Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel Three-sequence Alignment with Space-efficient

The sequence alignment is a fundamental problem in computational biology. Many sequence alignment methods have been proposed, such as pair-wise sequence alignment, multiple sequence alignment (MSA), syntenic alignment, constraint multiple sequence alignment, and etc. Among them, pair-wise sequence alignment is a most commonly used method. Recently, MSA is more and more important which has been used to solve many molecular biological problems. The sum-of-pairs MSA problem has been proved to be a NP-complete problem. A progressive algorithm was used to solve MSA problem which is based on the pair-wise sequence alignments. However, this progressive MSA has a problem. This problem may be solved by using three-sequence alignment as a basic step instead of pair-wise sequence alignment. Three-sequence alignment can be solved sequentially in O(mnl) time complexity and O(mn) space complexity, where m, n and l are the lengths of the sequences to be aligned. The complexities of three-sequence alignment limit its applicability. Hence, to reduce the complexities becomes an important issue. In this paper, we propose a parallel algorithm to solve this problem. Our parallel algorithm requires O((mn)/p) space complexity and O((mnl)/p) time complexity, where p is the number of processors. Both experimental results and theoretical analysis are presented. The experimental results show that our parallel algorithm is applicable and achieves a good speed up.
Scaling Laplacian Pyramids

Laplacian pyramid--based Laurent polynomial (LP$^2$) matrices are generated by Laurent polynomial column vectors and have long been studied in connection with Laplacian pyramidal algorithms in signal processing. In this paper, we investigate when such matrices are scalable, that is, when right multiplication by Laurent polynomial diagonal matrices results in paraunitary matrices. The notion of scalability has recently been introduced in the context of finite frame theory and can be considered as a preconditioning method for frames. This paper significantly extends the current research on scalable frames to the setting of polyphase representations of filter banks. Furthermore, as applications of our main results we propose new construction methods for tight wavelet filter banks and tight wavelet frames.
Analysis of programs

interpretation is a general framework for obtaining cheaper and more approximative solutions to program analysis problems. In its most general form it attempts to be independent of the semantic base, but usually it is formulated in either a structural operational or a denotational setting. Given the semantics v1 →p v2 of a program p, the first step is often to define the uncomputable collecting semantics s1 ⇒p s2. The intention is that
An algebraic/numerical formalism for one-loop multi-leg amplitudes

We present a formalism for the calculation of multi-particle one-loop amplitudes, valid for an arbitrary number N of external legs, and for massive as well as massless particles. A new method for the tensor reduction is suggested which naturally isolates infrared divergences by construction. We prove that for N ? 5, higher dimensional integrals can be avoided. We derive many useful relations which allow for algebraic simplifications of one-loop amplitudes. We introduce a form factor representation of tensor integrals which contains no inverse Gram determinants by choosing a convenient set of basis integrals. For the evaluation of these basis integrals we propose two methods: An evaluation based on the analytical representation, which is fast and accurate away from exceptional kinematical configurations, and a robust numerical one, based on multi-dimensional contour deformation. The formalism can be implemented straightforwardly into a computer program to calculate next-to-leading order corrections to multi-particle processes in a largely automated way.
Computing Surface Uniformization Using Discrete Beltrami Flow

In this paper, we propose a novel algorithm for computing surface uniformization for surfaces with arbitrary topology. According to the celebrated uniformization theorem, all Riemann surfaces can be classified as elliptic, parabolic, or hyperbolic. Our algorithm is able to work on all these cases by first constructing an initial map onto an appropriate domain, such as a sphere, or a polygon in the plane $\mathbb{R}^2$ or the hyperbolic disk $D$, and then morphing the diffeomorphism based on the discrete Beltrami flow algorithm. For high genus surfaces, both the final mapping and the target domain are unknown, which presents a challenge in general. Each such surface can be conformally mapped onto $D$ modulo a discrete subgroup of all fractional linear transforms on $D$. A conformal copy of the surface, which is also its uniformization domain, can be visualized as a fundamental polygon in $D$ corresponding to the discrete subgroup, where the generators of the discrete subgroup map each side of the fundament.
Round Randomized Learning Vector Quantization for Brain Tumor Imaging

