The quality of endoscopic images is critical to the success of polyp segmentation, highlighting the need for accurate exposure correction in endoscopy. While traditional deep learning methods are effective, they demand substantial computational resources during inference. To address this, we propose the Endoscopic Exposure Correction Spiking Neural Network (ECSNN), an efficient framework designed for resource-limited devices. Our approach features a Positive Incentive Learning Module that reduces noise in input images. These enhanced features are then processed by U-Shape Networks (USNet), which leverages spiking neural networks to learn deep representations for exposure correction. Additionally, we introduce a Brightness Prompt Module consisting of two components: the Brightness Spike Encoding Module (BSEM), which encodes brightness information into spike signals, and the Brightness-Aware Prompt Block (BAPB), which adjusts exposure by guiding the network through brightness-aware attention. We evaluate ECSNN on the Endo4IE and ECSEG datasets, where it outperforms six state-of-the-art methods and demonstrates its practical utility in clinical diagnosis.

As a high mortality disease, cancer seriously affects people's life and well-being. Reliance on pathologists to assess disease progression from pathological images is inaccurate and burdensome. Computer aided diagnosis (CAD) system can effectively assist diagnosis and make more credible decisions. However, a large number of labeled medical images that contribute to improve the accuracy of machine learning algorithm, especially for deep learning in CAD, are difficult to collect. Therefore, in this work, an improved few-shot learning method is proposed for medical image recognition. In addition, to make full use of the limited feature information in one or more samples, a feature fusion strategy is involved in our model. On the dataset of BreakHis and skin lesions, the experimental results show that our model achieved the classification accuracy of 91.22% and 71.20% respectively when only 10 labeled samples are given, which is superior to other state-of-the-art methods.

As we all know, the learning rate plays a vital role in deep neural network (DNN) training. This study introduces an incremental proportional-integral-derivative (PID) controller widely used in automatic control as a learning rate scheduler for stochastic gradient descent (SGD). To automatically calculate the current learning rate, we utilize feedback control to determine the relationship between training losses and learning rates, named incremental PID learning rates, which include PID-Base and PID-Warmup. The new schedulers reduce the dependence on the initial learning rate and achieve higher accuracy. Compared with multistep learning rates (MSLR), cyclical learning rates (CLR), and SGD with warm restarts (SGDR), incremental PID learning rates based on feedback control obtain higher accuracy on CIFAR-10, CIFAR-100, and Tiny-ImageNet-200. We believe that our methods can improve the performance of SGD.

The computational methods of protein-protein interaction sites prediction can effectively avoid the shortcomings of high cost and time in traditional experimental approaches. However, the serious class imbalance between interface and non-interface residues on the protein sequences limits the prediction performance of these methods. This work therefore proposed a new strategy, NearMiss-based under-sampling for unbalancing datasets and Random Forest classification (NM-RF), to predict protein interaction sites. Herein, the residues on protein sequences were represented by the PSSM-derived features, hydropathy index (HI) and relative solvent accessibility (RSA). In order to resolve the class imbalance problem, an under-sampling method based on NearMiss algorithm is adopted to remove some non-interface residues, and then the random forest algorithm is used to perform binary classification on the balanced feature datasets. Experiments show that the accuracy of NM-RF model reaches 87.6% and 84.3% on Dtestset72 and PDBtestset164 respectively, which demonstrate the effectiveness of the proposed NM-RF method in differentiating the interface or non-interface residues.

