Antonio Neme

• PhD
• Senior Researcher at National Autonomous University of Mexico

A lack of labeled examples is a problem in different domains, such as text and image processing, medicine, and static reservoir characterization, because supervised learning relies on vast volumes of these data to perform successfully, but this is quite expensive. However, large amounts of unlabeled data exist in these domains. The deep semi-superv...

Horizontal gene transference is a biological process that involves the donation of DNA or RNA from an organism to a second, unrelated organism. This process is different from the more common one, vertical transference, which is present whenever an organism or pair of organisms reproduce and transmit their genetic material to the descendants. The id...

Property prediction is a key interest in chemistry. For several decades there has been a continued and incremental development of mathematical models to predict properties. As more data is generated and accumulated, there seems to be more areas of opportunity to develop models with increased accuracy. The same is true if one considers the large dev...

Natural Language Processing has focused its efforts in sentiment analysis, token categorization, topic identification, translation, authorship attribution and many other relevant and useful tasks. In this contribution, we describe an algorithm able to characterize texts in a feature space from which, among other tasks, the authorship attribution pr...

Scene classification in autonomous navigation is a highly complex task due to variations, such as light conditions and dynamic objects, in the inspected scenes; it is also a challenge for small-factor computers to run modern and highly demanding algorithms. In this contribution, we introduce a novel method for classifying scenes in simultaneous loc...

An open problem in data science is that of anomaly detection. Anomalies are instances that do not maintain a certain property that is present in the remaining observations in a dataset. Several anomaly detection algorithms exist, since the process itself is ill-posed mainly because the criteria that separates common or expected vectors from anomali...

We propose a methodology to narrow down the selection of design parameters of phantoms for calibrating ultrasound devices. For doing so, we model the phantoms as composite materials. Through a mathematical homogenization technique, the global properties of the phantom are given in terms of the volume fractions of its components, their geometric sha...

Chagas disease, caused by the Trypanosoma cruzi (T. cruzi) parasite, is the third most common parasitosis worldwide. Most of the infected subjects can remain asymptomatic without an opportune and early detection or an objective diagnostic is not conducted. Frequently, the disease manifests itself after a long time, accompanied by severe heart disea...

The process of recognizing manufacturing parts in real time requires fast, accurate, small, and low-power-consumption sensors. Here, we describe a method to extract descriptors from several objects observed from a wide range of angles in a three-dimensional space. These descriptors define the dataset, which allows for the training and further valid...

The transcription factor vitamin D receptor (VDR) is the high affinity nuclear target of the biologically active form of vitamin D3 (1,25(OH)2D3). In order to identify pure genomic transcriptional effects of 1,25(OH)2D3, we used VDR cistrome, transcriptome and open chromatin data, obtained from the human monocytic cell line THP-1, for a novel hiera...

Vitamin D is essential for the function of the immune system. In this study, we treated peripheral blood mononuclear cells (PBMCs) of healthy adults with the biologically active form of vitamin D3, 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) using two different approaches: single repeats with PBMCs obtained from a cohort of 12 individuals and personali...

Writers tend to follow a certain style that can be detected or at least sketched by an appropriate algorithm. Columnists in newspapers, being also writers, follow their specific style. The style tends to be stable once writers reach maturity, but it is subject to change when internal or external circumstances differ. Here, we apply a bag-of-words a...

Chromatin accessibility illustrates the density of nucleosome packaging and is a key feature of epigenetic analysis. Genomic DNA at accessible chromatin regions can be bound by transcription factors, polymerases and other nuclear proteins and often represents promoters, enhancers and other gene regulatory elements. In the past these sites have been...

We tested whether lifelong modification of vitamin D signaling can alter the progression of early prostate carcinogenesis in studies using mice that develop high-grade prostatic intraepithelial neoplasia that is similar to humans. Two tissue-limited models showed that prostate vitamin D receptor (VDR) loss increased prostate carcinogenesis. In anot...

In the vitamin D intervention study VitDbol (NCT02063334) blood samples were drawn directly before an oral bolus (2000 μg vitamin D3) and 24 h later. The focus of phase II of VitDbol was the transcriptome-wide analysis of the effects of vitamin D gene expression in human peripheral blood mononuclear cells (PBMCs). All five participants responded in...