Brain magnetic resonance imaging (MRI) classification into normal and abnormal is a critical and challenging task. Owing to that, several medical imaging classification techniques have been devised in which Learning Vector Quantization (LVQ) is amongst the potential. The main goal of this paper is to enhance the performance of LVQ technique in order to gain higher accuracy detection for brain tumor in MRIs. The classical way of selecting the winner code vector in LVQ is to measure the distance between the input vector and the codebook vectors using Euclidean distance function. In order to improve the winner selection technique, round off function is employed along with the Euclidean distance function. Moreover, in competitive learning classifiers, the fitting model is highly dependent on the class distribution. Therefore this paper proposed a multiresampling technique for which better class distribution can be achieved. This multiresampling is executed by using random selection via preclassification. The test data sample used are the brain tumor magnetic resonance images collected from Universiti Kebangsaan Malaysia Medical Center and UCI benchmark data sets. Comparative studies showed that the proposed methods with promising results are LVQ1, Multipass LVQ, Hierarchical LVQ, Multilayer Perceptron, and Radial Basis Function.
Evaluation of the Psychometric Properties of Two Short Forms of the Social Interaction Anxiety Scale and the Social Phobia Scale

The Social Interaction Anxiety Scale and Social Phobia Scale are widely used measures of social anxiety. Using data from individuals with social anxiety disorder (n = 435) and nonanxious controls (n = 86), we assessed the psychometric properties of two independently developed short forms of these scales. Indices of convergent and discriminant validity, diagnostic specificity, sensitivity to treatment, and readability were examined. Comparisons of the two sets of short forms to each other and the original long forms were conducted. Both sets of scales demonstrated adequate internal consistency in the patient sample, showed expected patterns of correlation with measures of related and unrelated constructs, adequately discriminated individuals with social anxiety disorder from those without, and showed decreases in scores over the course of cognitive-behavioral therapy and/or pharmacotherapy. However, some significant differences in scale performance were noted. Implications for the clinical assessment of social anxiety are discussed.
Existing approaches of cultural studies and global dialogism: A study beginning with the debate around “cultural imperialism”

ABSTRACT Cultural studies has been dramatically internationalised recently, and a new theoretical framework is accordingly demanded. International cultural studies should have its own theoretical platform corresponding to its internationality. Starting from how to respond to the thesis “cultural imperialism,” this article categorises existing cultural studies into two approaches, the “modernity” and “post-modernity” moments, analysing their advantages and disadvantages respectively. A third approach, “globality,” transcends the previous two, the tenet of which is a philosophy of global dialogism that sublates (aufheben) both modernity and postmodernity simultaneously.
One-year outcomes in schizophrenia after switching from typical antipsychotics to olanzapine in Japan: an observational study

Background The purpose of this study was to assess the 1-year clinical, functional, and safety-related outcomes following a switch to olanzapine of at least one typical antipsychotic drug in the previous regimen in the treatment of patients of schizophrenia in Japan. Methods Using data from a large 1-year prospective, multicenter, naturalistic study of olanzapine for the treatment of schizophrenia in Japan, patients who were switched from any oral typical antipsychotic to olanzapine were identified. Mixed models for repeated measures, controlling for baseline demographics, were utilized to assess outcomes for clinical and functional measures. Results Of the 262 patients who switched from typical antipsychotics to olanzapine, 41% were outpatients and 59% were inpatients. Most of these patients were switched due to poor medication efficacy (71.0%) or medication intolerability (25.6%). Most patients (71.4%) completed the 1-year study. Clinically and statistically significant (P < 0.01) improvements were observed in patient illness severity and health-related quality of life, including improvements in global symptom severity and in positive, negative, depressive, and cognitive symptoms. Over half of the patients (58.3%) demonstrated a treatment response to olanzapine and 47.4% achieved symptom remission. Mean weight gain from baseline to endpoint was 2.31 ± 4.72 kg, with 30.4% of patients experiencing clinically significant weight gain (at least 7% of baseline weight). Conclusion During this 1-year naturalistic treatment of schizophrenia patients in Japan, switching from typical antipsychotics to olanzapine resulted in significant improvements in patients’ clinical and functional outcomes. Approximately one-third of patients had clinically significant weight gain. These findings highlight the favorable benefit to risk profile of switching to olanzapine following failure on typical antipsychotics.
¿Digo lo que siento y siento lo que digo? Una aproximación transcultural al uso de los emoticonos y emojis en los mensajes en CMC

The use of emoticons and emojis among online messaging users has achieved a globalized level. This article aims at examining how certain emojis and emoticons are chosen by message senders to regular the intensity of emotions in their messages. Or, by means of using them, message senders wish to blur textual rigidity and show interaction empathy during the communication process. This study analyzes the use of these symbols and graphic elements in message exchange through CMC and SNS, where users from different culture background convey their feeling. For it, two empirical studies of a methodological design were carried out: One pilot study was intended for the research instrument validation. The second was a survey study. By testing online messaging habit, this study enabled the researchers to observe whether the senders inclined to linguistic text use only, or they preferred including an additional emoticon or emoji in their message to communicate their feelings. Results of this research show that, at a certain extent, massage senders’ different culture background could influence on their emotional expressivity level.
8-Bit Approximations for Parallelism in Deep Learning

