Miracle-dz/UniFAR-FTUs huggingface dataset:
Library generation for linear transforms

The development of high-performance numeric libraries has become extraordinarily difficult due to multiple processor cores, vector instruction sets, and deep memory hierarchies. To make things worse, often each library has to be re-implemented and re-optimized, whenever a new platform is released. In this thesis we develop a library generator that completely automates the library development for one important numerical domain: linear transforms, which include the discrete Fourier transform, discrete cosine transforms, filters, and discrete wavelet transforms. The input to our generator is a specification of the transform and a set of recursive algorithms for the transform, represented in a high-level domain-specific language; the output is a C++ library that supports general input size, is vectorized and multithreaded, and provides an optional adaptation mechanism for the memory hierarchy. Further, as we show in extensive benchmarks, the runtime performance of our automatically generated libraries is comparable to and often even higher than the best existing human-written code, including the widely used library FFTW and the commercially developed and maintained Intel Integrated Performance Primitives (IPP) and AMD Performance Library (APL). Our generator automates all library development steps typically performed manually by programmers, such as analyzing the algorithm and finding the set of required recursive functions and base cases, the appropriate restructuring of the algorithm to parallelize for multiple threads and to vectorize for the available vector instruction set and vector length, and performing code level optimizations such as algebraic simplification and others. The key to achieving full automation as well as excellent performance is a proper set of abstraction layers in the form of domain-specific languages called SPL (Signal Processing Language), index-free ∑-SPL, regular ∑-SPL, and intermediate code representation, and the use of rewriting systems to perform all difficult optimizations at a suitable, high level of abstraction. In addition, we demonstrate that our automatic library generation framework enables various forms of customization that would be very costly to perform manually. As examples, we show generated trade-offs between code size and performance, generated Java libraries obtained by modifying the backend, and functional customization for important transform variants.
Specialized Cilia in Mammalian Sensory Systems

Cilia and flagella are highly conserved and important microtubule-based organelles that project from the surface of eukaryotic cells and act as antennae to sense extracellular signals. Moreover, cilia have emerged as key players in numerous physiological, developmental, and sensory processes such as hearing, olfaction, and photoreception. Genetic defects in ciliary proteins responsible for cilia formation, maintenance, or function underlie a wide array of human diseases like deafness, anosmia, and retinal degeneration in sensory systems. Impairment of more than one sensory organ results in numerous syndromic ciliary disorders like the autosomal recessive genetic diseases Bardet-Biedl and Usher syndrome. Here we describe the structure and distinct functional roles of cilia in sensory organs like the inner ear, the olfactory epithelium, and the retina of the mouse. The spectrum of ciliary function in fundamental cellular processes highlights the importance of elucidating ciliopathy-related proteins in order to find novel potential therapies.
Aspects of Socially Assistive Robots Design for Dementia Care

Increasing prevalence of dementia matched with higher demand on healthcare services poses a challenge to society. The use of innovative technologies such as robotics has been identified as one of the solutions to this predicament. The design of Socially Assistive Robots (SAR) is a multidisciplinary field that needs to incorporate the diverse requirements of people with dementia and their carers. This paper attempts to identify important considerations for the successful design of SARs and to categorize them. A taxonomy of SAR's features is proposed, best practice design approaches, technology acceptance and ethical issues are examined. Recommendations for future areas of research are outlined.
Interactive Task Learning for Simple Games

We present an agent, called RosieTAG, that is implemented in Soar and interacts with an external robotic environment. Rosie learns new games through interactive instruction with a human via restricted natural language. Instead of learning policy or strategy information, as is common in other game learners, Rosie learns multiple game formulations (the objects, players, and rules of a game) and then uses its own general strategies to solve them. We describe the structure and functionality of Rosie, and evaluate its competence, generality, communication efficiency, communication accessibility, and ability to continuously learn and accumulate new tasks and new task knowledge.
The observed relationship of cloud to surface longwave radiation and air temperature at Ny-Ålesund, Svalbard

