ACP-DRL: an anticancer peptides recognition method based on deep representation learning.

Increasing numbers of software vulnerabilities are discovered every year whether they are reported publicly or discovered internally in proprietary code. These vulnerabilities can pose serious risk of exploit and result in system compromise, information leaks, or denial of service. We leveraged the wealth of C and C++ open-source code available to develop a largescale function-level vulnerability detection system using machine learning. To supplement existing labeled vulnerability datasets, we compiled a vast dataset of millions of open-source functions and labeled it with carefully-selected findings from three different static analyzers that indicate potential exploits. Using these datasets, we developed a fast and scalable vulnerability detection tool based on deep feature representation learning that directly interprets lexed source code. We evaluated our tool on code from both real software packages and the NIST SATE IV benchmark dataset. Our results demonstrate that deep feature representation learning on source code is a promising approach for automated software vulnerability detection.

Centroids-guided deep multi-view K-means clustering

Anticancer peptides (ACPs) have natural cationic properties and can act on the anionic cell membrane of cancer cells to kill cancer cells. Therefore, ACPs have become a potential anticancer drug with good research value and prospect. In this article, we propose AACFlow, an end-to-end model for identification of ACPs based on deep learning. End-to-end models have more room to automatically adjust according to the data, making the overall fit better and reducing error propagation. The combination of attention augmented convolutional neural network (AAConv) and multi-layer convolutional neural network (CNN) forms a deep representation learning module, which is used to obtain global and local information on the sequence. Based on the concept of flow network, multi-head flow-attention mechanism is introduced to mine the deep features of the sequence to improve the efficiency of the model. On the independent test dataset, the ACC, Sn, Sp, and AUC values of AACFlow are 83.9%, 83.0%, 84.8%, and 0.892, respectively, which are 4.9%, 1.5%, 8.0%, and 0.016 higher than those of the baseline model. The MCC value is 67.85%. In addition, we visualize the features extracted by each module to enhance the interpretability of the model. Various experiments show that our model is more competitive in predicting ACPs.

Cancer has become one of the deadliest diseases,which causes catastrophic pressure on healthcare systems and kills massive lives each year. Anticancer peptides (ACPs) have attracted great interest as a new direction for cancer treatment. Thus, developing in silico approaches for ACPs prediction is necessary and urgent. Here, we propose a new computational model called inACP, combining deep sequential representation learning features embedding and predicted protein structure features as input and integrating three machine learning classifiers with an ensemble approach. Comparison results show that inACP has a better capability to recognize ACPs than several state-of-the-art approaches. Datasets and source code are available at https://github.com/lnr3/inACP/.

A Comprehensive Survey on Deep Graph Representation Learning

Although advancing the therapeutic alternatives for treating deadly cancers has gained much attention globally, still the primary methods such as chemotherapy have significant downsides and low specificity. Most recently, Anticancer peptides (ACPs) have emerged as a potential alternative to therapeutic alternatives with much fewer negative side-effects. However, the identification of ACPs through wet-lab experiments is expensive and time-consuming. Hence, computational methods have emerged as viable alternatives. During the past few years, several computational ACP identification techniques using hand-engineered features have been proposed to solve this problem. In this study, we propose a new multi headed deep convolutional neural network model called ACP-MHCNN, for extracting and combining discriminative features from different information sources in an interactive way. Our model extracts sequence, physicochemical, and evolutionary based features for ACP identification using different numerical peptide representations while restraining parameter overhead. It is evident through rigorous experiments using cross-validation and independent-dataset that ACP-MHCNN outperforms other models for anticancer peptide identification by a substantial margin on our employed benchmarks. ACP-MHCNN outperforms state-of-the-art model by 6.3%, 8.6%, 3.7%, 4.0%, and 0.20 in terms of accuracy, sensitivity, specificity, precision, and MCC respectively. ACP-MHCNN and its relevant codes and datasets are publicly available at: https://github.com/mrzResearchArena/Anticancer-Peptides-CNN. ACP-MHCNN is also publicly available as an online predictor at: https://anticancer.pythonanywhere.com/.

