Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of mislabelled microarrays using robust sparse logistic regression

MOTIVATION Previous studies reported that labelling errors are not uncommon in microarray datasets. In such cases, the training set may become misleading, and the ability of classifiers to make reliable inferences from the data is compromised. Yet, few methods are currently available in the bioinformatics literature to deal with this problem. The few existing methods focus on data cleansing alone, without reference to classification, and their performance crucially depends on some tuning parameters. RESULTS In this article, we develop a new method to detect mislabelled arrays simultaneously with learning a sparse logistic regression classifier. Our method may be seen as a label-noise robust extension of the well-known and successful Bayesian logistic regression classifier. To account for possible mislabelling, we formulate a label-flipping process as part of the classifier. The regularization parameter is automatically set using Bayesian regularization, which not only saves the computation time that cross-validation would take, but also eliminates any unwanted effects of label noise when setting the regularization parameter. Extensive experiments with both synthetic data and real microarray datasets demonstrate that our approach is able to counter the bad effects of labelling errors in terms of predictive performance, it is effective at identifying marker genes and simultaneously it detects mislabelled arrays to high accuracy. AVAILABILITY The code is available from http://cs.bham. ac.uk/∼jxb008. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
A Panel of Genetic Polymorphism for the Prediction of Prognosis in Patients with Early Stage Non-Small Cell Lung Cancer after Surgical Resection

Background This study was conducted to investigate whether a panel of eight genetic polymorphisms can predict the prognosis of patients with early stage non-small cell lung cancer (NSCLC) after surgical resection. Materials and Methods We selected eight single nucleotide polymorphisms (SNPs) which have been associated with the prognosis of lung cancer patients after surgery in our previous studies. A total of 814 patients with early stage NSCLC who underwent curative surgical resection were enrolled. The association of the eight SNPs with overall survival (OS) and disease-free survival (DFS) was analyzed. Results The eight SNPs (CD3EAP rs967591, TNFRSF10B rs1047266, AKT1 rs3803300, C3 rs2287845, HOMER2 rs1256428, GNB2L1 rs3756585, ADAMTSL3 rs11259927, and CD3D rs3181259) were significantly associated with OS and/or DFS. Combining those eight SNPs, we designed a prognostic index to predict the prognosis of patients. According to relative risk of death, a score value was assigned to each genotype of the SNPs. A worse prognosis corresponded to a higher score value, and the sum of score values of eight SNPs defined the prognostic index of a patient. When we categorized the patients into two groups based on the prognostic index, high risk group was significantly associated with worse OS and DFS compared to low risk group (aHR for OS = 2.21, 95% CI = 1.69–2.88, P = 8.0 x 10−9, and aHR for DFS = 1.58, 95% CI = 1.29–1.94, P = 1.0 x 10−5). Conclusions Prognostic index using eight genetic polymorphisms may be useful for the prognostication of patients with surgically resected NSCLC.
Proposal and application aware analysis of a wireless sensor network protocol

This paper proposes a simple protocol for low-power sensor networks with battery-operated sensing devices. The sensors are expected to become active only when certain events in the environment occur. Therefore, a scheme for the application and medium access cycles is developed which avoids common problems of energy loss due to idle actions. Subsequently, the protocol is evaluated according to sensor lifetime. In contrast to common performance analysis, the approach considers the application behavior as a main impact on the sensor lifetime. Options for energy savings are derived.
Gui --- phooey!: the case for text input

Information cannot be found if it is not recorded. Existing rich graphical application approaches interfere with user input in many ways, forcing complex interactions to enter simple information, requiring complex cognition to decide where the data should be stored, and limiting the kind of information that can be entered to what can fit into specific applications' data models. Freeform text entry suffers from none of these limitations but produces data that is hard to retrieve or visualize. We describe the design and implementation of Jourknow, a system that aims to bridge these two modalities, supporting lightweight text entry and weightless context capture that produces enough structure to support rich interactive presentation and retrieval of the arbitrary information entered.
Local convexity properties of digital curves

The paper studies local convexity properties of digital curves. We locally define convex and concave parts from the slope of maximal digital straight segments and arithmetically characterize the smallest digital pattern required for checking convexity. Moreover, we introduce the concepts of digital edge and digital hull, a digital hull being a sequence of increasing or decreasing digital edges. We show that any strictly convex or concave part has a unique digital hull and arithmetically characterize the smallest digital pattern that contains a point incident to two consecutive digital edges. These theoretical results lead to online and linear-time algorithms that are useful for polygonal representations: convex hull computation of convex digital curves, computation of a reversible polygon that respects the convex and concave parts of a digital curve and computation of the well-known minimum-perimeter polygon.
Impact of bi-directional crosstalk on power budget in wavelength reuse DWDM systems

