Miracle-dz/UniFAR-FTUs huggingface dataset:
DCMSVM: Distributed parallel training for single-machine multiclass classifiers

We present an algorithm and implementation for distributed parallel training of single-machine multiclass SVMs. While there is ongoing and healthy debate about the best strategy for multiclass classification, there are some features of the single-machine approach that are not available when training alternatives such as one-vs-all, and that are quite complex for tree based methods. One obstacle to exploring single-machine approaches on large datasets is that they are usually limited to running on a single machine! We build on a framework borrowed from parallel convex optimization - the alternating direction method of multipliers (ADMM) - to develop a new consensus based algorithm for distributed training of single-machine approaches. This is demonstrated with an implementation of our novel sequential dual algorithm (DCMSVM) which allows distributed parallel training with small communication requirements. Benchmark results show significant reduction in wall clock time compared to current state of the art multiclass SVM implementation (Liblinear) on a single node. Experiments are performed on large scale image classification including results with modern high-dimensional features.
Scheduling Workflows in Multi-cluster Environments

Scientific applications modeled as workflows can exhibit both task and data parallelism. Scheduling these workflows in a multi-cluster environment is challenging due to the large number of task mapping possibilities. Therefore, several heuristics have been proposed over the last years to address such a problem. A key limitation of existing heuristics for multi-cluster environments is that individual tasks are mapped onto single resources, which limits the resource options to reduce the time to the complete workflow executions. This paper introduces the Multi-Cluster Allocation-Heterogeneous Earliest Finish Time (MCA-HEFT) heuristic, which deploys single parallel tasks of a workflow into multiple clusters and schedules them accordingly. We evaluated MCA-HEFT against the Mixed-parallel Heterogeneous Earliest Finish Time (M-HEFT) heuristic, which is one of the most well-known workflow scheduling heuristics in literature. MCA-HEFT was able to produce make spans that were up to 42% shorter than those produced by M-HEFT, having only approximately 10% of tasks distributed on multiple clusters. Our experiments considered several metrics and parameters including critical path size, make span, number of clusters used to execute tasks, and the network impact when deploying the tasks in multiple clusters.
Design and analysis of a low power VLIW DSP core

Power consumption has been the primary issue in processor design, with various power reduction strategies being adopted from system-level to circuit-level. In order to develop a power efficient system, architecture design, compiler optimization, as well as user evaluation must be employed in a unified framework. This paper presents an architecture-level power/performance simulator for a VLIW DSP processor core. Relying on parameterized power models and cycle accurate simulation, it provides fast and accurate power estimation for architecture exploration. Furthermore, the proposed modeling methodology can be used with minimal changes in the evaluation of other VLIW processor cores or for characterizing the efficiency of compiler-driven power efficient transformations.
Consistent mesh parameterizations

A basic element of Digital Geometry Processing algorithms is the establishment of a smooth parameterization for a given model. In this paper we propose an algorithm which establishes parameterizations for a set of models. The parameterizations are called consistent because they share the same base domain and respect features. They give immediate correspondences between models and allow remeshes with the same connectivity. Such remeshes form the basis for a large class of algorithms, including principal component analysis, wavelet transforms, detail and texture transfer between models, and n-way shape blending. We demonstrate the versatility of our algorithm with a number of examples.
A Generalized Path Integral Control Approach to Reinforcement Learning

With the goal to generate more scalable algorithms with higher efficiency and fewer open parameters, reinforcement learning (RL) has recently moved towards combining classical techniques from optimal control and dynamic programming with modern learning techniques from statistical estimation theory. In this vein, this paper suggests to use the framework of stochastic optimal control with path integrals to derive a novel approach to RL with parameterized policies. While solidly grounded in value function estimation and optimal control based on the stochastic Hamilton-Jacobi-Bellman (HJB) equations, policy improvements can be transformed into an approximation problem of a path integral which has no open algorithmic parameters other than the exploration noise. The resulting algorithm can be conceived of as model-based, semi-model-based, or even model free, depending on how the learning problem is structured. The update equations have no danger of numerical instabilities as neither matrix inversions nor gradient learning rates are required. Our new algorithm demonstrates interesting similarities with previous RL research in the framework of probability matching and provides intuition why the slightly heuristically motivated probability matching approach can actually perform well. Empirical evaluations demonstrate significant performance improvements over gradient-based policy learning and scalability to high-dimensional control problems. Finally, a learning experiment on a simulated 12 degree-of-freedom robot dog illustrates the functionality of our algorithm in a complex robot learning scenario. We believe that Policy Improvement with Path Integrals (PI2) offers currently one of the most efficient, numerically robust, and easy to implement algorithms for RL based on trajectory roll-outs.
Analysis of Multiscale Products for Step Detection and Estimation