Cancer is the second leading cause of death globally, and use of therapeutic peptides to target and kill cancer cells has received considerable attention in recent years. Identification of anticancer peptides (ACPs) through wet-lab experimentation is expensive and often time consuming; therefore, development of an efficient computational method is essential to identify potential ACP candidates prior to in vitro experimentation. In this study, we developed support vector machine- and random forest-based machine-learning methods for the prediction of ACPs using the features calculated from the amino acid sequence, including amino acid composition, dipeptide composition, atomic composition, and physicochemical properties. We trained our methods using the Tyagi-B dataset and determined the machine parameters by 10-fold cross-validation. Furthermore, we evaluated the performance of our methods on two benchmarking datasets, with our results showing that the random forest-based method outperformed the existing methods with an average accuracy and Matthews correlation coefficient value of 88.7% and 0.78, respectively. To assist the scientific community, we also developed a publicly accessible web server at www.thegleelab.org/MLACP.html.

Despite the continuous evolution and significant improvement of cybersecurity mechanisms, malware threats remain one of the most important concerns in cyberspace. Meanwhile, Android malware plays a big role in these ever-growing threats. In recent years, deep learning has become the dominant machine learning technique for malware detection and continues to make outstanding achievements. Deep graph representation learning is the task of embedding graph-structured data into a low-dimensional space using deep learning models. Recently, autoencoders have proven to be an effective way for deep representation learning. However, it is not straightforward to apply the idea of autoencoder to graph-structured data because of their irregular structure. In this paper, we present DroidMalGNN, a novel deep learning technique that combines autoencoders with graph neural networks (GNNs) to detect Android malware in an end-to-end manner. DroidMalGNN represents each Android application with an attributed function call graph (AFCG) that allows it to model complex relationships between data. For more efficiency, DroidMalGNN performs graph representation learning in a supervised manner where two autoencoders are trained with benign and malicious AFCGs separately. In this way, it generates two informative embedding vectors for each AFCG in a low-dimensional space and feeds them into a dense neural network to classify the AFCG as benign or malicious. Our experimental results show that DroidMalGNN can achieve good detection performance in terms of different evaluation measures.

Image cyberbullying detection and recognition using transfer deep machine learning

Smart grids integrate advanced information and communication technologies (ICTs) into traditional power grids for more efficient and resilient power delivery and management, but also introduce new security vulnerabilities that can be exploited by adversaries to launch cyber attacks, causing severe consequences such as massive blackout and infrastructure damages. Existing machine learning-based methods for detecting cyber attacks in smart grids are mostly based on supervised learning, which need the instances of both normal and attack events for training. In addition, supervised learning requires that the training dataset includes representative instances of various types of attack events to train a good model, which is sometimes hard if not impossible. This paper presents a new method for detecting cyber attacks in smart grids using PMU data, which is based on semi-supervised anomaly detection and deep representation learning. Semi-supervised anomaly detection only employs the instances of normal events to train detection models, making it suitable for finding unknown attack events. A number of popular semi-supervised anomaly detection algorithms were investigated in our study using publicly available power system cyber attack datasets to identify the best-performing ones. The performance comparison with popular supervised algorithms demonstrates that semi-supervised algorithms are more capable of finding attack events than supervised algorithms. Our results also show that the performance of semi-supervised anomaly detection algorithms can be further improved by augmenting with deep representation learning.

