Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial evaluation for optimized compilation of actor-oriented models

One major achievement of traditional computer science is systematically abstracting away the physical world. The Von Neumann model provides a universal abstraction for sequential computation. The concept is so simple and powerful for transformational systems (vs. reactive systems [Berry1989]) that any traditional program can run regardless of underlying platform—whether it is a supercomputer or a desktop. Embedded software systems, however, engage the physical world. Time, concurrency, liveness, continuums and reactivity must be remarried to computation [Lee2006J. In order to reason about these properties, a programming model must be able to express these properties directly. The traditional techniques for doing concurrent programming on top of sequential programming languages like C use threads complemented with synchronization mechanisms like semaphores and mutual exclusion locks. These methods are at best retrofits to the fundamentally sequential formalism and are hard to understand, difficult to debug, brittle and error-prone. Actor-oriented design presents a high level abstraction for composing concurrent components. There is a rich variety of concurrency formalisms that span the whole spectrum from most expressive to most analyzable. In particular, I will focus on one particular model of computation called heterochronous dataflow (HDF) which strikes a nice balance between expressiveness and analyzability. However, high level abstraction often introduces overhead and results in slower systems. In component based design, generic components are highly parameterized for reusability and thus are less efficient. The well-defined interface between components results in flexible composition but increases the cost of inter-component communication through the interface. In the second part of this thesis, I will address the problem of generating an efficient implementation from a high level specification. I use partial evaluation as an optimized compilation technique for actor-oriented models. Compared with traditional compiler optimization, partial evaluation for embedded software works at the component level and heavily leverages domain-specific knowledge. Through model analysis—the counterpart of binding-time analysis in the use of partial evaluation for general purpose software [Jones1993], the tool can discover the static parts in the model including data types, buffer sizes, parameter values, model structures and execution schedules, etc. and then exploit the already known information to reach a very efficient implementation. I use a helper-based mechanism, which leads to flexible and extensible code generation framework. The end result is that the benefit offered by high level abstraction comes with (almost) no performance penalty. The code generation framework described in this dissertation has been released in open source as part of Ptolemy II and can be downloaded from http://ptolemy.org/.
NAUTILUS: Fishing for Deep Bugs with Grammars

Fuzz testing is a well-known method for efficiently identifying bugs in programs. Unfortunately, when programs that require highly-structured inputs such as interpreters are fuzzed, many fuzzing methods struggle to pass the syntax checks: interpreters often process inputs in multiple stages, first syntactic and then semantic correctness is checked. Only if both checks are passed, the interpreted code gets executed. This prevents fuzzers from executing “deeper” — and hence potentially more interesting — code. Typically, two valid inputs that lead to the execution of different features in the target program require too many mutations for simple mutation-based fuzzers to discover: making small changes like bit flips usually only leads to the execution of error paths in the parsing engine. So-called grammar fuzzers are able to pass the syntax checks by using ContextFree Grammars. Feedback can significantly increase the efficiency of fuzzing engines and is commonly used in state-of-the-art mutational fuzzers which do not use grammars. Yet, current grammar fuzzers do not make use of code coverage, i.e., they do not know whether any input triggers new functionality. In this paper, we propose NAUTILUS, a method to efficiently fuzz programs that require highly-structured inputs by combining the use of grammars with the use of code coverage feedback. This allows us to recombine aspects of interesting inputs, and to increase the probability that any generated input will be syntactically and semantically correct. We implemented a proofof-concept fuzzer that we tested on multiple targets, including ChakraCore (the JavaScript engine of Microsoft Edge), PHP, mruby, and Lua. NAUTILUS identified multiple bugs in all of the targets: Seven in mruby, three in PHP, two in ChakraCore, and one in Lua. Reporting these bugs was awarded with a sum of 2600 USD and 6 CVEs were assigned. Our experiments show that combining context-free grammars and feedback-driven fuzzing significantly outperforms state-of-the-art approaches like AFL by an order of magnitude and grammar fuzzers by more than a factor of two when measuring code coverage.
Cirurgia espiritual: uma investigação