Functional near-infrared spectroscopy (fNIRS) is a promising neuroimaging technology. The fNIRS classification problem has always been the focus of the brain-computer interface (BCI). Inspired by the success of Transformer based on self-attention mechanism in the fields of natural language processing and computer vision, we propose an fNIRS classification network based on Transformer, named fNIRS-T. We explore the spatial-level and channel-level representation of fNIRS signals to improve data utilization and network representation capacity. Besides, a preprocessing module, which consists of one-dimensional average pooling and layer normalization, is designed to replace filtering and baseline correction of data preprocessing. It makes fNIRS-T an end-to-end network, called fNIRS-PreT. Compared with traditional machine learning classifiers, convolutional neural network (CNN), and long short-term memory (LSTM), the proposed models obtain the best accuracy on three open-access datasets. Specifically, in the most extensive ternary classification task (30 subjects) that includes three types of overt movements, fNIRS-T, CNN, and LSTM obtain 75.49%, 72.89%, and 61.94% on test sets, respectively. Compared to traditional classifiers, fNIRS-T is at least 27.41% higher than statistical features and 6.79% higher than well-designed features. In the individual subject experiment of the ternary classification task, fNIRS-T achieves an average subject accuracy of 78.22% and surpasses CNN and LSTM by a large margin of +4.75% and +11.33%. fNIRS-PreT using raw data also achieves competitive performance to fNIRS-T. Therefore, the proposed models improve the performance of fNIRS-based BCI significantly.

The presence of haze significantly reduces the quality of images. Researchers have designed a variety of algorithms for image dehazing (ID) to restore the quality of hazy images. However, there are few studies that summarize the deep learning (DL) based dehazing technologies. In this paper, we conduct a comprehensive survey on the recent proposed dehazing methods. Firstly, we conclude the commonly used datasets, loss functions and evaluation metrics. Secondly, we group the existing researches of ID into two major categories: supervised ID and unsupervised ID. The core ideas of various influential dehazing models are introduced. Finally, the open issues for future research on ID are pointed out.

Protein-protein interactions play essential roles in various biological progresses. Identifying protein interaction sites can facilitate researchers to understand life activities and therefore will be helpful for drug design. However, the number of experimental determined protein interaction sites is far less than that of protein sites in protein-protein interaction or protein complexes. Therefore, the negative and positive samples are usually imbalanced, which is common but bring result bias on the prediction of protein interaction sites by computational approaches. In this work, we presented three imbalance data processing strategies to reconstruct the original dataset, and then extracted protein features from the evolutionary conservation of amino acids to build a predictor for identification of protein interaction sites. On a dataset with 10,430 surface residues but only 2,299 interface residues, the imbalance dataset processing strategies can obviously reduce the prediction bias, and therefore improve the prediction performance of protein interaction sites. The experimental results show that our prediction models can achieve a better prediction performance, such as a prediction accuracy of 0.758, or a high F-measure of 0.737, which demonstrated the effectiveness of our method.

In contrast to traditional dehazing methods, deep learning based single image dehazing (SID) algorithms have achieved better performances by creating a mapping function from haze to haze-free images. Usually, the images taken from the natural scenes have different haze levels, but deep SID algorithms only process the hazy images as one group. It makes the deep SID algorithms difficult to deal with the image set with some images having specific haze density. In this paper, a Discrete Haze Level Dehazing network (DHL-Dehaze), a very effective method to dehaze multiple different haze level images, is proposed. The proposed approach considers a single image dehazing problem as a multi-domain image-to-image translation, instead of grouping all hazy images into the same domain. DHL-Dehaze provides computational derivation to describe the role of different haze levels for image translation. To verify the proposed approach, we synthesize two largescale datasets with multiple haze level images based on the NYU-Depth and DIML/CVL datasets. The experiments show that DHL-Dehaze can obtain excellent quantitative and qualitative dehazing results, especially when the haze concentration is high.

BACKGROUND: Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past decades, detecting drug-target interactions (DTIs) remains to be extremely resource-intensive and time-consuming. Therefore, many computational approaches have been developed for predicting drug-target associations on a large scale. RESULTS: In this paper, we proposed an deep learning-based method to predict DTIs only using the information of drug structures and protein sequences. The final results showed that our method can achieve good performance with the accuracies up to 92.0%, 90.0%, 92.0% and 90.7% for the target families of enzymes, ion channels, GPCRs and nuclear receptors of our created dataset, respectively. Another dataset derived from DrugBank was used to further assess the generalization of the model, which yielded an accuracy of 0.9015 and an AUC value of 0.9557. CONCLUSION: It was elucidated that our model shows improved performance in comparison with other state-of-the-art computational methods on the common benchmark datasets. Experimental results demonstrated that our model successfully extracted more nuanced yet useful features, and therefore can be used as a practical tool to discover new drugs. AVAILABILITY: http://deeplearner.ahu.edu.cn/web/CnnDTI.htm.