The creation of practical deep learning data-products often requires parallelization across processors and computers to make deep learning feasible on large data sets, but bottlenecks in communication bandwidth make it difficult to attain good speedups through parallelism. Here we develop and test 8-bit approximation algorithms which make better use of the available bandwidth by compressing 32-bit gradients and nonlinear activations to 8-bit approximations. We show that these approximations do not decrease predictive performance on MNIST, CIFAR10, and ImageNet for both model and data parallelism and provide a data transfer speedup of 2x relative to 32-bit parallelism. We build a predictive model for speedups based on our experimental data, verify its validity on known speedup data, and show that we can obtain a speedup of 50x and more on a system of 96 GPUs compared to a speedup of 23x for 32-bit. We compare our data types with other methods and show that 8-bit approximations achieve state-of-the-art speedups for model parallelism. Thus 8-bit approximation is an efficient method to parallelize convolutional networks on very large systems of GPUs.
A Multi-Resolution Methodology for the 3D Modeling of Large and Complex Archeological Areas

This article reports on a multi-resolution and multi-sensor approach developed for the accurate and detailed 3D modeling of the entire Roman Forum in Pompei, Italy. The archaeological area, approximately 150 × 80 m, contains more than 350 finds spread all over the forum as well as larger mural structures of previous buildings and temples. The interdisciplinary 3D modeling work consists of a multi-scale image- and range-based digital documentation method developed to fulfill all the surveying and archaeological needs and exploit all the intrinsic potentialities of the actual 3D modeling techniques. The data resolution spans from a few decimeters down to few millimeters. The employed surveying methodologies have pros and cons which will be addressed and discussed. The results of the integration of the different 3D data in seamlessly textured 3D model are finally presented and discussed.
Realistic evaluation of real-time forecasts in the Survey of Professional Forecasters

Each quarter, the Federal Reserve Bank of Philadelphia publishes the Survey of Professional Forecasters (SPF). This quarterly survey polls professional economists on their views about the economy over the next few years. Previously conducted by the National Bureau of Economic Research and the American Statistical Association, the survey provides forecasts for nominal GDP and the GDP price index, corporate profits, real GDP and its components, and a number of monthly business indicators, such as interest rates, housing starts, industrial production, and the consumer price index. The Philadelphia Fed has conducted this survey since the second quarter of 1990. How accurate are the SPF forecasts? On first look, this seems like a straightforward question. The Philadelphia Fed posts the entire history of the survey’s projections on its website, and it is easy to compare these projections with the historical data. On second look, as Dean Croushore and I have noted in our work over the last 10 years, macroeconomic historical data are revised often — and, in many cases, significantly. Such revisions complicate the evaluation of forecasts. In this note, I report on the survey’s accuracy using alternative values of the historical realizations from the Philadelphia Fed’s real-time data set for macroeconomists. I quantify the extent to which the data revisions matter and study the survey’s performance relative to that of simple benchmark time-series models, estimated on the same real-time realizations that the panelists would have used at the time.
Importance of positive reputation for Smartphone adoption

This study is aimed at investigating the importance of positive reputation from external experience sources for diffusion of a mobile convergent device, Smartphone. We categorized the different reputation sources into four; personal, expert, consumers, and mass media. By conducting a conjoint analysis with 53 samples from a university, we found that the prior experience of consumer group has the largest importance for the purchasing decision of the potential adopters. Moreover, early adopters and female consumers give more importance on the prior consumers' opinions. The reputation from expert and mass media was relatively lower than it from consumers and personal group. We discuss the implications for utilizing social networking service for diffusion of the innovative convergent device and the directions for further study.
Statics and dynamics of fluorescent lamps operating at high frequency: modeling and simulation

The static and dynamic response of a fluorescent lamp operating at high frequency was studied and modeled by a SPICE compatible behavioral equivalent circuit. Good agreement was found between model simulations and experimental results. It was also found analytically that the proposed model predicts a zero at the half right side of the complex plane as observed experimentally.
Incremental gain scheduling and eigenvalue tracking for robust pole assignment in extended linearization of nonlinear control systems

The principle of extended linearization is widely used for the control of nonlinear continuous-time processes which can be described in a quasi-linear form. For this class of systems, the gain matrix of linear state feedback controllers is usually adapted in such a way that the eigenvalues of the closed-loop control system are equal to predefined values and such that they remain fixed in spite of the system's nonlinearity. However, classical numerical routines for pole assignment for multiple-input multiple-output systems do not allow for real-time application in rapid control prototyping environments. Therefore, a novel algorithm based on the online solution of initial value problems for the desired controller gains is presented in this paper. Simulations and experimental results are given to highlight the applicability and robustness of this approach. An overview of suitable extensions to further observer-based control tasks concludes this paper.
Generalized Segment Posterior Probability for Automatic Mandarin Pronunciation Evaluation

