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Many complex physical systems exhibit a rich variety of discrete behavioural modes. Often, the system complexity limits the applicability of standard modelling tools. Hence, understanding the underlying physics of different behaviours and distinguishing between them is challenging. Although traditional machine learning techniques could predict and classify behaviour well, typically they do not provide any meaningful insight into the underlying physics of the system. In this paper we present a novel method for extracting physically meaningful clusters of discrete behaviour from limited experimental observations. This method obtains a set of physically plausible functions that both facilitate behavioural clustering and aid in system understanding. We demonstrate the approach on the V-shaped falling paper system, a new falling paper type system that exhibits four distinct behavioural modes depending on a few morphological parameters. Using just 49 experimental observations, the method discovered a set of candidate functions that distinguish behaviours with an error of 2.04%, while also aiding insight into the physical phenomena driving each behaviour. © 2019 Howison et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Author summary Conferences are great venues for disseminating algorithmic bioinformatics results, but they unfortunately do not offer an opportunity to make major revisions in the way that journals do. As a result, it is not possible for authors to fix mistakes that might be easily correctable but nevertheless can cause the paper to be rejected. As a reviewer, I wish that I had the opportunity to tell the authors, “Hey, you forgot to do this really important thing, without which it is hard to accept the paper, but if you could go back and fix it, you might have a great paper for the conference.” This lack of a back and forth can be especially problematic for first-time submitters or those from outside the field, e.g., biologists. In this article, I outline Ten Simple Rules to follow when writing an algorithmic bioinformatics conference paper to avoid having it rejected.

I review my scientific career in terms of eight areas and 16 papers. The first two areas are associated with childhood. The other six are associated with residual maximum likelihood (REML), canonical transformation, inbreeding in selected populations, average information residual maximum likelihood (AIREML), the computer program ASReml and sampling-based estimation.

The Semantic Link Network is a general semantic model for modeling the structure and the evolution of complex systems. Various semantic links play different roles in rendering the semantics of complex system. One of the basic semantic links represents cause-effect relation, which plays an important role in representation and understanding. This paper verifies the role of the Semantic Link Network in representing the core of text by investigating the contribution of cause-effect link to representing the core of scientific papers. Research carries out with the following steps: (1) Two propositions on the contribution of cause-effect link in rendering the core of paper are proposed and verified through a statistical survey, which shows that the sentences on cause-effect links cover about 65% of key words within each paper on average. (2) An algorithm based on syntactic patterns is designed for automatically extracting cause-effect link from scientific papers, which recalls about 70% of manually annotated cause-effect links on average, indicating that the result adapts to the scale of data sets. (3) The effects of cause-effect link on four schemes of incorporating cause-effect link into the existing instances of the Semantic Link Network for enhancing the summarization of scientific papers are investigated. The experiments show that the quality of the summaries is significantly improved, which verifies the role of semantic links. The significance of this research lies in two aspects: (1) it verifies that the Semantic Link Network connects the important concepts to render the core of text; and, (2) it provides an evidence for realizing content services such as summarization, recommendation and question answering based on the Semantic Link Network, and it can inspire relevant research on content computing.

Quantifying the impact of a scholarly paper is of great significance, yet the effect of geographical distance of cited papers has not been explored. In this paper, we examine 30,596 papers published in Physical Review C, and identify the relationship between citations and geographical distances between author affiliations. Subsequently, a relative citation weight is applied to assess the impact of a scholarly paper. A higher-order weighted quantum PageRank algorithm is also developed to address the behavior of multiple step citation flow. Capturing the citation dynamics with higher-order dependencies reveals the actual impact of papers, including necessary self-citations that are sometimes excluded in prior studies. Quantum PageRank is utilized in this paper to help differentiating nodes whose PageRank values are identical. Refereed/Peer-reviewed