We analyze discrete wavelet transform (DWT) multiscale products for detection and estimation of steps. Here the DWT is an over complete approximation to smoothed gradient estimation, with smoothing varied over dyadic scale, as developed by Mallat and Zhong (1992). The multiscale product approach was first proposed by Rosenfeld (1970) for edge detection. We develop statistics of the multiscale products, and characterize the resulting non-Gaussian heavy tailed densities. The results may be applied to edge detection with a false-alarm constraint. The response to impulses, steps, and pulses is also characterized. To facilitate the analysis, we employ a new general closed-form expression for the Cramer-Rao bound (CRB) for discrete-time step-change location estimation. The CRB can incorporate any underlying continuous and differentiable edge model, including an arbitrary number of steps. The CRB analysis also includes sampling phase offset effects and is valid in both additive correlated Gaussian and independent and identically distributed (i.i.d.) non-Gaussian noise. We consider location estimation using multiscale products, and compare results to the appropriate CRB.
Performance Evaluation and Comparison of Sahi Pro and Selenium Webdriver

Software testing is a crucial phase in software development life cycle that reduce errors, cut maintenance and overall software costs. Manual testing takes a lot of time and effort, so automation tools are used by testers. There are number of automation testing tools available, but to choose the appropriate tool for the task requires various parameters to be considered. In this paper an evaluation on web-based software testing tools; Sahi Pro and Selenium Webdriver, based on execution time, recording and playback efficiency, browser and platform compatibility, result reporting, ease of learning and cost has been presented. It will help testers to take informed decision to choose a tool according to their requirements and resources.
Pupillary Reaction in Children with Recurrent Abdominal Pain

An investigation was carried out with 3 groups of children to compare pupillary reactions (as an index of autonomic function) in response to stress induced by the cold pressor test. It was found that normal pupillary reactions are modified in children who have recurrent abdominal pain without physical cause and also in children with behaviour problems. It is suggested that disturbances of autonomic function merit further investigation in psychosomatic and emotional disorders, both as a method of diagnosis and to help elucidate the underlying mechanisms whereby symptoms may be produced.
In vitro effects of nitazoxanide on Echinococcus granulosus protoscoleces and metacestodes.

OBJECTIVES Infection of humans and domestic ruminants with the larval stage (metacestode) of Echinococcus granulosus results in cystic echinococcosis (CE). The metacestode causes a space-occupying lesion in visceral organs, most commonly in the liver. Benzimidazole carbamate derivatives, such as mebendazole and albendazole, are currently used for chemotherapeutic treatment of CE. In human patients, benzimidazoles have to be applied in high doses for extended periods of time, and adverse side effects are frequently observed. In order to evaluate alternative treatment options, the in vitro efficacy of nitazoxanide, a broad-spectrum drug used against intestinal parasites and bacteria, was investigated. METHODS Freshly isolated E. granulosus protoscoleces were subjected to nitazoxanide treatment (1, 5 and 10 microg/mL), and the effects on parasite viability were monitored by Trypan Blue staining and scanning electron microscopy. Protoscolex cultures were maintained further, until metacestode development took place. Metacestodes were then subjected to nitazoxanide treatment (10 microg/mL), and corresponding effects were visualized by scanning and transmission electron microscopy. RESULTS Dose-dependent protoscolex death within a few days of nitazoxanide treatment was observed. Subsequent in vitro culture of drug-treated protoscoleces confirmed the non-viability of parasites, while further cultivation of non-treated protoscoleces for a period of at least 3 months resulted in stage conversion and the formation of small metacestodes 3-4 mm in diameter. Nitazoxanide had a deleterious effect on these metacestodes, which was comparable to that of albendazole. CONCLUSIONS Our study indicates a potential for nitazoxanide as an alternative treatment option against CE.
A computational model for emergent dynamics in the kidney

In this paper, concepts from network automata are adapted and extended to model complex biological systems. Specifically, systems of nephrons, the operational units of the kidney, are modelled and the dynamics of such systems are explored. Nephron behaviour can fluctuate widely and, under certain conditions, become chaotic. However, the behaviour of the whole kidney remains remarkably stable and blood solute levels are maintained under a wide range of conditions even when many nephrons are damaged or lost. A network model is used to investigate the stability of systems of nephrons and interactions between nephrons. More sophisticated dynamics are explored including the observed oscillations in single nephron filtration rates and the development of stable ionic and osmotic gradients in the inner medulla which contribute to the countercurrent exchange mechanism. We have used the model to explore the effects of changes in input parameters including hydrostatic and osmotic pressures and concentrations of ions, such as sodium and chloride. The intrinsic nephron control, tubuloglomerular feedback, is included and the effects of coupling between nephrons are explored in two-, eight- and 72-nephron models.
Purification and molecular characterization of FAP, a feto-acinar protein associated with the differentiation of human pancreas.