A detailed investigation of multigigabit wavelength reuse DWDM system tolerance to bidirectional crosstalk, conditioned by the maximum seed power budget and channel spacing, was preformed. Maximum tolerated seed powers were measured for DSF and SMF, for 10 Gb/s NRZ US signal. We demonstrated that high power regime reveals that the most dominant nonlinear impairment arises for the seed frequency shift coinciding with the SBS anti-Stokes. We assess the optimal seed frequency shift range, allowing a successful trade-off between the seed power budget and enabled spectral efficiency.
Empirically Based Psychosocial Therapies for Schizophrenia: The Disconnection between Science and Practice

Empirically validated psychosocial therapies for individuals diagnosed with schizophrenia were described in the report of the Schizophrenia Patient Outcomes Research Team (PORT, 2009). The PORT team identified eight psychosocial treatments: assertive community treatment, supported employment, cognitive behavioral therapy, family-based services, token economy, skills training, psychosocial interventions for alcohol and substance use disorders, and psychosocial interventions for weight management. PORT listings of empirically validated psychosocial therapies provide a useful template for the design of effective recovery-oriented mental health care systems. Unfortunately, surveys indicate that PORT listings have not been implemented in clinical settings. Obstacles to the implementation of PORT psychosocial therapy listings and suggestions for changes needed to foster implementation are discussed. Limitations of PORT therapy listings that are based on therapy outcome efficacy studies are discussed, and cross-cultural and course and outcome studies of correlates of recovery are summarized.
UniPi: Recognition of Mentions of Disorders in Clinical Text

The paper describes our experiments addressing the SemEval 2014 task on the Analysis of Clinical text. Our approach consists in extending the techniques of NE recognition, based on sequence labelling, to address the special issues of this task, i.e. the presence of overlapping and discontiguous mentions and the requirement to map the mentions to unique identifiers. We explored using supervised methods in combination with word embeddings generated from unannotated data.
Single Women and the Transition to Marriage in Hong Kong, Shanghai and Tokyo

This paper considers the transition to adulthood in East Asia by exploring the experiences of single women between the ages of 25 and 45 years in the cities of Hong Kong, Shanghai and Tokyo. The paper argues that single women encounter difficulties negotiating marriage in the three cities due to problems in marriage markets, expectations of fertility upon marriage, and conflicts between educational and employment opportunities and marital roles. It also finds that in the three cities, women articulated two models of marriage, namely, a gender duty model based on expectations of gendered role fulfilment and a companionate model. The paper suggests that the specific configuration of marriage models differs in the three cities due to differences in the historical and social backgrounds of the cities and the larger national and regional contexts.
Compact Vehicular Trajectory Encoding ( extended version )

Many applications in vehicular communications require the collection of vehicular position traces. So far this has been done by recording and transmitting unencoded position samples. Depending on the frequency and resolution of these samples, the resulting data may be very large, consuming significant resources for storage and transmission. In this paper, we propose a method based on two-dimensional cubic spline interpolation that is able to reduce the amount of the measurement data significantly. Our approach allows for a configurable accuracy threshold and performs its task in O(n). We evaluate our approach with real vehicular GPS movement traces and show that it is able to reduce the volume of the measurement set by up to 80 % for an accuracy threshold of 20 centimeters.
201o International Conference on Computer and Communication Technologies in Agriculture Engineering

GML is an XML encoding for representation and exchange of geographic information. With the popularity of GML, more and more spatial data exists in GML format. It raises the problem of how to query the data in GML. Since GML is based on XML, query technologies for XML can be employed to GML. However, the fact that GML differs from XML in many aspects makes these technologies not so applicable for GML. The standard query language XQuery, which is recommended by W3C, only applies to GML non­ spatial queries. To query GML documents, we propose a GML query processor by extending XQuery in datatypes and spatial operators. The processor can deal with non­ spatial and spatial queries, and output the query results in GML format.
SoD-Toolkit: A Toolkit for Interactively Prototyping and Developing Multi-Sensor, Multi-Device Environments

