Benchmarking network propagation methods for disease gene identification

In-silico identification of potential target genes for disease is an essential aspect of drug target discovery. Recent studies suggest that successful targets can be found through by leveraging genetic, genomic and protein interaction information. Here, we systematically tested the ability of 12 varied algorithms, based on network propagation, to identify genes that have been targeted by any drug, on gene-disease data from 22 common non-cancerous diseases in OpenTargets. We considered two biological networks, six performance metrics and compared two types of input gene-disease association scores. The impact of the design factors in performance was quantified through additive explanatory models. Standard cross-validation led to over-optimistic performance estimates due to the presence of protein complexes. In order to obtain realistic estimates, we introduced two novel protein complex-aware cross-validation schemes. When seeding biological networks with known drug targets, machine learning and diffusion-based methods found around 2-4 true targets within the top 20 suggestions. Seeding the networks with genes associated to disease by genetics decreased performance below 1 true hit on average. The use of a larger network, although noisier, improved overall performance. We conclude that diffusion-based prioritisers and machine learning applied to diffusion-based features are suited for drug discovery in practice and improve over simpler neighbour-voting methods. We also demonstrate the large impact of choosing an adequate validation strategy and the definition of seed disease genesPeer ReviewedPostprint (published version

Experimental Study on 164 Algorithms Available in Software Tools for Solving Standard Non-Linear Regression Problems

In the specialized literature, researchers can find a large number of proposals for solving regression problems that come from different research areas. However, researchers tend to use only proposals from the area in which they are experts. This paper analyses the performance of a large number of the available regression algorithms from some of the most known and widely used software tools in order to help non-expert users from other areas to properly solve their own regression problems and to help specialized researchers developing well-founded future proposals by properly comparing and identifying algorithms that will enable them to focus on significant further developments. To sum up, we have analyzed 164 algorithms that come from 14 main different families available in 6 software tools (Neural Networks, Support Vector Machines, Regression Trees, Rule-Based Methods, Stacking, Random Forests, Model trees, Generalized Linear Models, Nearest Neighbor methods, Partial Least Squares and Principal Component Regression, Multivariate Adaptive Regression Splines, Bagging, Boosting, and other methods) over 52 datasets. A new measure has also been proposed to show the goodness of each algorithm with respect to the others. Finally, a statistical analysis by non-parametric tests has been carried out over all the algorithms and on the best 30 algorithms, both with and without bagging. Results show that the algorithms from Random Forest, Model Tree and Support Vector Machine families get the best positions in the rankings obtained by the statistical tests when bagging is not considered. In addition, the use of bagging techniques significantly improves the performance of the algorithms without excessive increase in computational times.This work was supported in part by the University of Córdoba under the project PPG2019-UCOSOCIAL-03, and in part by the Spanish Ministry of Science, Innovation and Universities under Grant TIN2015- 68454-R and Grant TIN2017-89517-P

BSUV-Net: a fully-convolutional neural network for background subtraction of unseen videos

Background subtraction is a basic task in computer vision and video processing often applied as a pre-processing step for object tracking, people recognition, etc. Recently, a number of successful background-subtraction algorithms have been proposed, however nearly all of the top-performing ones are supervised. Crucially, their success relies upon the availability of some annotated frames of the test video during training. Consequently, their performance on completely “unseen” videos is undocumented in the literature. In this work, we propose a new, supervised, background subtraction algorithm for unseen videos (BSUV-Net) based on a fully-convolutional neural network. The input to our network consists of the current frame and two background frames captured at different time scales along with their semantic segmentation maps. In order to reduce the chance of overfitting, we also introduce a new data-augmentation technique which mitigates the impact of illumination difference between the background frames and the current frame. On the CDNet-2014 dataset, BSUV-Net outperforms stateof-the-art algorithms evaluated on unseen videos in terms of several metrics including F-measure, recall and precision.Accepted manuscrip