BACKGROUND: The recognition of protein interaction sites is of great significance in many biological processes, signaling pathways and drug designs. However, most sites on protein sequences cannot be defined as interface or non-interface sites because only a small part of protein interactions had been identified, which will cause the lack of prediction accuracy and generalization ability of predictors in protein interaction sites prediction. Therefore, it is necessary to effectively improve prediction performance of protein interaction sites using large amounts of unlabeled data together with small amounts of labeled data and background knowledge today. RESULTS: In this work, three semi-supervised support vector machine-based methods are proposed to improve the performance in the protein interaction sites prediction, in which the information of unlabeled protein sites can be involved. Herein, five features related with the evolutionary conservation of amino acids are extracted from HSSP database and Consurf Sever, i.e., residue spatial sequence spectrum, residue sequence information entropy and relative entropy, residue sequence conserved weight and residual Base evolution rate, to represent the residues within the protein sequence. Then three predictors are built for identifying the interface residues from protein surface using three types of semi-supervised support vector machine algorithms. CONCLUSION: The experimental results demonstrated that the semi-supervised approaches can effectively improve prediction performance of protein interaction sites when unlabeled information is involved into the predictors and one of them can achieve the best prediction performance, i.e., the accuracy of 70.7%, the sensitivity of 62.67% and the specificity of 78.72%, respectively. With comparison to the existing studies, the semi-supervised models show the improvement of the predication performance.

BACKGROUND: The occurrence of cotton pests and diseases has always been an important factor affecting the total cotton production. Cotton has a great dependence on environmental factors during its growth, especially climate change. In recent years, machine learning and especially deep learning methods have been widely used in many fields and have achieved good results. METHODS: First, this papaer used the common Aprioro algorithm to find the association rules between weather factors and the occurrence of cotton pests. Then, in this paper, the problem of predicting the occurrence of pests and diseases is formulated as time series prediction, and an LSTM-based method was developed to solve the problem. RESULTS: The association analysis reveals that moderate temperature, humid air, low wind spreed and rain fall in autumn and winter are more likely to occur cotton pests and diseases. The discovery was then used to predict the occurrence of pests and diseases. Experimental results showed that LSTM performs well on the prediction of occurrence of pests and diseases in cotton fields, and yields the Area Under the Curve (AUC) of 0.97. CONCLUSION: Suitable temperature, humidity, low rainfall, low wind speed, suitable sunshine time and low evaporation are more likely to cause cotton pests and diseases. Based on these associations as well as historical weather and pest records, LSTM network is a good predictor for future pest and disease occurrences. Moreover, compared to the traditional machine learning models (i.e., SVM and Random Forest), the LSTM network performs the best.

BACKGROUND: Protein-protein interactions (PPIs) play important roles in biological functions. Studies of the effects of mutants on protein interactions can provide further understanding of PPIs. Currently, many databases collect experimental mutants to assess protein interactions, but most of these databases are old and have not been updated for several years. RESULTS: To address this issue, we manually curated a kinetic and thermodynamic database of mutant protein interactions (dbMPIKT) that is freely accessible at our website. This database contains 5291 mutants in protein interactions collected from previous databases and the literature published within the last three years. Furthermore, some data analysis, such as mutation number, mutation type, protein pair source and network map construction, can be performed online. CONCLUSION: Our work can promote the study on PPIs, and novel information can be mined from the new database. Our database is available in http://DeepLearner.ahu.edu.cn/web/dbMPIKT/ for use by all, including both academics and non-academics.