This work describes the purification of FAP, a feto-acinar pancreatic protein associated with the ontogenesis, differentiation, and transformation of the human exocrine pancreas. The protein was purified to homogeneity from pancreatic juices of patients with pancreatic pathology by a two-step chromatographic procedure which consisted of size exclusion on Sephacryl S-200 and affinity on heparin-Sepharose. The final preparation gave a single band at Mr 110,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis after Coomassie stain or autoradiography of the 125I-labeled protein. Immunodetection with the murine monoclonal antibody mAb J28 in nitrocellulose replicas demonstrated a main Mr 110,000 component and trace components in the Mr 100,000-80,000 range. The immunopattern was identical to that in the original crude pancreatic secretion, therefore showing that the molecular characteristics of the protein, i.e. molecular mass, microheterogeneity, and immunoreactivity, were not altered along the purification procedure. FAP was identified as an acidic protein (isoelectric point 4.2-4.8) consisting of a single polypeptide chain having no free SH residues. Analysis of the amino acid composition showed a high proline content. Twenty-two residues of the N-terminal sequence were determined. No significant homology between this peptide and other proteins was found following a search of the NBRF-18 data bank. Sugar analysis showed the presence of mannose which is consistent with N-linked carbohydrate chains and an unusual high ratio in N-acetylgalactosamine residues suggesting the presence of many O-linked carbohydrate chains. Sequential deglycosylation with neuraminidase, hexosaminidase, and O-glycanase yield a single Mr 58,000 peptide showing that, relative to a molecular mass of 110,000, the carbohydrate moiety of FAP accounts for at least 47% of its apparent Mr by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Multiscale modelling of acoustic porous materials

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Heritability of volumetric brain changes and height in children entering puberty

The human brain undergoes structural changes in children entering puberty, while simultaneously children increase in height. It is not known if brain changes are under genetic control, and whether they are related to genetic factors influencing the amount of overall increase in height. Twins underwent magnetic resonance imaging brain scans at age 9 (N = 190) and 12 (N = 125). High heritability estimates were found at both ages for height and brain volumes (49–96%), and high genetic correlation between ages were observed (rg > 0.89). With increasing age, whole brain (+1.1%), cerebellum (+4.2%), cerebral white matter (+5.1%), and lateral ventricle (+9.4%) volumes increased, and third ventricle (−4.0%) and cerebral gray matter (−1.6%) volumes decreased. Children increased on average 13.8 cm in height (9.9%). Genetic influences on individual difference in volumetric brain and height changes were estimated, both within and across traits. The same genetic factors influenced both cerebral (20% heritable) and cerebellar volumetric changes (45%). Thus, the extent to which changes in cerebral and cerebellar volumes are heritable in children entering puberty are due to the same genes that influence change in both structures. The increase in height was heritable (73%), and not associated with cerebral volumetric change, but positively associated with cerebellar volume change (rp = 0.24). This association was explained by a genetic correlation (rg = 0.48) between height and cerebellar change. Brain and body each expand at their own pace and through separate genetic pathways. There are distinct genetic processes acting on structural brain development, which cannot be explained by genetic increase in height. Hum Brain Mapp, 2013. © 2011 Wiley Periodicals, Inc.
P-wave Amplification by Near-Surface Deposits at Different Excitation Levels

Possible nonlinearity in the response of sedimentary layers to incident P waves is studied using the strong-motion data from a vertical array in Taiwan at the site where a significant nonlinear response to S waves had been found. Soil transfer functions are analyzed at different excitation levels with a maximum vertical acceleration at surface reaching -0.1 g, corresponding to the compressional strain of 7 × 10 -5. Weak-motion and strong-motion transfer functions are compared. No effects of reduced amplification or change in resonance frequencies with increasing strain level were observed, suggesting that the response remained linear in the range of strain under consideration.
Tailoring plasmonic properties of metal-dielectric nanocomposite thin films

Tuning of the plasmonic properties of nanocomposite thin films made by embedding metal nanoparticles in dielectric matrices has been investigated theoretically. The working formula for localized surface plasmon resonance (LSPR) position (λLSPR) was derived to be λLSPR=λp1+ed(K+f1−f)+χIB with λp,ed, K, f and χIB being respectively the plasma wavelength of Au, dielectric constant of matrix thin film, shape factor, volume fraction of AuNPs inside the matrix and real part of inter-band susceptibility. Using this formula, LSPR of nanocomposites can be varied by more than 300 nm the visible range. Analysis of the formula concludes that for a given volume fraction, changing shape has the maximum effect on shift in LSPR position
Interference-alignment-embedded iterative beamforming design for multi-cell MIMO broadcasting

