The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health.

Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge

Best practices for bioinformatic characterization of neoantigens for clinical utility

Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequencing technologies to identify neoantigens and to create personalized immunotherapies for cancer treatment. To create a personalized cancer vaccine, neoantigens must be computationally predicted from matched tumor-normal sequencing data, and then ranked according to their predicted capability in stimulating a T cell response. This candidate neoantigen prediction process involves multiple steps, including somatic mutation identification, HLA typing, peptide processing, and peptide-MHC binding prediction. The general workflow has been utilized for many preclinical and clinical trials, but there is no current consensus approach and few established best practices. In this article, we review recent discoveries, summarize the available computational tools, and provide analysis considerations for each step, including neoantigen prediction, prioritization, delivery, and validation methods. In addition to reviewing the current state of neoantigen analysis, we provide practical guidance, specific recommendations, and extensive discussion of critical concepts and points of confusion in the practice of neoantigen characterization for clinical use. Finally, we outline necessary areas of development, including the need to improve HLA class II typing accuracy, to expand software support for diverse neoantigen sources, and to incorporate clinical response data to improve neoantigen prediction algorithms. The ultimate goal of neoantigen characterization workflows is to create personalized vaccines that improve patient outcomes in diverse cancer types

Deep Learning based Recommender System: A Survey and New Perspectives

With the ever-growing volume of online information, recommender systems have been an effective strategy to overcome such information overload. The utility of recommender systems cannot be overstated, given its widespread adoption in many web applications, along with its potential impact to ameliorate many problems related to over-choice. In recent years, deep learning has garnered considerable interest in many research fields such as computer vision and natural language processing, owing not only to stellar performance but also the attractive property of learning feature representations from scratch. The influence of deep learning is also pervasive, recently demonstrating its effectiveness when applied to information retrieval and recommender systems research. Evidently, the field of deep learning in recommender system is flourishing. This article aims to provide a comprehensive review of recent research efforts on deep learning based recommender systems. More concretely, we provide and devise a taxonomy of deep learning based recommendation models, along with providing a comprehensive summary of the state-of-the-art. Finally, we expand on current trends and provide new perspectives pertaining to this new exciting development of the field.Comment: The paper has been accepted by ACM Computing Surveys. https://doi.acm.org/10.1145/328502

Personalised Visual Art Recommendation by Learning Latent Semantic Representations

In Recommender systems, data representation techniques play a great role as they have the power to entangle, hide and reveal explanatory factors embedded within datasets. Hence, they influence the quality of recommendations. Specifically, in Visual Art (VA) recommendations the complexity of the concepts embodied within paintings, makes the task of capturing semantics by machines far from trivial. In VA recommendation, prominent works commonly use manually curated metadata to drive recommendations. Recent works in this domain aim at leveraging visual features extracted using Deep Neural Networks (DNN). However, such data representation approaches are resource demanding and do not have a direct interpretation, hindering user acceptance. To address these limitations, we introduce an approach for Personalised Recommendation of Visual arts based on learning latent semantic representation of paintings. Specifically, we trained a Latent Dirichlet Allocation (LDA) model on textual descriptions of paintings. Our LDA model manages to successfully uncover non-obvious semantic relationships between paintings whilst being able to offer explainable recommendations. Experimental evaluations demonstrate that our method tends to perform better than exploiting visual features extracted using pre-trained Deep Neural Networks.Comment: Accepted at SMAP202

Automatic generation of software interfaces for supporting decisionmaking processes. An application of domain engineering & machine learning

[EN] Data analysis is a key process to foster knowledge generation in particular domains or fields of study. With a strong informative foundation derived from the analysis of collected data, decision-makers can make strategic choices with the aim of obtaining valuable benefits in their specific areas of action. However, given the steady growth of data volumes, data analysis needs to rely on powerful tools to enable knowledge extraction. Information dashboards offer a software solution to analyze large volumes of data visually to identify patterns and relations and make decisions according to the presented information. But decision-makers may have different goals and, consequently, different necessities regarding their dashboards. Moreover, the variety of data sources, structures, and domains can hamper the design and implementation of these tools. This Ph.D. Thesis tackles the challenge of improving the development process of information dashboards and data visualizations while enhancing their quality and features in terms of personalization, usability, and flexibility, among others. Several research activities have been carried out to support this thesis. First, a systematic literature mapping and review was performed to analyze different methodologies and solutions related to the automatic generation of tailored information dashboards. The outcomes of the review led to the selection of a modeldriven approach in combination with the software product line paradigm to deal with the automatic generation of information dashboards. In this context, a meta-model was developed following a domain engineering approach. This meta-model represents the skeleton of information dashboards and data visualizations through the abstraction of their components and features and has been the backbone of the subsequent generative pipeline of these tools. The meta-model and generative pipeline have been tested through their integration in different scenarios, both theoretical and practical. Regarding the theoretical dimension of the research, the meta-model has been successfully integrated with other meta-model to support knowledge generation in learning ecosystems, and as a framework to conceptualize and instantiate information dashboards in different domains. In terms of the practical applications, the focus has been put on how to transform the meta-model into an instance adapted to a specific context, and how to finally transform this later model into code, i.e., the final, functional product. These practical scenarios involved the automatic generation of dashboards in the context of a Ph.D. Programme, the application of Artificial Intelligence algorithms in the process, and the development of a graphical instantiation platform that combines the meta-model and the generative pipeline into a visual generation system. Finally, different case studies have been conducted in the employment and employability, health, and education domains. The number of applications of the meta-model in theoretical and practical dimensions and domains is also a result itself. Every outcome associated to this thesis is driven by the dashboard meta-model, which also proves its versatility and flexibility when it comes to conceptualize, generate, and capture knowledge related to dashboards and data visualizations

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.[Background]: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. [Results]: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. [Conclusions]: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.This work was supported by funds provided through the Gene Partnership and the Manton Center for Orphan Disease Research at Boston Children’s Hospital and the Center for Biomedical Informatics at Harvard Medical School and by generous donations in-kind of genomic sequencing services by Life Technologies (Carlsbad, CA, USA) and Complete Genomics (Mountain View, CA, USA).Peer Reviewe