OBJETIVO: Uma modalidade de tratamento que capta muito a atencao da midia e a cirurgia espiritual, que, entretanto, tem sido pouco estudada cientificamente. Uma questao que se impoe e sobre a veracidade ou nao de tais fenomenos, porem pesquisas nesse sentido sao escassas. METODO: Apresentamos o relato de uma investigacao sobre um dos mais famosos cirurgioes espirituais do Brasil, o Sr. Joao Teixeira de Farias. Foram acompanhadas por volta de 30 "cirurgias", sendo que em seis dos pacientes foram realizados a anamnese, o exame fisico e coletados os tecidos extraidos para exames anatomo-patologicos. RESULTADOS: O "cirurgiao" verdadeiramente incisa a pele ou o epitelio ocular, alem de realizar raspados corneanos sem nenhuma tecnica anestesica ou antisseptica identificavel. Apesar disso, apenas um paciente queixou-se de dor moderada quando teve a mama incisada. Os pacientes foram examinados ate tres dias depois da cirurgia sem nenhum sinal de infeccao, bem como os relatos posteriores dos pacientes nao continham informacoes de infeccao. O exame histopatologico evidenciou que os tecidos extraidos eram compativeis com o local de origem e, com excecao de um lipoma de 210 gramas, eram tecidos normais, sem particularidades patologicas. Foi realizada revisao da literatura e discussao do efeito placebo. CONCLUSOES: As cirurgias sao reais, mas, apesar de nao ter sido possivel avaliar a eficacia do procedimento, aparentemente nao teriam efeito especifico na cura dos pacientes. Sem duvida, nossos achados sao mais exploratorios que conclusivos. Sao necessarios posteriores estudos para lancar luz sobre esse heterodoxo tratamento.
A Whole-Cell Screen Identifies Small Bioactives That Synergize with Polymyxin and Exhibit Antimicrobial Activities against Multidrug-Resistant Bacteria

The threat of diminished antibiotic discovery has global health care in crisis. In the United States, it is estimated each year that over 2 million bacterial infections are resistant to first-line antibiotic treatments and cost in excess of 20 billion dollars. ABSTRACT The threat of diminished antibiotic discovery has global health care in crisis. In the United States, it is estimated each year that over 2 million bacterial infections are resistant to first-line antibiotic treatments and cost in excess of 20 billion dollars. Many of these cases result from infection with the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), which are multidrug-resistant bacteria that often cause community- and hospital-acquired infections in both healthy and immunocompromised patients. Physicians have turned to last-resort antibiotics like polymyxins to tackle these pathogens, and as a consequence, polymyxin resistance has emerged and is spreading. Barring the discovery of new antibiotics, another route to successfully mitigate polymyxin resistance is to identify compounds that can complement the existing arsenal of antibiotics. We recently designed and performed a large-scale robotic screen to identify 43 bioactive compounds that act synergistically with polymyxin B to inhibit the growth of polymyxin-resistant Escherichia coli. Of these 43 compounds, 5 lead compounds were identified and characterized using various Gram-negative bacterial organisms to better assess their synergistic activity with polymyxin. Several of these compounds reduce polymyxin to an MIC of <2 μg/ml against polymyxin-resistant and polymyxin-heteroresistant Gram-negative pathogens. Likewise, four of these compounds exhibit antimicrobial activity against Gram-positive bacteria, one of which rapidly eradicated methicillin-resistant Staphylococcus aureus. We present multiple first-generation (i.e., not yet optimized) compounds that warrant further investigation and optimization, since they can act both synergistically with polymyxin and also as lone antimicrobials for combating ESKAPE pathogens.
Improving the Robustness to Data Inconsistency between Training and Testing for Code Completion by Hierarchical Language Model

In the field of software engineering, applying language models to the token sequence of source code is the state-of-art approach to build a code recommendation system. The syntax tree of source code has hierarchical structures. Ignoring the characteristics of tree structures decreases the model performance. Current LSTM model handles sequential data. The performance of LSTM model will decrease sharply if the noise unseen data is distributed everywhere in the test suite. As code has free naming conventions, it is common for a model trained on one project to encounter many unknown words on another project. If we set many unseen words as UNK just like the solution in natural language processing, the number of UNK will be much greater than the sum of the most frequently appeared words. In an extreme case, just predicting UNK at everywhere may achieve very high prediction accuracy. Thus, such solution cannot reflect the true performance of a model when encountering noise unseen data. In this paper, we only mark a small number of rare words as UNK and show the prediction performance of models under in-project and cross-project evaluation. We propose a novel Hierarchical Language Model (HLM) to improve the robustness of LSTM model to gain the capacity about dealing with the inconsistency of data distribution between training and testing. The newly proposed HLM takes the hierarchical structure of code tree into consideration to predict code. HLM uses BiLSTM to generate embedding for sub-trees according to hierarchies and collects the embedding of sub-trees in context to predict next code. The experiments on inner-project and cross-project data sets indicate that the newly proposed Hierarchical Language Model (HLM) performs better than the state-of-art LSTM model in dealing with the data inconsistency between training and testing and achieves averagely 11.2\% improvement in prediction accuracy.
WHALETRANS: E2E WHisper to nAturaL spEech conversion using modified TRANSformer network