In this paper, we consider downlink multi-cell multi-user multi-antenna systems, where the users experience interference from adjacent cells as well as other users in the same cell. We design an iterative beamforming algorithm towards sum-rate maximization. Specifically, we propose an interference-alignment-embedded structure in the iteration, where a two-layer precoder approximately aligns the intra-cell interference with the inter-cell interference, and a max-SINR detector maximizes the achievable data rate. Simulation results show that the algorithm converges rapidly and achieves superior performance in noise-limited environments.
Grab a mug - Object detection and grasp motion planning with the Nao robot

In this paper we introduce an online grasping system for the Nao robot [1] manufactured by Aldebaran Robotics. The proposed system consists of an object detector and a grasp motion planner. Thereby, known objects are detected by a stereo contour-based object detector and hand motion paths are planned by an A*-based algorithm while avoiding obstacles. Compared to skilled robots such as Justin [2] or ASIMO [3] online grasping with the Nao constitute as particular problem due to the limited processing power and the hand design. The methods proposed allow detecting and grasping objects in real-time on an affordable humanoid robot.
An Audio-based Real-time Beat Tracking System and Its Applications

This paper describes a real-time beat tracking system that recognizes a rhythmic structure in real-world audio signals sampled from popular-music compact discs. Most previous beat-tracking systems dealt with MIDI signals and had difficulty in processing, in real time, audio signals containing sounds of various instruments and in tracking beats above the quarter-note level. Our system can process music without drums and music with drums and can — on the basis of three kinds of musical knowledge (of onset times, of chord changes, and of drum patterns) — recognize the hierarchical beat structure comprising the quarter-note, half-note, and measure levels. This paper also introduces several beat-tracking applications, such as beat-driven real-time computer graphics and lighting control.
The Future of Virtual Compound Screening

We provide a future perspective of the virtual screening field. A number of challenges will be highlighted that virtual screening will likely face when compound data will further grow at or beyond current rates and when much more target information will become available. These challenges go beyond computational efficiency issues (that will of course also play a critical role). For example, for structure‐based approaches, the accuracy of scoring functions and energy calculations will need to be improved. For ligand‐based approaches, the compound class‐dependence of similarity methods needs to be further explored and relationships between molecular similarity and activity similarity need to be established. We also comment on the current and future value of virtual screening. Opportunities for further development in a postgenome era are also discussed. It is hoped that some of the views and hypotheses we articulate might stimulate further discussion about the virtual screening field going forward.
Nucleocytoplasmic Distribution of the Ovalbumin Serpin PI-9 Requires a Nonconventional Nuclear Import Pathway and the Export Factor Crm1

ABSTRACT Proteinase inhibitor 9 (PI-9) is a human serpin present in the cytoplasm of cytotoxic lymphocytes and epithelial cells. It inhibits the cytotoxic lymphocyte granule proteinase granzyme B (graB) and is thought to protect cytotoxic lymphocytes and bystander cells from graB-mediated apoptosis. Following uptake into cells, graB promotes DNA degradation, rapidly translocating to the nucleus, where it binds a nuclear component. PI-9 should therefore be found in cytotoxic lymphocyte and bystander cell nuclei to ensure complete protection against graB. Here we demonstrate by microscopy and subcellular fractionation experiments that PI-9 is present in the nuclei of human cytotoxic cells, endothelial cells, and epithelial cells. We also show that the related serpins, PI-6, monocyte neutrophil elastase inhibitor (MNEI), PI-8, plasminogen activator inhibitor 2 (PAI-2), and the viral serpin CrmA exhibit similar nucleocytoplasmic distributions. Because these serpins lack classical nuclear localization signals and are small enough to diffuse through nuclear pores, we investigated whether import occurs actively or passively. Large (∼70 kDa) chimeric proteins comprising PI-9, PI-6, PI-8, MNEI, or PAI-2 fused to green fluorescent protein (GFP) show similar nucleocytoplasmic distributions to the parent proteins, indicating that nuclear import is active. By contrast, CrmA-GFP is excluded from nuclei, indicating that CrmA is not actively imported. In vitro nuclear transport assays show that PI-9 accumulates at a rate above that of passive diffusion, that it requires cytosolic factors but not ATP, and that it does not bind an intranuclear component. Furthermore, PI-9 is exported from nuclei via a leptomycin B-sensitive pathway, implying involvement of the export factor Crm1p. We conclude that the nucleocytoplasmic distribution of PI-9 and related serpins involves a nonconventional nuclear import pathway and Crm1p.