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Modern research in the biomedical sciences is data-driven utilizing high-throughput technologies to generate big genomic data. The Library of Integrated Network-based Cellular Signatures (LINCS) is an example for a large-scale genomic data repository providing hundred thousands of high-dimensional gene expression measurements for thousands of drugs and dozens of cell lines. However, the remaining challenge is how to use these data effectively for pharmacogenomics. In this paper, we use LINCS data to construct drug association networks (DANs) representing the relationships between drugs. By using the Anatomical Therapeutic Chemical (ATC) classification of drugs we demonstrate that the DANs represent a systems pharmacogenomic landscape of drugs summarizing the entire LINCS repository on a genomic scale meaningfully. Here we identify the modules of the DANs as therapeutic attractors of the ATC drug classes.

The concept of a digital twin is intriguing as it presents an innovative approach to solving numerous real-world challenges. Initially emerging from the domains of manufacturing and engineering, digital twin research has transcended its origins and now finds applications across a wide range of disciplines. This multidisciplinary expansion has impressively demonstrated the potential of digital twin research. While the simulation aspect of a digital twin is often emphasized, the role of artificial intelligence (AI) and machine learning (ML) is severely understudied. For this reason, in this paper, we highlight the pivotal role of AI and ML for digital twin research. By recognizing that a digital twin is a component of a broader Digital Twin System (DTS), we can fully grasp the diverse applications of AI and ML. In this paper, we explore six AI techniques—(1) optimization (model creation), (2) optimization (model updating), (3) generative modeling, (4) data analytics, (5) predictive analytics and (6) decision making—and their potential to advance applications in health, climate science, and sustainability. [ABSTRACT FROM AUTHOR]

The concept of a digital twin (DT) has gained significant attention in academia and industry because of its perceived potential to address critical global challenges, such as climate change, healthcare, and economic crises. Originally introduced in manufacturing, many attempts have been made to present proper definitions of this concept. Unfortunately, there remains a great deal of confusion surrounding the underlying concept, with many scientists still uncertain about the distinction between a simulation, a mathematical model and a DT. The aim of this paper is to propose a formal definition of a digital twin. To achieve this goal, we utilize a data science framework that facilitates a functional representation of a DT and other components that can be combined together to form a larger entity we refer to as a digital twin system (DTS). In our framework, a DT is an open dynamical system with an updating mechanism, also referred to as complex adaptive system (CAS). Its primary function is to generate data via simulations, ideally, indistinguishable from its physical counterpart. On the other hand, a DTS provides techniques for analyzing data and decision-making based on the generated data. Interestingly, we find that a DTS shares similarities to the principles of general systems theory. This multi-faceted view of a DTS explains its versatility in adapting to a wide range of problems in various application domains such as engineering, manufacturing, urban planning, and personalized medicine. [ABSTRACT FROM AUTHOR]

The idea of a digital twin has recently gained widespread attention. While, so far, it has been used predominantly for problems in engineering and manufacturing, it is believed that a digital twin also holds great promise for applications in medicine and health. However, a problem that severely hampers progress in these fields is the lack of a solid definition of the concept behind a digital twin that would be directly amenable for such big data-driven fields requiring a statistical data analysis. In this paper, we address this problem. We will see that the term 'digital twin', as used in the literature, is like a Matryoshka doll. For this reason, we unstack the concept via a data-centric machine learning perspective, allowing us to define its main components. As a consequence, we suggest to use the term Digital Twin System instead of digital twin because this highlights its complex interconnected substructure. In addition, we address ethical concerns that result from treatment suggestions for patients based on simulated data and a possible lack of explainability of the underling models. [ABSTRACT FROM AUTHOR]

As a consequence of technological progress, nowadays, one is used to the availability of big data generated in nearly all fields of science. However, the analysis of such data possesses vast challenges. One of these challenges relates to the explainability of methods from artificial intelligence (AI) or machine learning. Currently, many of such methods are nontransparent with respect to their working mechanism and for this reason are called black box models, most notably deep learning methods. However, it has been realized that this constitutes severe problems for a number of fields including the health sciences and criminal justice and arguments have been brought forward in favor of an explainable AI (XAI). In this paper, we do not assume the usual perspective presenting XAI as it should be, but rather provide a discussion what XAI can be. The difference is that we do not present wishful thinking but reality grounded properties in relation to a scientific theory beyond physics. This article is categorized under:Fundamental Concepts of Data and Knowledge > Explainable AIAlgorithmic Development > StatisticsTechnologies > Machine Learning [ABSTRACT FROM AUTHOR]

Social media data, for instance from Twitter or Facebook, provide a new type of data that consist of a mixture of text, image and video information. From a scientific point of view, the capabilities of this type of data from such microblogs are not well explored and to date it is largely unknown what principal knowledge can be extracted thereof. In this paper, we present a discussion of the capabilities of data from microblogs for performing a psychoanalysis. This could allow an analysis of the human personality of individual users. Such prospects raises serious concerns regarding the privacy of users of social media platforms. [ABSTRACT FROM AUTHOR]

The LINCS L1000 data repository contains almost two million gene expression profiles for thousands of small molecules and drugs. However, due to the complexity and the size of the data repository and a lack of an interoperable interface, the creation of pharmacologically meaningful workflows utilizing these data is severely hampered. In order to overcome this limitation, we developed the L1000 Viewer, a search engine and graphical web interface for the LINCS data repository. The web interface serves as an interactive platform allowing the user to select different forms of perturbation profiles, e.g., for specific cell lines, drugs, dosages, time points and combinations thereof. At its core, our method has a database we created from inferring and utilizing the intricate dependency graph structure among the data files. The L1000 Viewer is accessible via http://L1000viewer.bio-complexity.com/. [ABSTRACT FROM AUTHOR]

The article examines the meaning and goals of data science as well as the process of analyzing data.

• We examine further the measure δ for measuring symmetry in networks. • We establish bounds for δ for graphs with a given number of orbit sizes. • These results can be used to classify graphs. • We perform an analysis to explore symmetry on isomers. • The analysis of the chemical graphs reveal that only a very few chemical graphs are highly symmetric. In this paper, we prove bounds for the unique, positive zero of O G ★ (z) : = 1 − O G (z) , where O G (z) is the so-called orbit polynomial [1]. The orbit polynomial is based on the multiplicity and cardinalities of the vertex orbits of a graph. In [1] , we have shown that the unique, positive zero δ ≤ 1 of O G ★ (z) can serve as a meaningful measure of graph symmetry. In this paper, we study special graph classes with a specified number of orbits and obtain bounds on the value of δ. [ABSTRACT FROM AUTHOR]

Binary decision making is a topic of great interest for many fields, including biomedical science, economics, management, politics, medicine, natural science and social science, and much effort has been spent for developing novel computational methods to address problems arising in the aforementioned fields. However, in order to evaluate the effectiveness of any prediction method for binary decision making, the choice of the most appropriate error measures is of paramount importance. Due to the variety of error measures available, the evaluation process of binary decision making can be a complex task. The main objective of this study is to provide a comprehensive survey of error measures for evaluating the outcome of binary decision making applicable to many data‐driven fields. This article is categorized under: Fundamental Concepts of Data and Knowledge > Key Design Issues in Data MiningTechnologies > PredictionAlgorithmic Development > Statistics [ABSTRACT FROM AUTHOR]