A miRNA-Target Prediction Case Study

Giansanti, V., Castelli, M., Beretta, S., & Merelli, I. (2019). Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study. In V. V. Krzhizhanovskaya, M. H. Lees, P. M. A. Sloot, J. J. Dongarra, J. M. F. Rodrigues, P. J. S. Cardoso, J. Monteiro, ... R. Lam (Eds.), Computational Science – ICCS 2019: 19th International Conference, Faro, Portugal, June 12–14, 2019, Proceedings, Part III (pp. 31-44). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11538 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-030-22744-9_3MicroRNAs (miRNAs) are small non-coding RNAs with a key role in the post-transcriptional gene expression regularization, thanks to their ability to link with the target mRNA through the complementary base pairing mechanism. Given their role, it is important to identify their targets and, to this purpose, different tools were proposed to solve this problem. However, their results can be very different, so the community is now moving toward the deployment of integration tools, which should be able to perform better than the single ones. As Machine and Deep Learning algorithms are now in their popular years, we developed different classifiers from both areas to verify their ability to recognize possible miRNA-mRNA interactions and evaluated their performance, showing the potentialities and the limits that those algorithms have in this field. Here, we apply two deep learning classifiers and three different machine learning models to two different miRNA-mRNA datasets, of predictions from 3 different tools: TargetScan, miRanda, and RNAhybrid. Although an experimental validation of the results is needed to better confirm the predictions, deep learning techniques achieved the best performance when the evaluation scores are taken into account.authorsversionpublishe

Evaluating the benefits of key-value databases for scientific applications

The convergence of Big Data applications with High-Performance Computing requires new methodologies to store, manage and process large amounts of information. Traditional storage solutions are unable to scale and that results in complex coding strategies. For example, the brain atlas of the Human Brain Project has the challenge to process large amounts of high-resolution brain images. Given the computing needs, we study the effects of replacing a traditional storage system with a distributed Key-Value database on a cell segmentation application. The original code uses HDF5 files on GPFS through an intricate interface, imposing synchronizations. On the other hand, by using Apache Cassandra or ScyllaDB through Hecuba, the application code is greatly simplified. Thanks to the Key-Value data model, the number of synchronizations is reduced and the time dedicated to I/O scales when increasing the number of nodes.This project/research has received funding from the European Unions Horizon 2020 Framework Programme for Research and Innovation under the Speci c Grant Agreement No. 720270 (Human Brain Project SGA1) and the Speci c Grant Agreement No. 785907 (Human Brain Project SGA2). This work has also been supported by the Spanish Government (SEV2015-0493), by the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P), and by Generalitat de Catalunya (contract 2017-SGR-1414).Postprint (author's final draft

Investigation on Data Adaptation Techniques for Neural Named Entity Recognition

Data processing is an important step in various natural language processing tasks. As the commonly used datasets in named entity recognition contain only a limited number of samples, it is important to obtain additional labeled data in an efficient and reliable manner. A common practice is to utilize large monolingual unlabeled corpora. Another popular technique is to create synthetic data from the original labeled data (data augmentation). In this work, we investigate the impact of these two methods on the performance of three different named entity recognition tasks.Comment: ACL SRW 2021 - camera read

12th International Conference on Sustainable Energy Information Technology (SEIT 2022)

A way to reduce carbon emissions in cities is through movement by bicycle or on foot. However, it sometimes means to pass through high-pollution zones and consequently breath low quality air. We then propose a green Intelligent Transportation System (ITS) for zero-emission mobility users, providing users with low-pollution routes to avoid the high-pollution zones. This proposal uses ITS to promote the use of alternative transportation to classical motor vehicles to reduce carbon emissions. This is based on Complex Event Processing (CEP) technology to gather and process real-time data, a Decision Support System designed as a Fuzzy Inference System (FIS) to make decisions about recommended transit zones, taking also into account the user experience level and specific weather data, and Colored Petri Nets (CPN) as a tool to compute the routes. This is therefore an all-in-one solution to provide green routes, with the benefits of each one of the technologies used

Attention-based bidirectional GRU networks for efficient HTTPS traffic classification

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordDistributed and pervasive web services have become a major platform for sharing information. However, the hypertext transfer protocol secure (HTTPS), which is a crucial web encryption technology for protecting the information security of users, creates a supervisory burden for network management (e.g., quality-of-service guarantees and traffic engineering). Identifying various types of encrypted traffic is crucial for cyber security and network management. In this paper, we propose a novel deep learning model called BGRUA to identify the web services running on HTTPS connections accurately. BGRUA utilizes a bidirectional gated recurrent unit (GRU) and attention mechanism to improve the accuracy of HTTPS traffic classification. The bidirectional GRU is used to extract the forward and backward features of the byte sequences in a session. The attention mechanism is adopted to assign weights to features according to their contributions to classification. Additionally, we investigate the effects of different hyperparameters on the performance of BGRUA and present a set of optimal values that can serve as a basis for future relevant studies. Comparisons to existing methods based on three typical datasets demonstrate that BGRUA outperforms state-of-the-art encrypted traffic classification approaches in terms of accuracy, precision, recall, and F1-score

SimAnMo — A parallelized runtime model generator

In this article, we present the novel features of the recent version of SimAnMo, the Simulated Annealing Modeler. The tool creates models that correlate the size of one input parameter of an application to the corresponding runtime and thus SimAnMo allows predictions for larger input sizes. A focus lies on applications whose runtime grows exponentially in the input parameter size. Such programs are, for example, of high interest for cryptanalysis to analyze practical security of traditional and post‐quantum secure schemes. However, SimAnMo also generates reliable models for the widespread case of polynomial runtime behavior and also for the important case of factorial runtime increase. SimAnMo's model generation is based on a parallelized simulated annealing procedure and heuristically minimizes the costs of a model. Those may rely on different quality metrics. Insights into SimAnMo's software design and its usage are provided. We demonstrate the quality of SimAnMo's models for different algorithms from various application fields. We show that our approach also works well on ARM architectures