BACKGROUND: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures. RESULTS: This paper proposes a dynamic ensemble approach to identify protein-ligand binding residues by using sequence information only. To avoid problems resulting from highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we constructed several balanced data sets and we trained a random forest classifier for each of them. We dynamically selected a subset of classifiers according to the similarity between the target protein and the proteins in the training data set. The combination of the predictions of the classifier subset to each query protein target yielded the final predictions. The ensemble of these classifiers formed a sequence-based predictor to identify protein-ligand binding sites. CONCLUSIONS: Experimental results on two Critical Assessment of protein Structure Prediction datasets and the ccPDB dataset demonstrated that of our proposed method compared favorably with the state-of-the-art. AVAILABILITY: http://www2.ahu.edu.cn/pchen/web/LigandDSES.htm.

More and more studies have shown many complex diseases are contributed jointly by alterations of numerous genes. In this paper, we propose a gene differential coexpression analysis algorithm in the level of gene sets and apply the algorithm to a publicly available type 2 diabetes (T2D) expression dataset. The experimental results on simulated data show that the new approach performed well. Moreover, we apply the new approach to clinical data, many additional discoveries can be found through our method.

BACKGROUND: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics. RESULTS: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model. CONCLUSIONS: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques.

Eigengene extracted by independent component analysis (ICA) is one kind of effective feature for tumor classification. In this letter, a novel tumor classification approach is proposed by using eigengene and support vector machine (SVM) based classifier committee learning (CCL) algorithm. In this method, a strategy of random feature subspace division is designed to improve the diversity of weaker classifiers. Gene expression data constructed by different feature subspaces are modeled by ICA, respectively. And the corresponding eigengene sets extracted by the ICA algorithm are used as the inputs of the weaker SVM classifiers. Moreover, a strategy of Bayesian sum rule (BSR) is designed to integrate the outputs of the weaker SVM classifiers, and used to provide a final decision for the tumor category. Experimental results on three DNA microarray datasets demonstrate that the proposed method is effective and feasible for tumor classification.

In current proteomics research, a big challenge is to differentiate the correlative proteins for a given biological function from all existing proteins, and if it does, how strong is the relationship between the proteins and function. Statistical significance testing can be used to address this question. However, every traditional statistical test method may suffer from the inability to identify important differentially expressed proteins if the biological samples do not completely meet the assumptions of each test method [ 1 ]. To detect the regulated proteins for differential proteomics, we analyze multiple significance test methods and discover some significance proteins. We use the four statistical methods, i.e., Kolmogorov-Smirnov test (KS-test), Baumgartner-Weib-Schindler test (BWS-test), T-test, Brunner-Munzel test (BM-test) to measure the difference of the expression level of individual protein under two experimental conditions, respectively. The results had been successfully used for the discovery of protein biomarkers in breast cancer.

Microarray data prediction is a hard task due to the small sample and high dimension property. This paper proposes a classifier fusion approch to solve this problem based on genetic algorithm (GA). In this fusion strategy, GA is applied to select proper feature subsets and weight value for the fusion of classifiers. The experimental results show that the proposed scheme can improve the prediction accuracy.

This paper presents a novel multi-sub-swarm Particle Swarm Optimization (PSO) algorithm. The proposed algorithm can effectively imitate a natural ecosystem, in which the different sub-populations can compete with each other. After competing, the winner will continue to explore the original district, while the loser will be obliged to explore another district. Four benchmark multimodal functions of varying difficulty are used as test functions. The experimental results show that the proposed method has a stronger adaptive ability and a better performance for complicated multimodal functions with respect to other methods.

In this paper an efficient shape matching approach based on fuzzy discrete particle swarm optimization (FDPSO) is proposed. Based on fuzzy theory and PSO method, we applied this optimization method to a special combinatorial optimization problem: shape matching and recognition. Firstly, an original shape is approximated to a polygone and a shape representation of invariant attributes sequence is used. Then fuzzy matrices were adopted to represent the position and velocity of the particles in PSO. Finally, the superiority of our proposed method over traditional approaches to shape matching is demonstrated by experiments. The experimental results showed that our proposed method can achieve good results due to its robustness.