The myeloid master regulator CCAAT enhancer-binding protein alpha (CEBPA) is known as a pioneer factor. In this study, we report the CEBPA cistrome of THP-1 human monocytes after stimulation with the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) for 2, 8 and 24 h. About a third of the genomic VDR binding sites co-located w...

No single-omic approach completely elucidates the multitude of alterations taking place in Alzheimer's disease (AD). Here, we coupled transcriptomic and phosphoproteomic approaches to determine the temporal sequence of changes in mRNA, protein, and phosphopeptide expression levels from human temporal cortical samples, with varying degree of AD-rela...

The micronutrient vitamin D significantly modulates the human epigenome via enhancing genome-wide the rate of accessible chromatin and vitamin D receptor (VDR) binding. This study focuses on histone marks of active chromatin at promoter and enhancer regions and investigates, whether these genomic loci are sensitive to vitamin D. The epigenome of TH...

The vitamin D-modulated transcriptome of highly responsive human cells, such as THP-1 monocytes, comprises more than 500 genes, half of which are primary targets. Recently, we proposed a chromatin model of vitamin D signaling demonstrating that nearly all vitamin D target genes are located within vitamin D-modulated topologically associated domains...

Electoral fraud can be committed along several stages. Different tools have been applied to detect the existence of such undesired actions. One particular undesired activity is that of vote-buying. It can be thought of as an economical influence of a candidate over voters that in other circumstances could have decided to vote for a different candid...

Pedestrian dynamics have been widely studied in the context of crowds in panic situations. In this contribution, however, we have condensed the research undertaken on the dynamics of users inside high-capacity buses under normal conditions. The dynamics and distribution followed by users inside the bus lead to spatial distributions in which several...

The physiological functions of vitamin D are mediated by its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) activating the transcription factor vitamin D receptor (VDR). In THP-1 human monocytes we demonstrated epigenome-wide effects of 1,25(OH)2D3 at 8979 loci with significantly modulated chromatin accessibility. Maximal chromatin opening was...

Monocytes are important cells of the innate immune system that can differentiate into macrophages and dendritic cells. The biologically active form of vitamin D, 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3), serves as a ligand of the nuclear receptor vitamin D receptor (VDR). A key physiological function of 1,25(OH)2D3 is the defense against pathogens,...

Vitamin D 3 has transcriptome-and genome-wide effects and activates, via the binding of its metabolite 1α,25-dihydroxyvitamin D 3 to the transcription factor vitamin D receptor (VDR), several hundred target genes. Using samples from a 5-month vitamin D 3 intervention study (VitDmet), we recently reported that the expression of 12 VDR target genes i...

The style followed by authors can be thought of as a collection of attributes that defines the stylistics space. Texts from the same author tend to be similar in that space. However, the identification of stylistics spaces has proven to be challenging. Associated with the stylistics space is the authorship attribution task. On it, a text of unknown...

Scope: Vitamin D₃, its biologically most active metabolite 1α,25-dihydroxyvitamin D₃ (1,25(OH)₂D₃), and the vitamin D receptor (VDR) are important for adipose tissue biology. Methods and results: We extrapolated genomic VDR association loci in adipocytes from 55 conserved genome-wide VDR-binding sites in nonfat tissues. Taking the genes DUSP10,...

The genome-wide analysis of the binding sites of the transcription factor vitamin D receptor (VDR) is essential for a global appreciation the physiological impact of the nuclear hormone 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). Genome-wide analysis of lipopolysaccharide (LPS)-polarized THP-1 human monocytic leukemia cells via chromatin immunoprecipi...

The vitamin D receptor (VDR) is a transcription factor that mediates the genomic effects of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). Genome-wide there are several thousand binding sites and hundreds of primary 1,25(OH)2D3 target genes, but their functional relation is largely elusive. In this study, we used ChIA-PET data of the transcription factor...

Decreasing neighborhood with distance has been identified as one of a few conditions to achieve final states in the self-organizing map (SOM) that resemble the distribution of high-dimensional input data. In the classic SOM model, best matching units (BMU) decrease their influence area as a function of distance. We introduce a modification to the S...