This article proposes an Enhanced Memetic Differential Evolution (EMDE) for designing digital filters which aim at detecting defects of the paper produced during an industrial process. Defect detection is handled by means of two Gabor filters and their design is performed by the EMDE. The EMDE is a novel adaptive evolutionary algorithm which combines the powerful explorative features of Differential Evolution with the exploitative features of three local search algorithms employing different pivot rules and neighborhood generating functions. These local search algorithms are the Hooke Jeeves Algorithm, a Stochastic Local Search, and Simulated Annealing. The local search algorithms are adaptively coordinated by means of a control parameter that measures fitness distribution among individuals of the population and a novel probabilistic scheme. Numerical results confirm that Differential Evolution is an efficient evolutionary framework for the image processing problem under investigation and show that the EMDE performs well. As a matter of fact, the application of the EMDE leads to a design of an efficiently tailored filter. A comparison with various popular metaheuristics proves the effectiveness of the EMDE in terms of convergence speed, stagnation prevention, and capability in detecting solutions having high performance.

With the rapid development of information technology, scientific social networks (SSNs) have become the fastest and most convenient way for researchers to communicate with each other. Many published papers are shared via SSNs every day, resulting in the problem of information overload. How to appropriately recommend personalized and highly valuable papers for researchers is becoming more urgent. However, when recommending papers in SSNs, only a small amount of positive instances are available, leaving a vast amount of unlabelled data, in which negative instances and potential unseen positive instances are mixed together, which naturally belongs to One-Class Collaborative Filtering (OCCF) problem. Therefore, considering the extreme data imbalance and data sparsity of this OCCF problem, a hybrid approach of Social and Content aware One-class Recommendation of Papers in SSNs, termed SCORP, is proposed in this study. Unlike previous approaches recommended to address the OCCF problem, social information, which has been proved playing a significant role in performing recommendations in many domains, is applied in both the profiling of content-based filtering and the collaborative filtering to achieve superior recommendations. To verify the effectiveness of the proposed SCORP approach, a real-life dataset from CiteULike was employed. The experimental results demonstrate that the proposed approach is superior to all of the compared approaches, thus providing a more effective method for recommending papers in SSNs.

Cyclic dominance of three species is a commonly occurring interaction dynamics, often denoted the rock-paper-scissors (RPS) game. Such a type of interactions is known to promote species coexistence. Here, we generalize recent results of Reichenbach et al. [Nature (London) 448, 1046 (2007)] of a four-state variant of the RPS game. We show that spiral formation takes place only without a conservation law for the total density. Nevertheless, in general, fast diffusion can destroy species coexistence. We also generalize the four-state model to slightly varying reaction rates. This is shown both analytically and numerically not to change pattern formation, or the effective wavelength of the spirals, and therefore not to alter the qualitative properties of the crossover to extinction.

Procedures for grouping students into homogeneous subsets have long interested educational researchers. The research reported in this paper is an investigation of a set of objective grouping procedures based on multivariate analysis considerations. Four multivariate functions that might serve as criteria for adequate grouping are given and discussed; a method for optimizing these functions is also described. The set of procedures is illustrated through application to data from two samples of students, each student with scores on either ten or eleven subtests of a criterion referenced mathematics inventory. The results indicate that the procedures discussed provide a promising means for grouping students to minimize classroom heterogeneity. (Author)

Research paper recommenders emerged over the last decade to ease finding publications relating to researchers' area of interest. The challenge was not just to provide researchers with very rich publications at any time, any place and in any form but to also offer the right publication to the right researcher in the right way. Several approaches exist in handling paper recommender systems. However, these approaches assumed the availability of the whole contents of the recommending papers to be freely accessible, which is not always true due to factors such as copyright restrictions. This paper presents a collaborative approach for research paper recommender system. By leveraging the advantages of collaborative filtering approach, we utilize the publicly available contextual metadata to infer the hidden associations that exist between research papers in order to personalize recommendations. The novelty of our proposed approach is that it provides personalized recommendations regardless of the research field and regardless of the user's expertise. Using a publicly available dataset, our proposed approach has recorded a significant improvement over other baseline methods in measuring both the overall performance and the ability to return relevant and useful publications at the top of the recommendation list.