Abstract Ten-year (2004–2013) observations of cloud and surface shortwave (SW) and longwave (LW) fluxes at Ny-Ålesund were analysed to investigate monthly variations in cloudiness and their impacts on the surface LW radiation budget and near-surface temperature (Ts). The cloud fraction (CF) showed distinct monthly variations, high in summer (0.90) and lower in winter (0.79). The downward SW flux increased from March and showed a peak (~200 W m−2) in June. In contrast, the downward LW (LWD) flux increased from ~200 W m−2 in February to ~300 W m−2 in July. Both LWD and upward LW (LWU) fluxes and their difference increased during winter as lowest cloud base height (LCBH) decreased and CF increased. Ts difference and both LW fluxes difference (ΔLWD and ΔLWU), calculated as the difference in monthly mean Ts and LW between all-sky and cloud-free conditions, were highly correlated (R2 = 0.68 for LWD and R2 = 0.92 for LWU). Dramatic changes in Ts, CF and LW fluxes at Ny-Ålesund were closely associated with cold and warm air mass advection on a multi-day time scale. The average Ts under low-level clouds (LCBH ≤ 2 km) was estimated as −7.4 ± 6.1 °C due to warm air masses advected from the North Atlantic Ocean and Barents Sea, whereas the average Ts on cloud-free days was −14.5 ± 5.7 °C because of cold air mass advection from the pole. However, the duration of low-level clouds may not be long enough to drive such large Ts variations. 75-percentile of low-level cloud conditions at Ny-Ålesund persisted up to 2.3 days, whereas cloud-free and high-altitude cloud (LCBH > 2 km) conditions lasted for approximately 0.8 and 0.5 days, respectively. This implies that cloud LW effects on several warm days may be larger than the monthly average, but may not be accumulated enough to induce surface warming due to abrupt Ts drop associated with cold air mass advection.
Prediction of wrist arteriovenous fistula maturation with preoperative vein mapping with ultrasonography.

OBJECTIVE The purpose of this study was to determine whether the preoperative minimal cephalic vein size in the forearm was predictive of successful wrist fistula maturation to a functional hemodialysis access. METHODS Forty-four consecutive patients underwent evaluation before surgery with ultrasound scan imaging to map the entire cephalic vein in preparation for the construction of an arteriovenous fistula at the wrist. Measurements of the vein diameter were obtained from the ultrasound scan images at eight representative sites. Patients were clinically followed to determine maturation of the fistula to provide a functional hemodialysis access. The smallest diameter of the cephalic vein then was used as a preoperative predictor of fistula maturation. RESULTS Successful maturation of the arteriovenous fistula was achieved in 22 of the procedures (50%). Cephalic veins with a minimal diameter of 2.0 mm or less were used for anastamosis in 19 patients (43%), and three of these procedures (16%) led to a functional access site. The remaining 25 patients (57%) had minimal cephalic vein diameters greater than 2.0 mm, producing a successful maturation in 19 of the fistula creations (76%). A significantly higher rate of successful fistula maturation in those patients with a preoperative minimal cephalic vein size greater than 2.0 mm was realized (P =.0002, chi(2) test, with Yates correction for continuity). CONCLUSION In patients with a minimal cephalic vein size of 2.0 mm or less, a procedure other than wrist fistula should be considered for optimization of dialysis access.
Label optimal regret bounds for online local learning

We resolve an open question from (Christiano, 2014b) posed in COLT'14 regarding the optimal dependency of the regret achievable for online local learning on the size of the label set. In this framework the algorithm is shown a pair of items at each step, chosen from a set of $n$ items. The learner then predicts a label for each item, from a label set of size $L$ and receives a real valued payoff. This is a natural framework which captures many interesting scenarios such as collaborative filtering, online gambling, and online max cut among others. (Christiano, 2014a) designed an efficient online learning algorithm for this problem achieving a regret of $O(\sqrt{nL^3T})$, where $T$ is the number of rounds. Information theoretically, one can achieve a regret of $O(\sqrt{n \log L T})$. One of the main open questions left in this framework concerns closing the above gap. In this work, we provide a complete answer to the question above via two main results. We show, via a tighter analysis, that the semi-definite programming based algorithm of (Christiano, 2014a), in fact achieves a regret of $O(\sqrt{nLT})$. Second, we show a matching computational lower bound. Namely, we show that a polynomial time algorithm for online local learning with lower regret would imply a polynomial time algorithm for the planted clique problem which is widely believed to be hard. We prove a similar hardness result under a related conjecture concerning planted dense subgraphs that we put forth. Unlike planted clique, the planted dense subgraph problem does not have any known quasi-polynomial time algorithms. Computational lower bounds for online learning are relatively rare, and we hope that the ideas developed in this work will lead to lower bounds for other online learning scenarios as well.
Hand-Camera Coordination Varies over Time in Users of the Argus® II Retinal Prosthesis System