Exploratory data analysis is a fundamental stage in data mining of high-dimensional datasets. Several algorithms have been implemented to grasp a general idea of the geometry and patterns present in high-dimensional data. Here, we present a methodology based on the distance matrix of the input data. The algorithm is based in the number of points co...

Cancer cells present several mutations that allow them to grow faster than normal cells, at the time that enables them to avoid apotosis and other control processes. Cancer cell may be affected by synthetic lethality, which refers to the induction of one or more mutations that affect them, but affect normal cells as little as possible. It is one of...

The style authors follow to express their ideas has been a subject of great debate. Several perspectives have been followed to try to analyze the style. In this contribution we present a computational methodology to study the writing style in a collection of hundreds of texts. For each text several attributes, which include different time series, a...

Authorship attribution has attracted the attention of the natural language processing and machine learning communities in the past few years. Here we are interested in finding a general measure of the style followed in the texts from the three main candidates in the Mexican presidential elections of 2012. We analyzed dozens of texts (discourses) fr...

Multilayer perceptrons can be trained with several algorithms and with different quantities that correlate the expected output and the achieved state. Among the most common of those quantities is the mean square error, but information-theoretic quantities have been applied with great success. A common scheme to train multilayer perceptrons is based...

A model of spatial pattern formation of electoral preferences is presented. In some voting districts, patterns of electoral preferences emerge, such that in nearby areas citizens tend to vote for the same candidate whereas in geographically distant areas the most voted candidate is that whose political position is distant to the latter. Those patte...

Air pollution in big cities is a major health problem. Pollutants in the air may have severe consequences in humans, creating conditions for several illness and also affect tissues and organs, and also affect other animals and crop productivity. From several years now, the air quality has been monitored by stations distributed over major cities, an...

Cities are instances of complex structures. They present several conflicting dynamics, emergence of unexpected patterns of mobility and behavior, as well as some degree of adaptation. To make sense of several aspects of cities, such as traffic flow, mobility, social welfare, social exclusion, and commodities, data mining may be an appropriate techn...

We propose the use of self-organizing maps as models of social processes, in particular, of electoral preferences. In some voting districts patterns of electoral preferences emerge, such that in nearby areas citizens tend to vote for the same candidate whereas in geographically distant areas the most voted candidate is that whose political position...

Visualization of high-dimensional data is a major task in data mining. The main idea of visualization is to map data from the high-dimensional space onto a certain position in a low-dimensional space. From all mappings, only those that lead to maps that are good approximations of the data distribution observed in the high-dimensional space are of i...

Writers tend to express their ideas with different styles, defined with the so called firm or stylome, which is an abstraction of the general constraints and specific combinations of words within their language they decide to follow. Although capturing this style has proven to be very difficult, some advances have been achieved. Here, we present a...

The training scheme in self-organizing maps consists of two phases: i) competition, in which all units intend to become the best matching unit (BMU), and ii) cooperation, in which the BMU allows its neighbor units to adapt their weight vector. In order to study the relevance of cooperation, we present a model in which units do not necessarily coope...

Natural computing finds its source of inspiration in diverse biological phenomena and social behaviors from mainly insects and birds. In this chapter, we instead propose human social phenomena. The presented algorithms have been applied in optimization endeavours with success or are promising tools in the design of optimization techniques.

Learning how to count in different bases has been seen as a trivial task in almost all introductory mathematics courses. However, the low performance shown by many students, while performing this task, is appalling. This situation has motivated serious research in this matter. In order to study a model of count learning, we analyze the performance...

Cluster analysis applications of the SOM require it to be sensible to features, or groupings, of different sizes in the input data. On the other hand, the SOM’s behavior while the organization process is taking place also exhibits regularities of different scales, such as periodic behaviors of different frequencies, or changes of different magnitud...

Decreasing neighborhood has been identified as a necessary condition for self-organization to hold in the self-organizing map (SOM). In the SOM, each best matching unit (BMU) decreases its influence area as a function of time and this area is always radial. Here, we present a model in which the BMU does not reduce its neighborhood, but the rest of...