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Prognostic biomarkers can have an important role in the clinical practice because they allow stratification of patients in terms of predicting the outcome of a disorder. Obstacles for developing such markers include lack of robustness when using different data sets and limited concordance among similar signatures. In this paper, we highlight a new problem that relates to the biological meaning of already established prognostic gene expression signatures. Specifically, it is commonly assumed that prognostic markers provide sensible biological information and molecular explanations about the underlying disorder. However, recent studies on prognostic biomarkers investigating 80 established signatures of breast and prostate cancer demonstrated that this is not the case. We will show that this surprising result is related to the distinction between causal models and predictive models and the obfuscating usage of these models in the biomedical literature. Furthermore, we suggest a falsification procedure for studies aiming to establish a prognostic signature to safeguard against false expectations with respect to biological utility. publishedVersion

High-throughput technologies do not only provide novel means for basic biological research but also for clinical applications in hospitals. For instance, the usage of gene expression profiles as prognostic biomarkers for predicting, e.g., cancer progression, has found widespread interest. Aside from predicting the progression of patients it is generally believed that such prognostic biomarkers provide also valuable information about disease mechanisms and the underlying molecular processes that are causal for a disorder. However, the latter assumption has been challenged. In this paper, we study this problem for prostate cancer. Specifically, we investigate a large number of previously published prognostic signatures of prostate cancer based on gene expression profiles and show that none of these can provide unique information about the underlying disease etiology of prostate cancer. Hence, our analysis reveals that none of the studied signatures has a sensible biological meaning. Overall, this shows that all studied prognostic signatures are merely black-box models allowing sensible predictions of prostate cancer outcome but are not capable of providing causal explanations to enhance the understanding of prostate cancer. publishedVersion

Background: Cancer is a complex disease with a lucid etiology and in understanding the causation, we need to appreciate this complexity. Objective: Here we are aiming to gain insights into the genetic associations of prostate cancer through a network-based systems approach using the BC3Net algorithm. Methods: Specifically, we infer a prostate cancer Gene Regulatory Network (GRN) from a large-scale gene expression data set of 333 patient RNA-seq profiles obtained from The Cancer Genome Atlas (TCGA) database. Results: We analyze the functional components of the inferred network by extracting subnetworks based on biological process information and interpret the role of known cancer genes within each process. Fur-thermore, we investigate the local landscape of prostate cancer genes and discuss pathological associa-tions that may be relevant in the development of new targeted cancer therapies. Conclusion: Our network-based analysis provides a practical systems biology approach to reveal the collective gene-interactions of prostate cancer. This allows a close interpretation of biological activity in terms of the hallmarks of cancer.

The size of the orbits or similar vertices of a network provides important information regarding each individual component of the network. In this paper, we investigate the entropy or information content and the symmetry index for several classes of graphs and compare the values of this measure with that of the symmetry index of certain graphs. publishedVersion

The field artificial intelligence (AI) was founded over 65 years ago. Starting with great hopes and ambitious goals the field progressed through various stages of popularity and has recently undergone a revival through the introduction of deep neural networks. Some problems of AI are that, so far, neither the “intelligence” nor the goals of AI are formally defined causing confusion when comparing AI to other fields. In this paper, we present a perspective on the desired and current status of AI in relation to machine learning and statistics and clarify common misconceptions and myths. Our discussion is intended to lift the veil of vagueness surrounding AI to reveal its true countenance. publishedVersion

The orbit polynomial is a new graph counting polynomial which is defined as OG(x)=&sum, i=1rx|Oi|, where O1, &hellip, Or are all vertex orbits of the graph G. In this article, we investigate the structural properties of the automorphism group of a graph by using several novel counting polynomials. Besides, we explore the orbit polynomial of a graph operation. Indeed, we compare the degeneracy of the orbit polynomial with a new graph polynomial based on both eigenvalues of a graph and the size of orbits.

Symmetry is an important visual feature for humans and its application in architecture is completely evident. This paper aims to investigate the role of symmetry in the aesthetics judgment of residential building fa&ccedil, ades and study the pattern of eye movement based on the expertise of subjects in architecture. In order to implement this in the present paper, we have created images in two categories: symmetrical and asymmetrical fa&ccedil, ade images. The experiment design allows us to investigate the preference of subjects and their reaction time to decide about presented images as well as record their eye movements. It was inferred that the aesthetic experience of a building fa&ccedil, ade is influenced by the expertise of the subjects. There is a significant difference between experts and non-experts in all conditions, and symmetrical fa&ccedil, ades are in line with the taste of non-expert subjects. Moreover, the patterns of fixational eye movements indicate that the horizontal or vertical symmetry (mirror symmetry) has a profound influence on the observer&rsquo, s attention, but there is a difference in the points watched and their fixation duration. Thus, although symmetry may attract the same attention during eye movements on fa&ccedil, ade images, it does not necessarily lead to the same preference between the expert and non-expert groups.