In this article, we investigate whispered-to natural-speech conversion method using sequence to sequence generation approach by proposing modified transformer architecture. We investigate different kinds of features such as mel frequency cepstral coefficients (MFCCs) and smoothed spectral features. The network is trained end-to-end (E2E) using supervised approach. We investigate the effectiveness of embedded auxillary decoder used after N encoder sub-layers, and is trained with the frame level objective function for identifying source phoneme labels. We predict target audio features and generate audio using these for testing. We test on standard wTIMIT dataset and CHAINS dataset. We report results as word-error-rate (WER) generated by using automatic speech recognition (ASR) system and also BLEU scores. %intelligibility and naturalness using mean opinion score and additionally using word error rate using automatic speech recognition system. In addition, we measure spectral shape of an output speech signal by measuring formant distributions w.r. t the reference speech signal, at frame level. In relation to this aspect, we also found that the whispered-to-natural converted speech formants probability distribution is closer to ground truth distribution. To the authors' best knowledge, this is the first time transformer with auxiliary decoder has been applied for whispered-to-natural speech conversion. [This pdf is TASLP submission draft version 1.0, 14th April 2020. ]
SiegeBreaker: An SDN Based Practical Decoy Routing System

Abstract Decoy Routing (DR), a promising approach to censorship circumvention, uses routers (rather than end hosts) as proxy servers. Users of censored networks, who wish to use DR, send specially crafted packets, nominally addressed to an uncensored website. Once safely out of the censored network, the packets encounter a special router (the Decoy Router) which identifies them using a secret handshake, and proxies them to their true destination (a censored site). However, DR has implementation problems: it is infeasible to reprogram routers for the complex operations required. Existing DR solutions fall back on using commodity servers as a Decoy Router. But as servers are not efficient at routing, most web applications show poor performance when accessed over DR. A further concern is that the Decoy Router has to inspect all flows in order to identify the ones that need DR. This may itself be a breach of privacy for other users (who neither require DR nor want to be monitored). In this paper, we present a novel DR system, Siege- Breaker (SB), which solves the aforementioned problems using an SDN-based architecture. Previous proposals involve a single unit which performs all major operations (inspecting all flows, identifying the DR requests and proxying them). In contrast, SB distributes the tasks for DR among three independent modules. (1) The SDN controller identifies DR requests via a covert, privacy preserving scheme, and does not need to inspect all flows. (2) The reconfigurable SDN switch intercepts packets, and forwards them to a secret proxy efficiently. (3) The secret proxy server proxies the client’s traffic to the censored site. Our modular, lightweight design achieves performance comparable to direct TCP downloads, for both in-lab setups, and Internet based tests involving commercial SDN switches.
Numerical Simulation of H2/O2 Continuous Spin Detonation with a Detailed Chemical Mechanism

Very high energy release rates, which can be achieved in detonations, for many years attract attention of engineers to possible practical applications of this phenomenon. As was shown for the first time by Ya. B. Zel’dovich [1], the detonation regime of combustion is also more efficient thermodynamically than the deflagration under the same initial conditions. One can hope that development of detonation-based fuel-burning devices will eventually lead to the design of more cost-effective and compact engines for of sub-orbital spacecraft and other high-speed vehicles. In recent years, significant efforts were undertaken for a detailed research on the concept of Pulse Detonation Engine (PDE), a device which creates propulsion by burning the fuel in a combustion chamber where a traveling detonation wave is periodically initiated. Nevertheless, it seems that, owing to the difficulties of fast exhaust of the combustion products and recharging of the combustion chamber by the fresh fuel mixture, the current generation PDEs are not yet capable of running at high frequencies needed for efficiency. There are a few alternative concepts of detonation-based engines. In particular, a promising idea that can be traced back to the work of B. V. Voitsekhovskii [2] is to use a detonation wave spinning in an annular tube, which is constantly refilled by a combustible mixture from one end. It is the so-called Continuous Detonation Wave Engine (CDWE), which was mostly studied in the Lavrent’yev Instutute of Hydrodynamics, Novosibirsk, Russia. In many aspects, CDWE is close to PDE operating at very high frequency (several kHz). For a review of this concept and its comparison with PDE, see the recent publications [3,4]. In the present work, the detonation wave propagation in CDWE is simulated numerically by solving the Euler equations for a chemically reacting flow. A detailed chemical model (6 species, 7 reactions) is used to describe the combustion of stoichiometric hydrogen-oxygen mixture. The governing equations are solved with a highresolution shock-capturing WENO (weighted essentially non-oscillatory) scheme. The numerical simulations are used to obtain a clear picture of processes in the combustion chamber of CDWE, elucidate the underlying physical mechanisms, and investigate the influence of different parameters on this phenomenon.
RV-FuseNet: Range View Based Fusion of Time-Series LiDAR Data for Joint 3D Object Detection and Motion Forecasting

