Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of Clinical and Genomic Data for Decision Support in Cancer

Computer aided medical diagnosis is one of the most important research fields in biomedical engineering. Most of the efforts made focus on diagnosis based on clinical features. The latest breakthroughs of the technology in the biomolecular sciences are a direct cause of the explosive growth of biological data available to the scientific community. New technologies allow for high volume affordable production and collection of information on biological sequences, gene expression levels and proteins structure on almost every aspect of the molecular architecture of living organisms. For this reason, bioinformatics is asked to provide tools for biological information processing, representing today’s key in understanding the molecular basis of physiological and pathological genotypes. The exploitation of bioinformatics for medical diagnosis appears as an emerging field for the integration of clinical and genomic features, maximizing the information regarding the patient’s health status and the quality of the computer aided diagnosis. Yorgos Goletsis University of Ioannina, Greece
Applying Discrete Homotopy Analysis Method for Solving Fractional Partial Differential Equations

In this paper we developed a space discrete version of the homotopy analysis method (DHAM) to find the solutions of linear and nonlinear fractional partial differential equations with time derivative α (0<α≤1). The DHAM contains the auxiliary parameter ℏ, which provides a simple way to guarantee the convergence region of solution series. The efficiency and accuracy of the proposed method is demonstrated by test problems with initial conditions. The results obtained are compared with the exact solutions when α=1. It is shown they are in good agreement with each other.
Assessing Phrase-Based Translation Models with Oracle Decoding

Extant Statistical Machine Translation (SMT) systems are very complex softwares, which embed multiple layers of heuristics and embark very large numbers of numerical parameters. As a result, it is difficult to analyze output translations and there is a real need for tools that could help developers to better understand the various causes of errors. In this study, we make a step in that direction and present an attempt to evaluate the quality of the phrase-based translation model. In order to identify those translation errors that stem from deficiencies in the phrase table (PT), we propose to compute the oracle BLEU-4 score, that is the best score that a system based on this PT can achieve on a reference corpus. By casting the computation of the oracle BLEU-1 as an Integer Linear Programming (ILP) problem, we show that it is possible to efficiently compute accurate lower-bounds of this score, and report measures performed on several standard benchmarks. Various other applications of these oracle decoding techniques are also reported and discussed.
The WENSS & Dwingeloo surveys and the Galactic magnetic field

Aims. We investigate the structure of the Galactic magnetic field in the 2nd Galactic quadrant using radio continuum polarization data from the 325 MHz WENSS (WEsterbork Northern Sky Survey) survey in combination with earlier single-dish observations. Methods. We study gradients in polarization angle along Galactic longitude and latitude in the region 130 degrees less than or similar to l less than or similar to 173 degrees and -5 degrees less than or similar to b less than or similar to 31 degrees. These gradients were determined with a new method that we developed to efficiently and reliably fit linear gradients to periodic data like polarization angles. Since the WENSS data were obtained with a synthesis array they suffer from the "missing short spacing" problem. We have tried to repair this by adding an estimate of the large-scale emission based on the single-dish (Dwingeloo) data obtained by Brouw and Spoelstra. Combining all available data we derive a rotation measure map of the area, from which we estimate all 3 components of the magnetic field vector. Results. In the part of WENSS where large-scale structure in polarized intensity is relatively unimportant, we find that the magnetic field is predominantly perpendicular to the line-of-sight, and parallel to the Galactic plane. The magnetic field components along the line-of-sight and along Galactic latitude have comparable values, and the strength of these components is much smaller than the strength of the total magnetic field. Our observations also cover part of the so-called "fan" region, an area of strong polarized intensity, where large-scale structure is missing from our WENSS data. We tentatively show that Faraday rotation occurring in front of the Perseus arm is causing both the WENSS RM and the RM towards the fan region observed in previous single-dish surveys, and we suggest that the fan is formed by local emission that originates in front of the emission we see in WENSS.
Optimising mHealth helpdesk responsiveness in South Africa: towards automated message triage