Introduction: Most visual neuroprostheses use an external camera for image acquisition. This adds two complications to phosphene perception: (1) stimulation locus will not change with eye movements; and (2) external cameras can be aimed in directions different from the user’s intended direction of gaze. Little is known about the stability of where users perceive light sources to be or whether they will adapt to changes in camera orientation. Methods: Three end-stage retinitis pigmentosa patients implanted with the Argus II participated in this study. This prosthesis stimulated the retina based on an 18° × 11° area selected within the camera’s 66° × 49° field of view. The center of the electrode array’s field of view mapped within the camera’s field of view is the camera alignment position (CAP). Proper camera alignments minimize errors in localizing visual percepts in space. Subjects touched single white squares in random locations on a darkened touchscreen 40 or more times. To study adaptation, subjects were given intentional CAP misalignments of 15–40° for 5–6 months. Subjects performed this test with auditory feedback during (bi-)weekly lab sessions. Misaligned CAPs were maintained for another 5–6 months without auditory feedback. Touch alignment was tracked to detect any adaptation. To estimate localization stability, data for when CAPs were set to minimize errors were tracked. The same localization test as above was used. Localization errors were tracked every 1–2 weeks for up to 40 months. Results: Two of three subjects used auditory feedback to improve accuracy with misaligned CAPs at an average rate of 0.02°/day (p < 0.05, bootstrap analysis of linear regression). The rates observed here were ~4000 times slower than those seen in normally-sighted subjects adapting to prism glasses. Removal of auditory feedback precipitated error increases for all subjects. Optimal CAPs varied significantly across test sessions (p < 10−4, bootstrap multivariate analysis of variance (MANOVA)), up to 21–29° within subjects over the observed period. Across subjects, optimal CAPs showed an average rate of change of 0.39°/day (SD 0.36°/day). Conclusions: Optimal CAPs varied dramatically over time for all subjects. Subjects displayed no adaptation to misaligned CAPs without feedback. Regular recalibration of CAPs may be required to maintain hand-camera coordination.
Defects in lamin B 1 expression or processing affect interphase chromosome position and gene expression

Chromosomes occupy discrete, mutually exclusive volumes in interphase nuclei (Cremer and Cremer, 2001). These chromosome territories do not intermingle, except at their boundaries (Zink et al., 1998; Edelmann et al., 2001; Branco and Pombo, 2006), and their size is approximately related to DNA content (Gilbert et al., 2005). Although most proteins diffuse rapidly throughout nuclei (Misteli, 2001), the diffusion of individual chromosome territories is constrained (Manders et al., 2003; Walter et al., 2003). Territories are not randomly distributed, and the rules governing positioning are incompletely understood and vary between cell types (Parada et al., 2004) and growth state (Parada et al., 2002). The most constant fi nding is of a conserved radial organization; gene-poor chromosomes (e.g., human chromosome 18) are found at the periphery, and gene-rich chromosomes (e.g., human chromosome 19) are found more centrally (Croft et al., 1999; Cremer and Cremer, 2001; Tanabe et al., 2005). A similar although weaker radial organization with gene-poor chromosomes more peripheral has recently been reported for the mouse, based on position analysis of chromosomes 1, 2, 9, 11, 14, and X in a range of cell types (Mayer et al., 2005). No specifi c nuclear envelope (NE) component has been implicated in these large-scale localizations, and the inner nuclear membrane protein emerin and lamina protein lamin A have been excluded (Boyle et al., 2001; Meaburn et al., 2005). The signifi cance of the nonrandom distribution of chromosome territories within the interphase nucleus remains poorly understood. The nonrandom organization of territories may refl ect functional associations between specifi c chromatin regions and other nuclear structures, the nucleolus being one obvious example. The inner face of the nuclear periphery, consisting of an inner nuclear membrane decorated with a nuclear lamina pierced by nuclear pore complexes (NPCs) represents another large domain for potential chromatin interaction. Experimental evidence from several groups has shown that associations between certain gene loci and the nuclear periphery may play important roles in the transcriptional regulation of those genes. The association has been shown to act at the level of chromosomal subregions and generally has a repressive or silencing role, with activation involving movement away from the periphery into the nuclear interior (Hewitt et al., 2004; Zink et al., 2004; Chuang et al., 2006). Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression
Hyper-Minimization for Deterministic Tree Automata

Hyper-minimization is a recent automaton compression technique that can reduce the size of an automaton beyond the limits imposed by classical minimization. The additional compression power is enabled by allowing a finite difference in the represented language. The necessary theory for hyper-minimization is developed for (bottom-up) deterministic tree automata. The hyper-minimization problem for deterministic tree automata is reduced to the hyper-minimization problem for deterministic finite-state string automata, for which fast algorithms exist. The fastest algorithm obtained in this way runs in time , where m is the size of the transition table and n is the number of states of the input tree automaton.
Transport proteins determine drug sensitivity and resistance in a protozoan parasite, Trypanosoma brucei