In this paper, we investigate the automatic pronunciation evaluation method for native Mandarin. Multi-space distribution (MSD) hidden Markov model (HMM) is adopted to train the gold standard model. Machine scores derived from the generalized segment posterior probability on both syllables and phone level are proposed and investigated to measure the goodness of pronunciation (GOP). They are evaluated on the database collected internally and shown better performance than other well-known methods. In addition, detailed analyses of human scoring such as inter/intra-rater on utterance/speaker level are also given.
The e ! ects of irreversibility and uncertainty on capital accumulation q

Irreversibility and uncertainty increase the user cost of capital which tends to reduce the capital stock. Working in the opposite direction is a hangover e! ect, which arises because irreversibility prevents the "rm from selling capital even when the marginal revenue product of capital is low. Neither the user cost e! ect nor the hangover e! ect dominates globally, so that irreversibility may increase or decrease capital accumulation. Furthermore, an increase in uncertainty can either increase or decrease the long-run capital stock under irreversibility relative to that under reversibility. Other e! ects that we consider, however, have unambiguous e! ects on long-run capital accumulation. ( 1999 Published by Elsevier Science B.V. All rights reserved. 0304-3932/99/$ see front matter ( 1999 Published by Elsevier Science B.V. All rights reserved. PII: S 0 3 0 4 3 9 3 2 ( 9 9 ) 0 0 0 2 9 X 1Throughout this paper we will use the term &reversibility' to refer to the situation in which the "rm can purchase and sell capital at the same price without any transactions costs or adjustment costs. JEL classixcation: E22
V3885 SAGITTARIUS: A COMPARISON WITH A RANGE OF STANDARD MODEL ACCRETION DISKS

A analysis of standard model accretion disk synthetic spectrum fits to combined Far Ultraviolet Spectroscopic Explorer and Space Telescope Imaging Spectrograph spectra of V3885 Sagittarius, on an absolute flux basis, selects a model that accurately represents the observed spectral energy distribution. Calculation of the synthetic spectrum requires the following system parameters. The cataclysmic variable secondary star period–mass relation calibrated by Knigge in 2006 and 2007 sets the secondary component mass. A mean white dwarf (WD) mass from the same study, which is consistent with an observationally determined mass ratio, sets the adopted WD mass of 0.7 M☉, and the WD radius follows from standard theoretical models. The adopted inclination, i = 65°, is a literature consensus, and is subsequently supported by analysis. The mass transfer rate is the remaining parameter to set the accretion disk Teff profile, and the Hipparcos parallax constrains that parameter to by a comparison with observed spectra. The fit to the observed spectra adopts the contribution of a 57, 000 ± 5000 K WD. The model thus provides realistic constraints on and Teff for a large system above the period gap.
Models of the Shoemaker-Levy 9 Impacts. II. Radiative-Hydrodynamic Modeling of the Plume Splashback

We model the plume "splashback" phase of the Shoemaker-Levy 9 (SL9) collisions with Jupiter. We modified the ZEUS-3D hydrodynamic code to include radiative transport in the gray approximation and present validation tests. After initializing with a model Jovian atmosphere, we couple mass and momentum fluxes of SL9 plume material, as calculated by the ballistic Monte Carlo plume model of Paper I of this series. A strong and complex shock structure results. The shock temperatures produced by the model agree well with observations, and the structure and evolution of the modeled shocks account for the appearance of high-excitation molecular line emission after the peak of the continuum light curve. The splashback region cools by radial expansion as well as by radiation. The morphology of our synthetic continuum light curves agrees with observations over a broad wavelength range (0.9-12 μm). Much of the complex structure of these light curves is a natural consequence of the temperature dependence of the Planck function and the plume velocity distribution. A feature of our ballistic plume is a shell of mass at the highest velocities, which we term the "vanguard. " Portions of the vanguard ejected on shallow trajectories produce a lateral shock front, whose initial expansion accounts for the "third precursors" seen in the 2 μm light curves of the larger impacts and for hot methane emission at early times observed by Dinelli and coworkers. Continued propagation of this lateral shock approximately reproduces the radii, propagation speed, and centroid positions of the large rings observed at 3-4 μm by McGregor and coworkers. The portion of the vanguard ejected closer to the vertical falls back with high z-component velocities just after maximum light, producing CO emission and the "flare" seen at 0.9 μm. The model also produces secondary maxima ("bounces"), whose amplitudes and periods are in agreement with observations.