In South Africa, a national-level helpdesk was established in August 2014 as a social accountability mechanism for improving governance, allowing recipients of public sector services to send complaints, compliments and questions directly to a team of National Department of Health (NDoH) staff members via text message. As demand increases, mechanisms to streamline and improve the helpdesk must be explored. This work aims to evaluate the need for and feasibility of automated message triage to improve helpdesk responsiveness to high-priority messages. Drawing from 65 768 messages submitted between October 2016 and July 2017, the quality of helpdesk message handling was evaluated via detailed inspection of (1) a random sample of 481 messages and (2) messages reporting mistreatment of women, as identified using expert-curated keywords. Automated triage was explored by training a naïve Bayes classifier to replicate message labels assigned by NDoH staff. Classifier performance was evaluated on 12 526 messages withheld from the training set. 90 of 481 (18.7%) NDoH responses were scored as suboptimal or incorrect, with median response time of 4.0 hours. 32 reports of facility-based mistreatment and 39 of partner and family violence were identified; NDoH response time and appropriateness for these messages were not superior to the random sample (P>0.05). The naïve Bayes classifier had average accuracy of 85.4%, with ≥98% specificity for infrequently appearing (<50%) labels. These results show that helpdesk handling of mistreatment of women could be improved. Keyword matching and naïve Bayes effectively identified uncommon messages of interest and could support automated triage to improve handling of high-priority messages.
Constructing concept clouds from company websites

Word clouds are used for the visual representation of texts. The font size and color of a word show its importance, and the position of a word in the cloud can be arbitrary or reflect its relation to other words. In this paper, we present a tool that generates concept clouds from German company websites. The main idea of the visualization is to show the overall work and main interests of companies in a detailed information cloud based solely on their own web page. The concepts are taken from the STW Thesaurus of Economics. The colors of the concepts show the categories of the concepts in the thesaurus while the cloud layout is organized by semantic proximity of the concepts. To compute the similarity between concepts we use the semantic representation that is generated from DeWaC corpus. The distributional similarity is fundamentally different from the co-occurrence statistics which often used to generate word clouds.
First Report of Vannellidae Amoebae (Vannella Spp.) Isolated From Biofilm Source

Background Members of the Vannellidae family are free-living amoebae (FLA) distributed mainly in water and soil sources. The present study reports the first isolation of this genus in the biofilm source from hospital environment in Tehran, Iran. Methods Biofilm samples were collected from hospital environment. Cultivation was performed in non-nutrient agar covered with a heat-killed Escherichia coli. Cloning of the suspected amoebae was done. PCR amplification and Homology analysis using the Basic Local Alignment Search Tool (BLASTn) was performed to search for the most similar reference sequences. Results Microscopic examination showed numerous fan-shaped amoebae and peculiar cysts different to the usual shape of typical FLA. Sequence analysis of the PCR- product revealed that the suspected amoebae are highly homologous with Vannella spp. gene (99% identity and 100% query coverage) available in the gene bank database. Conclusion Although Vannella spp. is not proved to be pathogenic itself, but they are capable of harboring pathogenic intracellular organisms such as Microsporidian parasites. Thus, identification of such amoebae can be of clinical importance, as they could lead to transmission of other pathogens to human.
Automated Refactoring of Software using Version History and a Code Element Recentness Measure

This paper proposes a multi-objective genetic algorithm to automate software refactoring and validates the approach using a tool, MultiRefactor, and a set of open source Java programs. The tool uses a metric function to measure quality in a software system and tests a second objective to measure the recentness of the code elements being refactored. Previous versions of the software project are analyzed and a recentness measure is then calculated with respect to previous versions of code. The multi-objective setup refactors the input program to improve its quality using the quality objective, while also focusing on the recentness of the code elements inspected. An experiment has been constructed to measure the multi-objective approach against an alternative mono-objective approach that does not use an objective to measure element recentness. The two approaches are validated using six different open source Java programs. The multi-objective approach is found to give significantly better recentness scores across all inputs in a similar time, while also generating improvements in the quality score.
Factors Affecting the Improvement of the Initial Peak Urinary Flow Rate after Transurethral Resection of the Prostate or Photoselective Vaporization of the Prostate for Treating Benign Prostatic Hyperplasia