Cancer is one of the most dangerous threats to human health. One of the issues is drug resistance action, which leads to side effects after drug treatment. Numerous therapies have endeavored to relieve the drug resistance action. Recently, anticancer peptides could be a novel and promising anticancer candidate, which can inhibit tumor cell proliferation, migration, and suppress the formation of tumor blood vessels, with fewer side effects. However, it is costly, laborious and time consuming to identify anticancer peptides by biological experiments with a high throughput. Therefore, accurately identifying anti-cancer peptides becomes a key and indispensable step for anticancer peptides therapy. Although some existing computer methods have been developed to predict anticancer peptides, the accuracy still needs to be improved. Thus, in this study, we propose a deep learning-based model, called ACPNet, to distinguish anticancer peptides from non-anticancer peptides (non-ACPs). ACPNet employs three different types of peptide sequence information, peptide physicochemical properties and auto-encoding features linking the training process. ACPNet is a hybrid deep learning network, which fuses fully connected networks and recurrent neural networks. The comparison with other existing methods on ACPs82 datasets shows that ACPNet not only achieves the improvement of 1.2% Accuracy, 2.0% F1-score, and 7.2% Recall, but also gets balanced performance on the Matthews correlation coefficient. Meanwhile, ACPNet is verified on an independent dataset, with 20 proven anticancer peptides, and only one anticancer peptide is predicted as non-ACPs. The comparison and independent validation experiment indicate that ACPNet can accurately distinguish anticancer peptides from non-ACPs.

Anti-cancer peptides (ACPs) are a promising alternative to traditional chemotherapy. To aid wet-lab and clinical research, there is a growing interest in using machine learning techniques to help identify good ACP candidates computationally. In this paper, we describe DeepACPpred, a novel deep learning model composed of a hybrid CNN-RNN architecture for predicting ACPs. Using several gold-standard ACP datasets, we demonstrate that DeepACPpred is highly effective compared to state-of-the-art ACP prediction models.

The recent development in learning deep representations has demonstrated its wide applications in traditional vision tasks like classification and detection. However, there has been little investigation on how we could build up a deep learning framework in a weakly supervised setting. In this paper, we attempt to model deep learning in a weakly supervised learning (multiple instance learning) framework. In our setting, each image follows a dual multi-instance assumption, where its object proposals and possible text annotations can be regarded as two instance sets. We thus design effective systems to exploit the MIL property with deep learning strategies from the two ends; we also try to jointly learn the relationship between object and annotation proposals. We conduct extensive experiments and prove that our weakly supervised deep learning framework not only achieves convincing performance in vision tasks including classification and image annotation, but also extracts reasonable region-keyword pairs with little supervision, on both widely used benchmarks like PASCAL VOC and MIT Indoor Scene 67, and also a dataset for image-and patch-level annotations.

Cancer remains a major global health burden, and conventional treatments such as surgery, radiotherapy, and chemotherapy are often limited by systemic toxicity, drug resistance, and high cost. Anticancer peptides (ACPs) have emerged as promising therapeutic candidates because of their selective activity against tumor cells; however, experimental identification of ACPs is labor-intensive and time-consuming, and peptide activity may vary across tissue contexts. Although many computational models have been developed for general ACP prediction, tissue-specific ACP classification remains insufficiently explored. In this study, we developed ACP-Boost, a tissue-aware machine learning framework for tissue-specific ACP classification across nine cancer-related tissues: blood, brain, breast, cervix, colon, liver, lung, prostate, and skin. Experimentally validated peptide records were integrated from CancerPPD2 and DCTPep, followed by preprocessing, redundancy control, and tissue annotation. Peptide sequences were encoded into 473-dimensional feature vectors comprising amino acid composition (AAC), dipeptide composition (DPC), physicochemical property composition (PCP), and pseudo-amino acid composition (PseAAC). To address class imbalance while preserving the original sequence distribution, we formulated the task as a one-versus-rest classification problem, applied group-aware train-test splitting based on peptide sequences, and emphasized evaluation metrics suitable for imbalanced data. We systematically compared five machine learning algorithms, including support vector machine, random forest, logistic regression, k-nearest neighbors, and XGBoost. Among them, XGBoost showed the most stable overall performance across tissues. The results indicate that peptide sequence-derived descriptors contain measurable tissue-associated signals, although predictive separability remains moderate for several cancer types. Feature importance analysis further suggested that both shared charge-related properties and tissue-dependent sequence descriptors contribute to model discrimination. Overall, this study provides a comparative computational framework for tissue-specific ACP classification and highlights the importance of incorporating biological heterogeneity into peptide prediction tasks.

Chapter 6 - Multiview learning with shallow 1D-CNN for anticancer activity classification of therapeutic peptides