The number of scientific publications in the literature is steadily growing, containing our knowledge in the biomedical, health, and clinical sciences. Since there is currently no automatic archiving of the obtained results, much of this information remains buried in textual details not readily available for further usage or analysis. For this reason, natural language processing (NLP) and text mining methods are used for information extraction from such publications. In this paper, we review practices for Named Entity Recognition (NER) and Relation Detection (RD), allowing, e.g., to identify interactions between proteins and drugs or genes and diseases. This information can be integrated into networks to summarize large-scale details on a particular biomedical or clinical problem, which is then amenable for easy data management and further analysis. Furthermore, we survey novel deep learning methods that have recently been introduced for such tasks. publishedVersion

Afullerene is a cubic three-connected graph whose faces are entirely composed of pentagons and hexagons. Entropy applied to graphs is one of the significant approaches to measuring the complexity of relational structures. Recently, the research on complex networks has received great attention, because many complex systems can be modelled as networks consisting of components as well as relations among these components. Information-theoretic measures have been used to analyze chemical structures possessing bond types and hetero-atoms. In the present article, we reviewed various entropy-based measures on fullerene graphs. In particular, we surveyed results on the topological information content of a graph, namely the orbit-entropy Ia(G), the symmetry index, a degree-based entropy measure Iλ(G), the eccentric-entropy ifσ(G) and the Hosoya entropy H(G). publishedVersion

Deep learning models stand for a new learning paradigm in artificial intelligence (AI) and machine learning. Recent breakthrough results in image analysis and speech recognition have generated a massive interest in this field because also applications in many other domains providing big data seem possible. On a downside, the mathematical and computational methodology underlying deep learning models is very challenging, especially for interdisciplinary scientists. For this reason, we present in this paper an introductory review of deep learning approaches including Deep Feedforward Neural Networks (D-FFNN), Convolutional Neural Networks (CNNs), Deep Belief Networks (DBNs), Autoencoders (AEs), and Long Short-Term Memory (LSTM) networks. These models form the major core architectures of deep learning models currently used and should belong in any data scientist's toolbox. Importantly, those core architectural building blocks can be composed flexibly—in an almost Lego-like manner—to build new application-specific network architectures. Hence, a basic understanding of these network architectures is important to be prepared for future developments in AI. publishedVersion

The wind field is an essential factor that affects accurate homing and flare landing of parafoil systems. In order to obtain the ambient wind field during the descent of a parafoil system, a combination method of in-flight wind field identification and prediction is proposed. First, a wind identification method only using global position system information is derived based on the flight dynamics of parafoil systems. Then a wind field prediction model is constructed using the atmospheric dynamics, and the low-altitude wind field is predicted based on the identified wind field of high-altitude. Finally, simulations of wind field identification and prediction are conducted. The results demonstrate that the proposed method can identify the wind fields precisely and also predict the wind fields reasonably. This method can potentially be applied in practical parafoil systems to provide wind field information for homing tasks. publishedVersion

Research on the structural complexity of networks has produced many useful results in graph theory and applied disciplines such as engineering and data analysis. This paper is intended as a further contribution to this area of research. Here we focus on measures designed to compare graphs with respect to symmetry. We do this by means of a novel characteristic of a graph G, namely an 'orbit polynomial.' A typical term of this univariate polynomial is of the form czn, where c is the number of orbits of size n of the automorphism group of G. Subtracting the orbit polynomial from 1 results in another polynomial that has a unique positive root, which can serve as a relative measure of the symmetry of a graph. The magnitude of this root is indicative of symmetry and can thus be used to compare graphs with respect to that property. In what follows, we will prove several inequalities on the unique positive roots of orbit polynomials corresponding to different graphs, thus showing differences in symmetry. In addition,we present numerical results relating to several classes of graphs for the purpose of comparing the new symmetry measure with existing ones. Finally, it is applied to a set of isomers of the chemical compound adamantane C10H16. We believe that the measure can be quite useful for tackling applications in chemistry, bioinformatics, and structure-oriented drug design.

The number of scientific publications in the literature is steadily growing, containing our knowledge in the biomedical, health, and clinical sciences. Since there is currently no automatic archiving of the obtained results, much of this information remains buried in textual details not readily available for further usage or analysis. For this reason, natural language processing (NLP) and text mining methods are used for information extraction from such publications. In this paper, we review practices for Named Entity Recognition (NER) and Relation Detection (RD), allowing, e.g., to identify interactions between proteins and drugs or genes and diseases. This information can be integrated into networks to summarize large-scale details on a particular biomedical or clinical problem, which is then amenable for easy data management and further analysis. Furthermore, we survey novel deep learning methods that have recently been introduced for such tasks.

In this paper, we define novel graph measures for directed networks. The measures are based on graph polynomials utilizing the out- and in-degrees of directed graphs. Based on these polynomial, we define another polynomial and use their positive zeros as graph measures. The measures have meaningful properties that we investigate based on analytical and numerical results. As the computational complexity to compute the measures is polynomial, our approach is efficient and can be applied to large networks. We emphasize that our approach clearly complements the literature in this field as, to the best of our knowledge, existing complexity measures for directed graphs have never been applied on a large scale.