Purpose We evaluated the factors that affect the improvement of the initial peak flow rate after transurethral resection of the prostate (TURP) or photoselective vaporization of the prostate (PVP) for benign prostatic hyperplasia (BPH) patients by using noninvasive tools. Methods One hundred and twenty seven BPH patients who had undergone TURP or PVP between January 2005 and May 2009 were evaluated. They were divided into 2 groups: the postoperative initial peak urinary flow rate (Qmax) was less than 10 mL/sec (Group 1; n=37, TURP=11, PVP=26) and more than 10 mL/sec (Group 2; n=90, TURP=41, PVP=49). We confirmed the patients' preoperative check lists. The check list were the international prostate symptom score (IPSS), the quality of life score, a past history of acute urinary retention (AUR), body mass index and/or pyuria, the serum prostate-specific antigen (PSA) level and the prostate volume, the prostate transitional zone volume and prostatic calcification. The initial Qmax was measured at the outpatient clinic one week after discharge. Results The improvement rate was not significant difference between the TURP group (78.8%) and the PVP group (65.3%). The efficacy parameters were the IPSS-storage symptom score, the prostate volume, the PSA level and a past history of AUR. The IPSS-storage symptom scores of Group 1 (12.3±3.3) was higher than those of Group 2 (10.5±1.7). The prostate volume of Group 2 (42.3±16.6 g) was bigger than that of Group 1 (36.6±7.8 g). The PSA level of Group 2 (3.8±2.6 ng/mL) was higher than that of Group 1 (2.6±2.6 ng/mL). A past history of AUR in Group 1 (35.1%) was more prevalent than that of Group 2 (15.6%). Conclusions The non-invasive factors affecting the initial Qmax after TURP or PVP were the IPSS-storage symptom score, the prostate volume and a past history of AUR. Accordingly, in patients who have a higher IPSS-storage symptom score, a smaller prostate volume and a history of AUR, there might be a detrimental effect on the initial Qmax after TURP or PVP. These factors might also be used as long-term prognostic factors.
Snowcat Track Detection in Snowy Environments

This paper describes the image processing techniques designed to localize tracks of snowcats for the Italian mission in Antarctica within the ENEA R.A. S. (Surface Antarctic Robot) project for the autonomous driving of intelligent snowcats. The final goal is to enable snowcats to automatically follow preceding ones. A camera is used to acquire images of the scene in realtime; the image sequence is analyzed by a computer vision system which identifies the tracks and produces a high level description of the scene. This data is forwarded to a further software module in charge of the control of the snowcat movement. A further optional representation, in which markers highlighting the tracks are superimposed onto the acquired image, is transmitted to a human supervisor located off-board.
Efficient environmental monitoring using cost-aware path planning

This paper presents an efficient environmental monitoring strategy that considers the information gain along the trajectory of a robot. In order to monitor environmental parameters such as temperature and chemical concentration, an estimation method based on Gaussian process regression is used. The goal of this paper is to model accurate spatio-temporal phenomena by reducing the uncertainty over the surveillance region. A cost-aware path planning based environmental monitoring is desirable for mobile sensor networks since robots are coordinated to follow a trajectory with the maximum accumulated information gain, as well as the traveling distance. The proposed method with respect to different sampling methods is demonstrated in simulations.
RETROSPECTIVE : Space Efficient Conservative Garbage Collection

Both type-accurate and conservative garbage collectors have gained in importance since the original paper was written. Managing unnecessary retention by conservative collectors continues to be an important problem. There appear to be few reimplementations of the techniques we described, but significantly refined descendents of the original implementation are alive and well inside a large number of applications. There has been later work both on quantifying space retention by conservative collectors, and on theoretical bounds for such retention.
Vertical Data Migration in Large Near-Line Document Archives Based on Markov-Chain Predictions

Large multimedia document archives hold most of their data in near-line tertiary storage libraries for cost reasons. This paper develops an integrated approach to the vertical data migration hetween the tertiary and secondary storage in that it reconciles speculative preloading, to mask the high latency of the tertiary storage, with the replacement policy of the secondary storage. In addition, it considers the interaction of these policies with the tertiary storage scheduling and controls preloading aggressiveness by taking contention for tertiary storage drives into account. The integrated migration policy is based on a continuous-time Markov-chain (CTMC) model,fijr predicting the expected number of accesses to a document within a specified time horizon. The parameters of the CTMC model, the probabilities of co-accessing certain documents and the interaction times between successive accesses, are dynamically estimated and adjusted to evolving workload patterns by keeping online statistics. The integrated policy for vertical data migration has been implemented in a prototype system. Detailed simulation studies with Web-server-like synthetic workloads indicate sign$cant gains in terms of client response time. The studies also show that the overhead of the statistical bookkeeping and the computations for the access predictions is affordable.
Deterministic equivalents for certain functionals of large random matrices

Consider a $N\times n$ random matrix $ Y_n$ where the entries are independent but not identically distributed (matrices with a variance profile) Consider now a deterministic $N\times n$ matrix $A_n$ whose columns and rows are uniformly bounded for the Euclidean norm. Let $\Sigma_n=Y_n+A_n$. We prove in this article that there exists a deterministic equivalent to the empirical Stieltjes transform of the distribution of the eigenvalues of $\Sigma_n \Sigma_n^T$ which is itself the Stieltjes transform of a probability measure. This work is motivated by the context of performance evaluation of Multiple Inputs / Multiple Output (MIMO) wireless digital communication channels. As an application, we derive a deterministic equivalent to the mutual information of a wireless channel.
Differential Testing for Software

