced by linear discriminant analysis to prevent overfitting. Subsequently, MIC method was employed to select the important features binding classifiers to predict succinylation sites. From the compared experiments on 10-fold cross-validation and independent test data sets, SuccSPred2.0 obtained promising improvements. Comparative experiments showed that SuccSPred2.0 was superior to previous tools in identifying succinylation sites in the given proteins.

i2APP: A Two-Step Machine Learning Framework For Antiparasitic Peptides Identification.

Parasites can cause enormous damage to their hosts. Studies have shown that antiparasitic peptides can inhibit the growth and development of parasites and even kill them. Because traditional biological methods to determine the activity of antiparasitic peptides are time-consuming and costly, a method for large-scale prediction of antiparasitic peptides is urgently needed. We propose a computational approach called i2APP that can efficiently identify APPs using a two-step machine learning (ML) framework. First, in order to solve the imbalance of positive and negative samples in the training set, a random under sampling method is used to generate a balanced training data set. Then, the physical and chemical features and terminus-based features are extracted, and the first classification is performed by Light Gradient Boosting Machine (LGBM) and Support Vector Machine (SVM) to obtain 264-dimensional higher level features. These features are selected by Maximal Information Coefficient (MIC) and the features with the big MIC values are retained. Finally, the SVM algorithm is used for the second classification in the optimized feature space. Thus the prediction model i2APP is fully constructed. On independent datasets, the accuracy and AUC of i2APP are 0.913 and 0.935, respectively, which are better than the state-of-arts methods. The key idea of the proposed method is that multi-level features are extracted from peptide sequences and the higher-level features can distinguish well the APPs and non-APPs.

Self-supervised learning mechanism for identification of eyelid malignant melanoma in pathologic slides with limited annotation.

Purpose: The lack of finely annotated pathologic data has limited the application of deep learning systems (DLS) to the automated interpretation of pathologic slides. Therefore, this study develops a robust self-supervised learning (SSL) pathology diagnostic system to automatically detect malignant melanoma (MM) in the eyelid with limited annotation. Design: Development of a self-supervised diagnosis pipeline based on a public dataset, then refined and tested on a private, real-world clinical dataset. Subjects: A. Patchcamelyon (PCam)-a publicly accessible dataset for the classification task of patch-level histopathologic images. B. The Second Affiliated Hospital, Zhejiang University School of Medicine (ZJU-2) dataset - 524,307 patches (small sections cut from pathologic slide images) from 192 H&E-stained whole-slide-images (WSIs); only 72 WSIs were labeled by pathologists. Methods: Patchcamelyon was used to select a convolutional neural network (CNN) as the backbone for our SSL-based model. This model was further developed in the ZJU-2 dataset for patch-level classification with both labeled and unlabeled images to test its diagnosis ability. Then the algorithm retrieved information based on patch-level prediction to generate WSI-level classification results using random forest. A heatmap was computed for visualizing the decision-making process. Main outcome measures: The area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity were used to evaluate the performance of the algorithm in identifying MM. Results: ResNet50 was selected as the backbone of the SSL-based model using the PCam dataset. This algorithm then achieved an AUC of 0.981 with an accuracy, sensitivity, and specificity of 90.9, 85.2, and 96.3% for the patch-level classification of the ZJU-2 dataset. For WSI-level diagnosis, the AUC, accuracy, sensitivity, and specificity were 0.974, 93.8%, 75.0%, and 100%, separately. For every WSI, a heatmap was generated based on the malignancy probability. Conclusion: Our diagnostic system, which is based on SSL and trained with a dataset of limited annotation, can automatically identify MM in pathologic slides and highlight MM areas in WSIs by a probabilistic heatmap. In addition, this labor-saving and cost-efficient model has the potential to be refined to help diagnose other ophthalmic and non-ophthalmic malignancies.

A Self-Supervised Learning Based Framework for Eyelid Malignant Melanoma Diagnosis in Whole Slide Images.

Eyelid malignant melanoma (MM) is a rare disease with high mortality. Accurate diagnosis of such disease is important but challenging. In clinical practice, the diagnosis of MM is currently performed manually by pathologists, which is subjective and biased. Since the heavy manual annotation workload, most pathological whole slide image (WSI) datasets are only partially labeled (without region annotations), which cannot be directly used in supervised deep learning. For these reasons, it is of great practical significance to design a laborsaving and high data utilization diagnosis method. In this paper, a self-supervised learning (SSL) based framework for automatically detecting eyelid MM is proposed. The framework consists of a self-supervised model for detecting MM areas at the patch-level and a second model for classifying lesion types at the slide level. A squeeze-excitation (SE) attention structure and a feature-projection (FP) structure are integrated to boost learning on details of pathological images and improve model performance. In addition, this framework also provides visual heatmaps with high quality and reliability to highlight the likely areas of the lesion to assist the evaluation and diagnosis of the eyelid MM. Extensive experimental results on different datasets show that our proposed method outperforms other state-of-the-art SSL and fully supervised methods at both patch and slide levels when only a subset of WSIs are annotated. It should be noted that our method is even comparable to supervised methods when all WSIs are fully annotated. To the best of our knowledge, our work is the first SSL method for automatic diagnosis of MM at the eyelid and has a great potential impact on reducing the workload of human annotations in clinical practice.