Question: 1—Echocardiography images Images were acquired from end of diastole to end of systole at different phases (7 phases) within a cardiac cycle by a Vivid 3 GE Health echocardiography machine. To obtain worthy images at denoted phases, it would be dependent to operator (for the best clinical examination). Of course, having assumed images not only were acquired from A4C and A2C but also from short-axis views. Short axis views have not been used at your papers, so some radial, circumferential and sample rotatory data would be missed. Response: It is simply possible for us to record and analyze images of short-axis views. However, according to American Society of Echocardiography (ASE) [1, 2], in the modified Simpson’s rule which is a method for LV volume computation from 2-D echocardiography images, it suffices to acquire apical two and four chamber views (A4C, A2C) for left ventricular (LV) volume computation. Question: 2—Observed data yi′ s Echocardiography images paly role of observed data and they are symbolized by yi′ s. there is a sequence of observed data y1, y2,…,yN. N is the number of obtained images. In fact we have made a chain of displacement, rotation and pure strain or nonrigid transformation (deformation) by these observed data that is started from y1 and is ended up to yN. This chain has some conceptual interpretations of the elasticity of the global left ventricular motion/function and the regional LV fiber arrangement/movement. Response: Yes, it is correct. Question: 3—Embed observed data to a high dimensional space Response: Yes, it is correct. Question: 4—Image processing on yi′ s and geodesic distance between yi′ s Observed data y1, y2,…,yN are embed to a meshed surface sized number of pixels of an image. Translation, rotation and pure deformation of y1, y2,…,yN are occurred/and studied at this surface utilizing the mathematical elasticity theory. A distance metric is defined that computes distances between observed points. Medical interpretations of observed points over the time should be checked/and stated clearly at your manuscripts. Images are not usual images but also are images from the left ventricle. Motion (displacement and velocity), deformation (strain and strain rate) and torsion of each myocardial sample have to be extracted during a cardiac cycle in the mentioned surface. These are used on the creation of graph G referred to their papers. Response: In this stage, we have just computed the distance between the two images in a cardiac cycle using non-rigid image registration regardless of relationship between images over the time. Therefore by this method, the motion and longitudinal deformation (short-axis views are needed to get for radial and circumferential deformations) of LV myocardium between all of two images in a cardiac cycle are extracted (for example, between end systole image and end diastole image, etc.). Then, in other stage of our method (calculation of the matrix of pairwise geodesic distance and apply multidimensional scaling on the resulting geodesic distance matrix to construct the low dimensional data points xi), motion and longitudinal deformation of LV myocardium during a cardiac cycle are extracted. Question: 5—An Isomap f The main tool at this method is the function “f” which is an isometric map [2, 3]. I will be interested to know the structure/formula or relationship of this isometric function which has most probably a lot of practical information of the left ventricular function and structure. I mean, how we can get a good representation of such a this function “f” for heart science study? Is it “f” known as an algebraic function? What information has been coded to fibers (f−1) of this isometric function “f”? Response: Isomap algorithm is one of the most popular sets of nonlinear dimensionality reduction (NLDR) algorithms. This algorithm attempts to extract low-dimensional data points from input points in a high-dimensional space in such a way that pairwise geodesic distances (the distance between two points measured over the manifold) are preserved. So that nearby and far points in high-dimensional space map to nearby and far points in low-dimensional space. This method is frequently used for visualization of medial image set. Detail of this method is described in Tenenbaum et al. and Borg et al. [3, 4]. It should be noted that we do not change the structure or formula of isomap algorithm. We only define a new image distance function based on image registration in calculation of geodesic distance between yi′ s in isomap algorithm. With this modification, Isomap algorithm is specified for assessment of the left ventricular function and structure. However, precise mathematical descriptions of f and (f−1) applied to echocardiography images and using the other NLDR algorithms need further researches in the following of this article. Question: 6—A reconstructed curve on a 2D manifold space & hidden data xi′ s; f(yi) = xi Isometric function results in a reconstructive curve crossing from hidden data (xi′ s) in a surface. It’s natural that some information (maybe clinical information) would betransferred to these hidden points like the curve of LV volume changes and so on and so on. A main question is: what are these new points xi′ s exactly (medically point of view)? What the other data has been come out from these hidden points? I think all of these questions back to gain a good understanding of isometric function “f”. Response: These points xi′ s will probably enable physicians to diagnose and follow up many cardiac structures and functions that also open doors to much more research at imaging cardiology in the future. References 1. AlizadehSani Z, Shalbaf A, Behnam H, Shalbaf R: Automatic computation of left ventricularvolume changes over a cardiac cycle from echocardiography images by nonlinear dimensionality reduction. J Digit Imaging : July, 2014 2. Tenenbaum JB, de Silva V, Langford JC: global geometric framework for nonlinear dimensionalityreduction. Science 290:2319–2323, 2000. Reprint available online: http://web.mit.edu/cocosci/Papers/sci_reprint.pdf 3. Ledesma-Carbayo MJ, Kybic J, Desco M, et al.: Spatio-temporal nonrigid registration for ultrasoundcardiac motion estimation. IEEE Trans Med Imaging 24:1113–1126, 2005.

Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a "dying" paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing "offspring". Practically, this might be used to trace the successive published milestones of a research field., SCOPUS: ar.j, info:eu-repo/semantics/published

We study the oscillatory dynamics in the generic three-species rock-paper-scissors games with mutations. In the mean-field limit, different behaviors are found: (a) for high mutation rate, there is a stable interior fixed point with coexistence of all species; (b) for low mutation rates, there is a region of the parameter space characterized by a limit cycle resulting from a Hopf bifurcation; (c) in the absence of mutations, there is a region where heteroclinic cycles yield oscillations of large amplitude (not robust against noise). After a discussion on the main properties of the mean-field dynamics, we investigate the stochastic version of the model within an individual-based formulation. Demographic fluctuations are therefore naturally accounted and their effects are studied using a diffusion theory complemented by numerical simulations. It is thus shown that persistent erratic oscillations (quasi-cycles) of large amplitude emerge from a noise-induced resonance phenomenon. We also analytically and numerically compute the average escape time necessary to reach a (quasi-)cycle on which the system oscillates at a given amplitude., Comment: 25 pages, 9 figures. To appear in the Journal of Theoretical Biology

We study the cyclic dominance of three species in two-dimensional constrained Newman-Watts networks with a four-state variant of the rock-paper-scissors game. By limiting the maximal connection distance $R_{max}$ in Newman-Watts networks with the long-rang connection probability $p$, we depict more realistically the stochastic interactions among species within ecosystems. When we fix mobility and vary the value of $p$ or $R_{max}$, the Monte Carlo simulations show that the spiral waves grow in size, and the system becomes unstable and biodiversity is lost with increasing $p$ or $R_{max}$. These results are similar to recent results of Reichenbach \textit{et al.} [Nature (London) \textbf{448}, 1046 (2007)], in which they increase the mobility only without including long-range interactions. We compared extinctions with or without long-range connections and computed spatial correlation functions and correlation length. We conclude that long-range connections could improve the mobility of species, drastically changing their crossover to extinction and making the system more unstable., Comment: 6 pages, 7 figures

In this paper a reliable method is found for approximating the value of the Bivariate Normal Correlation Coefficient, rho, given values of the joint probability and the normal deviates, h and k, or the related areas. This technique finds useful application in the computation of the tetrachoric correlation coefficient, r, when the underlying distributions may be assumed to be normal. (Author)

We implemented three recently proposed approaches to the identification of overlapping and hierarchical substructures in graphs and applied the corresponding algorithms to a network of 492 information-science papers coupled via their cited sources. The thematic substructures obtained and overlaps produced by the three hierarchical cluster algorithms were compared to a content-based categorisation, which we based on the interpretation of titles and keywords. We defined sets of papers dealing with three topics located on different levels of aggregation: h-index, webometrics, and bibliometrics. We identified these topics with branches in the dendrograms produced by the three cluster algorithms and compared the overlapping topics they detected with one another and with the three pre-defined paper sets. We discuss the advantages and drawbacks of applying the three approaches to paper networks in research fields., Comment: 18 pages, 9 figures