As ubiquitous environments become increasingly commonplace with newer sensors and forms of computing devices (e.g. wearables, digital tabletops), researchers have continued to design and implement novel interaction possibilities. However, as the number of sensors and devices continues to rise, researchers still face numerous instrumentation, implementation and cost barriers before being able to take advantage of the additional capabilities. In this paper, we present the SoD-Toolkit -- a toolkit that facilitates the exploration and development of multi-device interactions, applications and ubiquitous environments by using combinations of low-cost sensors to provide spatial-awareness. The toolkit offers three main features. (1) A "plug and play" architecture for seamless multi-sensor integration, allowing for novel explorations and ad-hoc setups of ubiquitous environments. (2) Client libraries that integrate natively with several major device and UI platforms. (3) Unique tools that allow designers to prototype interactions and ubiquitous environments without a need for people, sensors, rooms or devices. We demonstrate and reflect on real-world case-studies from industry-based collaborations that influenced the design of our toolkit, as well as discuss advantages and limitations of our toolkit.
Rethinking Verification: Accuracy, Efficiency, and Scalability through Human-Machine Collaboration

With growing dependence on software in embedded and cyber-physical systems where vulnerabilities and malware can lead to disasters, efficient and accurate verification has become a crucial need for safety and cybersecurity. Formal verification of large software has remained an elusive target, riddled with problems of low accuracy and high computational complexity. The need for automating verification is undoubted, however human is indispensable to accurate real-world software verification. The automation should actually enable and simplify human cross-checking, which is especially important when the stakes are high. This technical briefing discusses the challenges of creating a powerful fusion of automation and human intelligence to solve software verification problems where complete automation has remained intractable. We will contrast with existing software verification approaches and reflect on their strengths and limitations as a human-machine collaboration framework and outline key software engineering research and practice challenges to be addressed in the future.
York_University at TRECVID 2010

In this paper, we describe our work done by members at York University in Canada for the KIS (Known-item search) task of TRECVID 2010. This is the rst time that we participate in the TRECVID. With rich experience in text retrieval, we mainly focus on the meta information of videos, and try to gure out the importance of these description corpus. In order to obtain this goal, we do not use any video or audio technologies. Only text retrieval methods are utilized to nd the know items. Traditional weighting models in text retrieval like BM25 and Lemur TF-IDF are used. Meanwhile, we also use query expansion methods to improve the performance. However, the results are not promising. We make a further discussion about the reason at the end of this paper.
Classification using a novel support vector machine fuzzy network for digital modulations in satellite communication

To make the modulation classification system more suitable for signals in a wide range of signal to noise rate (SNR), a novel support vector machine fuzzy network (SVMFN) is presented in this paper. The SVMFN employs a new definition of fuzzy density which incorporates accuracy and uncertainty of the classifiers to improve recognition reliability. Further, three efficient features with high robustness and less computation are extracted from intercepted signals to classify eleven digital modulation types (i.e. 2ASK, 4ASK, 2FSK, 4FSK, 2PSK, 4PSK, 8PSK, 16QAM, TFM, /spl pi//4QPSK and OQPSK). Computer simulation shows that the proposed scheme has the advantages of high accuracy and reliability (success rates are over 97.5% when SNR is not lower than 0 dB), and adapt to engineering applications.
Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus

Adult neurogenesis, the lifelong production of new neurons in the adult brain, is under complex genetic control but many of the genes involved remain to be identified. In this study, we have integrated publicly available gene expression data from the BXD and CXB recombinant inbred mouse lines to discover genes co-expressed in the adult hippocampus with Nestin, a common marker of the neural precursor cell population. In addition, we incorporated spatial expression information to restrict candidates to genes with high differential gene expression in the hippocampal dentate gyrus. Incorporating data from curated protein-protein interaction databases revealed interactions between our candidate genes and those already known to be involved in adult neurogenesis. Enrichment analysis suggested a link to the Wnt/β-catenin pathway, known to be involved in adult neurogenesis. In particular, our candidates were enriched in targets of Lef1, a modulator of the Wnt pathway. In conclusion, our combination of bioinformatics approaches identified six novel candidate genes involved in adult neurogenesis; Amer3, Eya3, Mtdh, Nr4a3, Polr2a, and Tbkbp1. Further, we propose a role for Lef1 transcriptional control in the regulation of adult hippocampal precursor cell proliferation.
Optimal magnetic sensor location for spherical harmonic identification applied to radiated electrical devices

This paper deals with the use of spherical harmonic representation to identify the magnetic multipolar sources associated to a given item, by measuring the near field around it. If the model presents many advantages, its use in an inverse problem approach requires special caution to critical points like the choice of sensor number and location. A method is presented that makes it possible, from a high number of information, to reduce the sensor number to a minimum and to optimize their location with respect to robustness. The robustness issue is solved by using an original method based on a genetic algorithm. A simple but didactic example illustrates the difficulties that can be met and our strategy to overcome them
Anticonvulsant effects of the BK‐channel antagonist paxilline

