MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to partially complementary regions within the 3’UTR of their target genes. Computational methods play an important role in target prediction and assume that the miRNA “seed region” (nt 2 to 8) is required for functional targeting, but typically only identify ∼80% of known bindings. Recent studies have highlighted a role for the entire miRNA, suggesting that a more flexible methodology is needed. We present a novel approach for miRNA target prediction based on Deep Learning (DL) which, rather than incorporating any knowledge (such as seed regions), investigates the entire miRNA and 3’TR mRNA nucleotides to learn a uninhibited set of feature descriptors related to the targeting process. We collected more than 150,000 experimentally validated homo sapiens miRNA:gene targets and cross referenced them with different CLIP-Seq, CLASH and iPAR-CLIP datasets to obtain ∼20,000 validated miRNA:gene exact target sites. Using this data, we implemented and trained a deep neural network—composed of autoencoders and a feed-forward network—able to automatically learn features describing miRNA-mRNA interactions and assess functionality. Predictions were then refined using information such as site location or site accessibility energy. In a comparison using independent datasets, our DL approach consistently outperformed existing prediction methods, recognizing the seed region as a common feature in the targeting process, but also identifying the role of pairings outside this region. Thermodynamic analysis also suggests that site accessibility plays a role in targeting but that it cannot be used as a sole indicator for functionality. Data and source code available at: https://bitbucket.org/account/user/bipous/projects/MIRAW. microRNAs are small RNA molecules that regulate biological processes by binding to the 3’UTR of a gene and their dysregulation is associated with several diseases. Computationally predicting these targets remains a challenge as they only partially match their target and so there can be hundreds of targets for a single microRNA. Current tools assume that most of the knowledge defining a microRNA-gene interaction can be captured by analysing the binding produced in the seed region (∼ the first 8nt in the miRNA). However, recent studies show that the whole microRNA can be important and form non-canonical targets. Here, we use a target prediction methodology that relies on deep neural networks to automatically learn the relevant features describing microRNA-gene interactions for predicting microRNA targets. This means we make no assumptions about what is important, leaving the task to the deep neural network. A key part of the work is obtaining a suitable dataset. Thus, we collected and curated more than 150,000 experimentally verified microRNA targets and used them to train the network. Using this approach, we are able to gain a better understanding of non-canonical targets and to improve the accuracy of state-of-the-art prediction tools.

Nowadays business process management is becoming a fundamental piece of many industrial processes. To manage the evolution and interactions between the business actions it is important to accurately model the steps to follow and the resources needed by a process. Workflows provide a way of describing the order of execution and the dependencies between the constituting activities of business processes. Workflow monitoring can help to improve and avoid delays in industrial environments where concurrent processes are carried out. In this article a new Petri net extension for modelling workflow activities together with their required resources is presented: resource-aware Petri nets (RAPN). An intelligent workflow management system for process monitoring and delay prediction is also introduced. Resource aware-Petri nets include time and resources within the classical Petri net workflow representation, facilitating the task of modelling and monitoring workflows. The workflow management system monitors the execution of workflows and detects possible delays using RAPN. In order to test this new approach, different services from a medical maintenance environment have been modelled and simulated.

Multi-attribute resource allocation problems involve the allocation of resources on the basis of several attributes, therefore, the definition of a fairness method for this kind of auctions should be formulated from a multi-dimensional perspective. Under such point of view, fairness should take into account all the attributes involved in the allocation problem, since focusing on just a single attribute may compromise the allocations regarding the remainder attributes (e.g. incurring in delayed or bad quality tasks). In this paper, we present a multi-dimensional fairness approach based on priorities. For that purpose, a recurrent auction scenario is assumed, in which the auctioneer keeps track of winner and losers. From that information, the priority methods are defined based on the lost auctions number, the number of consecutive loses, and the fitness of their loser bids. Moreover, some methods contain a probabilistic parameter that enables handling wealth ranking disorders due to fairness. We test our approach in real-data based simulator which emulates an industrial production environment where several resource providers compete to perform different tasks. The results pointed that multi-dimensional fairness incentives agents to remain in the market whilst it improves the equity of the wealth distribution without compromising the quality of the allocation attributesThis research project has been partially funded through the BR10/18 Scholarship granted to the first author of the paper. Work developed with the support of the research group SITES awarded with distinction by the Generalitat de Catalunya (SGR 2014-2016) and the MESC project funded by the Spanish MINECO (Ref. DPI2013-47450-C2-1-R

Medical applications have special features (interpretation of results in medical metrics, experiment reproducibility and dealing with complex data) that require the development of particular tools. The eXiT*CBR framework is proposed to support the development of and experimentation with new case-based reasoning (CBR) systems for medical diagnosis. Our framework offers a modular, heterogeneous environment that combines different CBR techniques for different application requirements. The graphical user interface allows easy navigation through a set of experiments that are pre-visualized as plots (receiver operator characteristics (ROC) and accuracy curves). This user-friendly navigation allows easy analysis and replication of experiments. Used as a plug-in on the same interface, eXiT*CBR can work with any data mining technique such as determining feature relevance. The results show that eXiT*CBR is a user-friendly tool that facilitates medical users to utilize CBR methods to determine diagnoses in the field of breast cancer, dealing with different patterns implicit in the data. Although several tools have been developed to facilitate the rapid construction of prototypes, none of them has taken into account the particularities of medical applications as an appropriate interface to medical users. eXiT*CBR aims to fill this gap. It uses CBR methods and common medical visualization tools, such as ROC plots, that facilitate the interpretation of the results. The navigation capabilities of this tool allow the tuning of different CBR parameters using experimental results. In addition, the tool allows experiment reproducibility.

In this work we propose a user-friendly medically oriented tool for prognosis development systems and experimentation under a case-based reasoning methodology. The tool enables health care collaboration practice to be mapped in cases where different doctors share their expertise, for example, or where medical committee composed of specialists from different fields work together to achieve a final prognosis. Each agent with a different piece of knowledge classifies the given cases through metrics designed for this purpose. Since multiple solutions for the same case are useless, agents collaborate among themselves in order to achieve a final decision through a coordinated schema. For this purpose, the tool provides a weighted voting schema and an evolutionary algorithm (genetic algorithm) to learn robust weights. Moreover, to test the experiments, the tool includes stratified cross-validation methods which take the collaborative environment into account. In this paper the different collaborative facilities offered by the tool are described. A sample usage of the tool is also providedThis research project has been partially funded through the projects labelled TIN2008-04547, DPI2011-24929 and CTQ2008-06865-C02-02 and the grants UDG-BR10/18 and FPU-AP2009-283

Motivation: Spatial transcriptomics (ST) enables the study of gene expression within its spatial context in histopathology samples. To date, a limiting factor has been the resolution of sequencing based ST products. The introduction of the Visium High Definition (HD) technology opens the door to cell resolution ST studies. However, challenges remain in the ability to accurately map transcripts to cells and in assigning cell types based on the transcript data. Results: We developed ENACT, a self-contained pipeline that integrates advanced cell segmentation with Visium HD transcriptomics data to infer cell types across whole tissue sections. Our pipeline incorporates novel bin-to-cell assignment methods, enhancing the accuracy of single-cell transcript estimates. Validated on diverse synthetic and real datasets, our approach is both scalable to samples with hundreds of thousands of cells and effective, offering a robust solution for spatially resolved transcriptomics analysis. Availability and implementation: ENACT source code is available at https://github.com/Sanofi-Public/enact-pipeline. Experimental data are available at https://zenodo.org/records/14748859.