Drug resistance in pathogenic protozoa is very often caused by changes to the ‘transportome’ of the parasites. In Trypanosoma brucei, several transporters have been implicated in uptake of the main classes of drugs, diamidines and melaminophenyl arsenicals. The resistance mechanism had been thought to be due to loss of a transporter known to carry both types of agents: the aminopurine transporter P2, encoded by the gene TbAT1. However, although loss of P2 activity is well-documented as the cause of resistance to the veterinary diamidine diminazene aceturate (DA; Berenil®), cross-resistance between the human-use arsenical melarsoprol and the diamidine pentamidine (melarsoprol/pentamidine cross resistance, MPXR) is the result of loss of a separate high affinity pentamidine transporter (HAPT1). A genome-wide RNAi library screen for resistance to pentamidine, published in 2012, gave the key to the genetic identity of HAPT1 by linking the phenomenon to a locus that contains the closely related T. brucei aquaglyceroporin genes TbAQP2 and TbAQP3. Further analysis determined that knockdown of only one pore, TbAQP2, produced the MPXR phenotype. TbAQP2 is an unconventional aquaglyceroporin with unique residues in the “selectivity region” of the pore, and it was found that in several MPXR lab strains the WT gene was either absent or replaced by a chimeric protein, recombined with parts of TbAQP3. Importantly, wild-type AQP2 was also absent in field isolates of T. b. gambiense, correlating with the outcome of melarsoprol treatment. Expression of a wild-type copy of TbAQP2 in even the most resistant strain completely reversed MPXR and re-introduced HAPT1 function and transport kinetics. Expression of TbAQP2 in Leishmania mexicana introduced a pentamidine transport activity indistinguishable from HAPT1. Although TbAQP2 has been shown to function as a classical aquaglyceroporin it is now clear that it is also a high affinity drug transporter, HAPT1. We discuss here a possible structural rationale for this remarkable ability.
Comorbidity of substance use and mental disorders.

INTRODUCTION Comorbidity is a term defined as the presence of two or more conditions occurring either at the same time or having a close relationship to the same individual. World Health Organization (WHO) define it as the "co-occurrence in the same individual of a psychoactive substance use disorder and another psychiatric disorder". Progressive deinstitutionalisation, despite indisputable benefits and improvement of life quality in psychiatric patients, resulted in appearance of new burdens, such as deterioration of family life. Furthermore, wide availability of alcoholic beverages and drugs in communities where the patients live, led comorbid substance abuse disorders to emerge as one of the biggest challenges in the modern psychiatry. There is a limited amount of data concerning the background of the patients with a dual diagnosis, available in the literature, and therefore our aim was to create a sociodemographic profile of such individuals. MATERIALS AND METHODS The study was conducted among the patients treated in a drug rehabilitation centre of the Upper Silesian Association "Familia" in Gliwice, Poland using authors' own questionnaire, consisting of 75 items. The study group consisted of 9 females and 91 males (n=100), average age of the patients equalled 29.7 years (95%CI: 28.5-31 years; min/max value: 20/48 years), all the patients had an established dual diagnosis. OUTCOMES 66% of the study group was single, with permanent residency, living with family either in city (47%) or in village (19%). Remaining 34% was spread through the other options (1-4%), with the highest percentage in "single, with permanent residency, living alone in the city" (4%). CONCLUSIONS Obtained data, demonstrated high homogeneity among the patients with a dual diagnosis in terms of a socio-demographical profile.
Machine translation in continuous space

We present a diﬀerent perspective on the machine translation problem that relies upon continuous-space probabilistic models for words and phrases. Within this perspective we propose a method called Tied-Mixture Machine Translation (TMMT) that uses a trainable parametric model employing Gaussian mixture probability density functions to represent word-and phrase–pairs. In the new perspective, machine translation is treated in the same way as acoustic modeling in speech recognition. This new treatment carries several potential advantages that may improve state-of-the-art machine translation systems, including better generalization to unseen events; adaptation to new domains, languages, genres, and speakers via methods such as Maximum-Likelihood Linear Regression (MLLR); and improved discrimination through discriminative training methods such as Maximum Mutual Information Estimation (MMIE). Our goal in this paper, however, is to introduce the new approach and demonstrate its viability, leaving investigation of some of the potential advantages to future work. To this end, we report some preliminary experiments demonstrating the viability of the proposed method.
Specialized Review Selection for Feature Rating Estimation

On participatory Websites, users provide opinions about products, with both overall ratings and textual reviews. In this paper, we propose an approach to accurately estimate feature ratings of the products. This approach selects user reviews that extensively discuss specific features of the products (called specialized reviews), using information distance of reviews on the features. Experiments on real data show that overall ratings of the specialized reviews can be used to represent their feature ratings. The average of these overall ratings can be used by recommender systems to provide feature specific recommendations that better help users make purchasing decisions.
A Sequential Model for Attentive Object Selection

A biologically motivated model for object selection is proposed which combines strategies for preattentive segmentation and attentive object selection to extract consistent descriptions of objects in a complex scene. Results from psychophysical experiments and neurophysiological data are discussed to account for the architecture of the human visual system and its computational principles. In this paper we present the implementation of the attentional component of the model and the application of the system to traac scene decomposition