Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences.

Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), and cytosine (C). Genes are DNA sequences containing the information to synthesize proteins. The genes of higher eukaryotic organisms contain coding sequences, known as exons and non-coding sequences, known as introns, which are removed on splice sites after the DNA is transcribed into RNA. Genome annotation is the process of identifying the location of coding regions and determining their function. This process is fundamental for understanding gene structure; however, it is time-consuming and expensive when done by biochemical methods. With technological advances, splice site detection can be done computationally. Although various software tools have been developed to predict splice sites, they need to improve accuracy and reduce false-positive rates. The main goal of this research was to generate Deep Splicer, a deep learning model to identify splice sites in the genomes of humans and other species. This model has good performance metrics and a lower false-positive rate than the currently existing tools. Deep Splicer achieved an accuracy between 93.55% and 99.66% on the genetic sequences of different organisms, while Splice2Deep, another splice site detection tool, had an accuracy between 90.52% and 98.08%. Splice2Deep surpassed Deep Splicer on the accuracy obtained after evaluating C. elegans genomic sequences (97.88% vs. 93.62%) and A. thaliana (95.40% vs. 94.93%); however, Deep Splicer's accuracy was better for H. sapiens (98.94% vs. 97.15%) and D. melanogaster (97.14% vs. 92.30%). The rate of false positives was 0.11% for human genetic sequences and 0.25% for other species' genetic sequences. Another splice prediction tool, Splice Finder, had between 1% and 3% of false positives for human sequences, while other species' sequences had around 4% and 10%.

Monitoring the Emotional Response to the COVID-19 Pandemic Using Sentiment Analysis: A Case Study in Mexico.

The world is facing the COVID-19 pandemic, leading to an unprecedented change in the lifestyle routines of millions. Beyond the general physical health, financial, and social repercussions of the pandemic, the adopted mitigation measures also present significant challenges in the population's mental health and health programs. It is complex for public organizations to measure the population's mental health in order to incorporate it into their own decision-making process. Traditional survey methods are time-consuming, expensive, and fail to provide the continuous information needed to respond to the rapidly evolving effects of governmental policies on the population's mental health. A significant portion of the population has turned to social media to express the details of their daily life, rendering this public data a rich field for understanding emotional and mental well-being. This study aims to track and measure the sentiment changes of the Mexican population in response to the COVID-19 pandemic. To this end, we analyzed 760,064,879 public domain tweets collected from a public access repository to examine the collective shifts in the general mood about the pandemic evolution, news cycles, and governmental policies using open sentiment analysis tools. Sentiment analysis polarity scores, which oscillate around -0.15, show a weekly seasonality according to Twitter's usage and a consistently negative outlook from the population. It also remarks on the increased controversy after the governmental decision to terminate the lockdown and the celebrated holidays, which encouraged the people to incur social gatherings. These findings expose the adverse emotional effects of the ongoing pandemic while showing an increase in social media usage rates of 2.38 times, which users employ as a coping mechanism to mitigate the feelings of isolation related to long-term social distancing. The findings have important implications in the mental health infrastructure for ongoing mitigation efforts and feedback on the perception of policies and other measures. The overall trend of the sentiment polarity is 0.0001110643.

Retinal vessel extraction using Lattice Neural Networks with Dendritic Processing.

Retinal images can be used to detect and follow up several important chronic diseases. The classification of retinal images requires an experienced ophthalmologist. This has been a bottleneck to implement routine screenings performed by general physicians. It has been proposed to create automated systems that can perform such task with little intervention from humans, with partial success. In this work, we report advances in such endeavor, by using a Lattice Neural Network with Dendritic Processing (LNNDP). We report results using several metrics, and compare against well known methods such as Support Vector Machines (SVM) and Multilayer Perceptrons (MLP). Our proposal shows better performance than other approaches reported in the literature. An additional advantage is that unlike those other tools, LNNDP requires no parameters, and it automatically constructs its structure to solve a particular problem. The proposed methodology requires four steps: (1) Pre-processing, (2) Feature computation, (3) Classification and (4) Post-processing. The Hotelling T(2) control chart was used to reduce the dimensionality of the feature vector, from 7 that were used before to 5 in this work. The experiments were run on images of DRIVE and STARE databases. The results show that on average, F1-Score is better in LNNDP, compared with SVM and MLP implementations. Same improvement is observed for MCC and the accuracy.