Successful commercial computer systems contain tens of millions of lines of handwritten software, all of which is subject to change as competitive pressures motivate the addition of new features in each release. As a practical matter, quality is not a question of correctness, but rather of how many bugs are fixed and how few are introduced in the ongoing development process. If the bug count is increasing, the software is deteriorating.
EMI Camera LSI (EMcam) with 12 × 4 on-chip loop antenna matrix in 65-nm CMOS to measure EMI noise distribution with 60-µm spatial precision

An EMI Camera LSI (EMcam) with a 12 × 4 on-chip 250µm × 50µm loop antenna matrix in 65nm CMOS is developed. EMcam achieves both the 2D electric scanning and 60µm-level spatial precision for the first time. The down-conversion architecture increases the bandwidth of EMcam and enables the measurement of EMI spectrum. Shared IF block scheme is proposed to alleviate the increasing power and area penalty inherent to the matrix measurement. ‘Mixer and antenna selector (MAS)’ reduces the switches and prevents the EMI attenuation due to the switches. EMI measurement with the smallest 32µm × 12µm antenna to date is also demonstrated.
Unsupervised language model adaptation using n-gram weighting

In this paper, we introduce the weighting of topic models in mixture language model adaptation using n-grams of the topic models. Topic clusters are formed by using a hard-clustering method assigning one topic to one document based on the maximum number of words chosen from a topic for that document in Latent Dirichlet Allocation (LDA) analysis. The n-grams of the topic generated by hard-clustering are used to compute the mixture weights of the component topic models. Instead of using all the words of the training vocabulary, selected words are used for LDA analysis, which are chosen by incorporating some information retrieval techniques. The proposed n-gram weighting approach shows significant reduction in perplexity and word error rate (WER) against a unigram weighting approach used in the literature.
Children's Acquisition of Values within the Fmily: Domains of Socialization Assessed with Autobiographical Narratives

The transmission and internalization of values are the primary processes that occur during socialization. A recent approach integrates existing theories and research findings into a comprehensive model of socialization. According to the domains of socialization approach, there is no general principle governing socialization but rather it occurs in different domains of caregiver-child interactions. Grusec and Davidov (2010) outlined five socialization domains, which involve controlling children’s behaviour by external means (control domain), protecting children from harm and relieving their distress (protection domain), teaching children information or skills outside of the discipline or distress setting (guided-learning domain), managing children’s environment to increase desirable role models (group participation domain), and accommodating each other’s wishes (mutual reciprocity domain). Previous work demonstrated the utility of the domains of socialization approach for the study and understanding of value acquisition (Vinik, Johnston, Grusec, & Farrell, 2013). The present study expanded on this work by focusing on processes within the family. A modified narrative methodology was used to explore aspects of the value acquisition process. Autobiographical narratives of 294 emerging adults about a time they learned an important value from a caregiver were analyzed. iii The sample included participants from four ethnic backgrounds. Findings provided further support for the usefulness of the domains of socialization approach to the study of value development, as events recalled in narratives were categorized into all domains but reciprocity. Values learned in the control domain were most frequently reported but were associated with the lowest levels of internalization. The highest level of value internalization was found to occur in the group participation domain, drawing attention to the importance of observing the behaviour of others. Socialization domains were associated with particular types of lesson content. The guided learning and group participation domains were associated with more positive and less negative emotional valence compared to the other domains. In turn, absence of negative valence was significantly related to better confidence in accuracy of memory reported in narratives, indicative of quality of information processing and learning. Most effects were not moderated by demographic variables providing support to the universal applicability of the domains of socialization approach.
Human error simulation as an aid to HCI design for critical systems

Human errors are understood as a combination of many factors. Among them are the limitations of human information processing and the difficult matching of automation and human abilities. In the conception of HCI for critical systems, the ability to identify possible human errors and their consequences is fundamental for designing defenses for these errors. However, the myriad of forms that human error can assume may distract the designer from this task. This paper describes S. PERERE (Simulation of Performance in Error), a human erroneous behavior computational simulator and its prospective usage as an aid to critical systems' HCI design. S. PERERE is based on ACT-R (Atomic Components of Thought -- Rational) cognitive architecture.