Isoform Function Prediction Using Deep Neural Network

Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA sequence, They may have a systematic effect on cell function and regulation. It is widely reported that isoforms of a gene have distinct or even contrasting functions. Most studies have shown that alternative splicing plays a significant role in human health and disease. Despite the wide range of gene function studies, there is little information about isoforms' functionalities. Recently, some computational methods based on Multiple Instance Learning have been proposed to predict isoform function using gene function and gene expression profile. However, their performance is not desirable due to the lack of labeled training data. In addition, probabilistic models such as Conditional Random Field (CRF) have been used to model the relation between isoforms. This project uses all the data and valuable information such as isoform sequences, expression profiles, and gene ontology graphs and proposes a comprehensive model based on Deep Neural Networks. The UniProt Gene Ontology (GO) database is used as a standard reference for gene functions. The NCBI RefSeq database is used for extracting gene and isoform sequences, and the NCBI SRA database is used for expression profile data. Metrics such as Receiver Operating Characteristic Area Under the Curve (ROC AUC) and Precision-Recall Under the Curve (PR AUC) are used to measure the prediction accuracy.

Encrypted Internet traffic classification using a supervised Spiking Neural Network

Internet traffic recognition is an essential tool for access providers since recognizing traffic categories related to different data packets transmitted on a network help them define adapted priorities. That means, for instance, high priority requirements for an audio conference and low ones for a file transfer, to enhance user experience. As internet traffic becomes increasingly encrypted, the mainstream classic traffic recognition technique, payload inspection, is rendered ineffective. This paper uses machine learning techniques for encrypted traffic classification, looking only at packet size and time of arrival. Spiking neural networks (SNN), largely inspired by how biological neurons operate, were used for two reasons. Firstly, they are able to recognize time-related data packet features. Secondly, they can be implemented efficiently on neuromorphic hardware with a low energy footprint. Here we used a very simple feedforward SNN, with only one fully-connected hidden layer, and trained in a supervised manner using the newly introduced method known as Surrogate Gradient Learning. Surprisingly, such a simple SNN reached an accuracy of 95.9% on ISCX datasets, outperforming previous approaches. Besides better accuracy, there is also a very significant improvement on simplicity: input size, number of neurons, trainable parameters are all reduced by one to four orders of magnitude. Next, we analyzed the reasons for this good accuracy. It turns out that, beyond spatial (i.e. packet size) features, the SNN also exploits temporal ones, mostly the nearly synchronous (within a 200ms range) arrival times of packets with certain sizes. Taken together, these results show that SNNs are an excellent fit for encrypted internet traffic classification: they can be more accurate than conventional artificial neural networks (ANN), and they could be implemented efficiently on low power embedded systems.