CircRNA has been shown to be involved in the occurrence of many diseases. Several computational frameworks have been proposed to identify circRNA-disease associations. Despite the existing computational methods have obtained considerable successes, these methods still require to be improved as their performance may degrade due to the sparsity of the data and the problem of memory overflow. We develop a novel computational framework called LGCDA to predict circRNA-disease associations by fusing local and global features to solve the above mentioned problems. First, we construct closed local subgraphs by using k-hop closed subgraph and label the subgraphs to obtain rich graph pattern information. Then, the local features are extracted by using graph neural network (GNN). In addition, we fuse Gaussian interaction profile (GIP) kernel and cosine similarity to obtain global features. Finally, the score of circRNA-disease associations is predicted by using the multilayer perceptron (MLP) based on local and global features. We perform five- fold cross validation on five datasets for model evaluation and our model surpasses other advanced methods. The code is available at https://github.com/lanbiolab/LGCDA

RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions. The two evidences give the reasoning for adopting knowledge-based deep learning methods in lincRNA detection. Similar to coding region transcription, non-coding regions are split at transcriptional sites. However, regulatory RNAs rather than message RNAs are generated. That is, the transcribed RNAs participate the biological process as regulatory units instead of generating proteins. Identifying these transcriptional regions from non-coding regions is the first step towards lincRNA recognition. The auto-encoder method achieves 100% and 92.4% prediction accuracy on transcription sites over the putative data sets. The experimental results also show the excellent performance of predictive deep neural network on the lincRNA data sets compared with support vector machine and traditional neural network. In addition, it is validated through the newly discovered lincRNA data set and one unreported transcription site is found by feeding the whole annotated sequences through the deep learning machine, which indicates that deep learning method has the extensive ability for lincRNA prediction. The transcriptional sequences of lincRNAs are collected from the annotated human DNA genome data. Subsequently, a two-layer deep neural network is developed for the lincRNA detection, which adopts the auto-encoder algorithm and utilizes different encoding schemes to obtain the best performance over intergenic DNA sequence data. Driven by those newly annotated lincRNA data, deep learning methods based on auto-encoder algorithm can exert their capability in knowledge learning in order to capture the useful features and the information correlation along DNA genome sequences for lincRNA detection. As our knowledge, this is the first application to adopt the deep learning techniques for identifying lincRNA transcription sequences.

CAPTCHA authentication has been challenged by recent technology advances in AI. However, many of the AI advances challenging CAPTCHA are either restricted by a limited amount of labeled CAPTCHA data or are constructed in an expensive or complicated way. In contrast, this paper illustrates a low-cost approach that takes advantage of the nature of open source libraries for an AI-based chosen-plaintext attack. The chosen-plaintext attack described here relies on a deep learning model created and trained on a simple personal computer in a low-cost way. It shows an efficient cracking rate over two open-source Python CAPTCHA Libraries, Claptcha and Captcha. This chosen-plaintext attack method has raised a potential security alert in the era of AI, particularly to small-business owners who use the open-source CAPTCHA libraries. The main contributions of this project include: (1) it is the first low-cost method based on chosen-plaintext attack by using the nature of open-source Python CAPTCHA libraries; (2) it is a novel way to combine TensorFlow object detection and our proposed peak segmentation algorithm with convolutional neural network to improve the recognition accuracy.

Regional rainfall forecasting is an important issue in hydrology and meteorology. Machine learning algorithms especially deep learning methods have emerged as a part of prediction tools for regional rainfall forecasting. This paper aims to design and implement a generic computing framework that can assemble a variety of machine learning algorithms as computational engines for regional rainfall forecasting in Upstate New York. The algorithms that have been bagged in the computing framework include the classical algorithms and the state-of-the-art deep learning algorithms, such as K-Nearest Neighbors, Support Vector Machine, Deep Neural Network, Wide Neural Network, Deep and Wide Neural Network, Reservoir Computing, and Long Short Term Memory methods. Through the experimental results and the performance comparisons of these various engines, we have observed that the SVM- and KNN-based method are outstanding models over other models in classification while DWNN- and KNN-based methods outstrip other models in regression, particularly those prevailing deep-learning-based methods, for handling uncertain and complex climatic data for precipitation forecasting. Meanwhile, the normalization methods such as Z-score and Minmax are also integrated into the generic computing framework for the investigation and evaluation of their impacts on machine learning models.

Patients with the same type of cancer often respond differently to identical drug treatments due to unique genomic traits. Accurately predicting a patient's response to drug is crucial in guiding treatment decisions, alleviating patient suffering, and improving cancer prognosis. Current computational methods utilize deep learning models trained on extensive drug screening data to predict anti-cancer drug responses based on features of cell lines and drugs. However, the interaction between cell lines and drugs is a complex biological process involving interactions across various levels, from internal cellular and drug structures to the external interactions among different molecules.To address this complexity, we propose a novel Hierarchical graph representation Learning with Multi-Granularity features (HLMG) algorithm for predicting anti-cancer drug responses. The HLMG algorithm combines features at two granularities: the overall gene expression and pathway substructures of cell lines, and the overall molecular fingerprints and substructures of drugs. Subsequently, it constructs a heterogeneous graph including cell lines, drugs, known cell line-drug responses, and the associations between similar cell lines and similar drugs. Through a graph convolutional network model, the HLMG learns the final cell line and drug representations by aggregating features of their multi-level neighbor in the heterogeneous graph. The multi-level neighbors consist of the node self, directly related drugs/cell lines, and indirectly related similar drugs/cell lines. Finally, a linear correlation coefficient decoder is employed to reconstruct the cell line-drug correlation matrix to predict anti-cancer drug responses. Our model was tested on the Genomics of Drug Sensitivity in Cancer (GDSC) and the Cancer Cell Line Encyclopedia (CCLE) databases. Results indicate that HLMG outperforms other state-of-the-art methods in accurately predicting anti-cancer drug responses.