Purpose: Mutations that enhance currents through the Ca2+‐ and voltage‐gated K+ channel BK (Slo, maxiK, KCNMA1) have been associated with seizure disorders in both rodent models and humans. Previously we have found that seizures themselves induce a gain‐of‐function in BK channels that is associated with elevated excitability in neocortical neurons. In this study, we sought to examine whether administration of BK‐channel antagonists possess anticonvulsant activity in vivo.
Clique-relaxed graph coloring

We define a generalization of the chromatic number of a graph G called the k-clique-relaxed chromatic number, denoted χ (k) (G). We prove bounds on χ (k) (G) for all graphs G, including corollaries for outerplanar and planar graphs. We also define the k-clique-relaxed game chromatic number, χ (k) g (G), of a graph G. We prove χ (2) g (G) ≤ 4 for all outerplanar graphs G, and give an example of an outerplanar graph H with χ (2) g (H) ≥ 3. Finally, we prove that if H is a member of a particular subclass of outerplanar graphs, then χ (2) g (H) ≤ 3.
Agent-oriented knowledge elicitation for modeling the winning of “hearts and minds”

Agent-oriented modeling is a top-down approach for modeling and simulating the behaviors of complex systems. This research addresses the application of agent-oriented modeling to eliciting and representing knowledge for social simulations. We provide an overview of agent-oriented modeling and describe a case study on conflict resolution that has an impact on winning “hearts and minds” of the occupied territory's population. After that we propose a method for eliciting and representing knowledge for social simulations by means of agent-oriented modeling. The models created by means of agent-oriented modeling can be implemented on several simulation platforms, such as NetLogo, Jason, and JADE.
Introduction to Mechanics and Symmetry: A Basic Exposition of Classical Mechanical Systems

A development of the basic theory and applications of mechanics with an emphasis on the role of symmetry. The book includes numerous specific applications, making it beneficial to physicists and engineers. Specific examples and applications show how the theory works, backed by up-to-date techniques, all of which make the text accessible to a wide variety of readers, especially senior undergraduates and graduates in mathematics, physics and engineering. This second edition has been rewritten and updated for clarity throughout, with a major revamping and expansion of the exercises. Internet supplements containing additional material are also available.
Novel algorithms for computation of inverse kinematics and inverse dynamics of Gough-Stewart platform

In this paper, we present new approaches for computation of the inverse kinematics and inverse dynamics of the Gough-Stewart platform. The new approach for the inverse kinematics, i.e., the calculation of joints velocity and acceleration, is based on using the projection matrices to directly related the mobile platform velocity and acceleration to active joints velocity and acceleration. The new approach for the inverse dynamics is rather unconventional, in the sense that it is based on implicit computation and the use of constraint forces. Our detailed analysis and comparison demonstrate that our new approach for computation of both inverse kinematics and inverse dynamics achieves a better computational efficiency than previously proposed methods.
SILVERVIZ : Extending SILVER for coordination in distributed collaborative modeling

0. ABSTRACT System Dynamics modeling projects commonly involve distributed team collaboration. Remote Collaboration can impose substantial burden of extra work for team project coordination, and research suggest that the difficulties of distance coordination have been a major contributing factor in shaping the success or failure of teams in some domains. (Gary M. Olson and Judith S. Olson. 2000). It is currently difficult for modelers to keep track of what changes fellow collaborators have made as a modeling project evolves. While proper information technology support is known to lessen the difficulties of remote collaborations, there is limited software support available for collaboration across System Dynamics modeling projects. The use of general technology such as email systems and wikis can lead to much needless effort to establish common understanding regarding the current status of work and in communicating recent changes. This paper describes the design of an extension to the open source SILVER system that provides a visual workspace that reduces such effort by keeping modelers notified on fellow modelers’ past activities and changes within modeling project, and to identify commonalities shared by multiple elements of a model.
Identifying Infection Sources and Regions in Large Networks

Identifying the infection sources in a network, including the index cases that introduce a contagious disease into a population network, the servers that inject a computer virus into a computer network, or the individuals who started a rumor in a social network, plays a critical role in limiting the damage caused by the infection through timely quarantine of the sources. We consider the problem of estimating the infection sources and the infection regions (subsets of nodes infected by each source) in a network, based only on knowledge of which nodes are infected and their connections, and when the number of sources is unknown a priori. We derive estimators for the infection sources and their infection regions based on approximations of the infection sequences count. We prove that if there are at most two infection sources in a geometric tree, our estimator identifies the true source or sources with probability going to one as the number of infected nodes increases. When there are more than two infection sources, and when the maximum possible number of infection sources is known, we propose an algorithm with quadratic complexity to estimate the actual number and identities of the infection sources. Simulations on various kinds of networks, including tree networks, small-world networks and real world power grid networks, and tests on two real data sets are provided to verify the performance of our estimators.