Robust real-time detection and motion forecasting of traffic participants is necessary for autonomous vehicles to safely navigate urban environments. In this paper, we present RV-FuseNet, a novel end-to-end approach for joint detection and trajectory estimation directly from time-series LiDAR data. Instead of the widely used bird’s eye view (BEV) representation, we utilize the native range view (RV) representation of LiDAR data. The RV preserves the full resolution of the sensor by avoiding the voxelization used in the BEV. Furthermore, RV can be processed efficiently due to its compactness. Previous approaches project time-series data to a common viewpoint for temporal fusion, and often this viewpoint is different from where it was captured. This is sufficient for BEV methods, but for RV methods, this can lead to loss of information and data distortion which has an adverse impact on performance. To address this challenge we propose a simple yet effective novel architecture, Incremental Fusion, that minimizes the information loss by sequentially projecting each RV sweep into the viewpoint of the next sweep in time. We show that our approach significantly improves motion forecasting performance over the existing state-of-the-art. Furthermore, we demonstrate that our sequential fusion approach is superior to alternative RV based fusion methods on multiple datasets.
Finger-Vein Recognition Based on Densely Connected Convolutional Network Using Score-Level Fusion With Shape and Texture Images

Biometrics using finger-veins is a recognition method based on the shape of veins in fingers, and it has the advantage of difficulty to be forged. However, a shade is inevitably produced due to the bones and fingernails, and a change in illumination occurs when acquiring the images of finger-veins. Previous studies have conducted finger-vein recognition using a single-type texture image or finger-vein segmented image (shape image). A texture image provides numerous features, but it is vulnerable to the changes in illumination during recognition and contains noises in regions other than the finger-vein region. A shape image is less affected by noises; however, the recognition accuracy is significantly reduced due to fewer features available and mis-segmented regions caused by shades. In this study, therefore, rough finger-vein regions in an image are detected to reduce the effect of mis-segmented regions, to complement the drawbacks of shape image-based finger-vein recognition. Furthermore, score-level fusion is performed for two output scores of deep convolutional neural network extracted from the texture and shape images, which can reduce the sensitivity to noise, while diverse features provided in the texture image are used efficiently. Two open databases, the Shandong University homologous multi-modal traits finger-vein database and Hong Kong Polytech University finger image database, are used for experiments, and the proposed method shows better recognition performance than the state-of-the-art method.
Addition of Wheat Bran and/or Rice Straw on Chemical Composition and in vitro Rumen Fermentation Characteristics of Ensiled Water Hyacinth

Abstract Li, J.D. , Liu, J.X. , Wu, Y.M. and Ye, J.A. 2007. Addition of wheat bran and/or rice straw on chemical composition and in vitro rumen fermentation characteristics of ensiled water hyacinth. J. Appl. Anim. Res., 31: 137–142. This work was conducted to investigate the quality of water hyacinth (WH) silage prepared with or without wheat bran (WB) and/or rice straw (RS). The WH silages were prepared in experimental glass containers to create four treatments: 1. 100% (fresh basis) WH (control); 2. 90% (WH) + 10% WB (WB10); 3. 90% WH + 10% RS (RS10), and 4. 90% WH + 5% WB + 5% RS (WB5RS5). The WH silage alone was of poor quality with undesirable odour and colour. Addition of 10% WB increased the content of dry matter, crude protein and lactate, improved fermentation characteristics and lowered pH value, percentage of ammonia-N in total N and butyrate concentration of silage (P<0.05). Addition of 10% RS increased dry matter content, reduced proportion of ammonia-N of total N and pH value as well as crude protein concentration (P<0.05), but had little effect on lactate concentration as well as fermentation characteristics (P>0.05). Addition of 5% rice straw and 5% wheat bran resulted in intermediate quality silage. It may be concluded that ensiling of water hyacinth with 10% WB was an efficient way to improve the silage quality.
Erratum

By Quentin Giai Gianetto et al., vol. 16, issue 1, pp. 29–32 DOI 10.1002/pmic.201500189. Due to an error after reformatting of the reference list, the sentence on page 32 of this contribution, which reads: “CP4P allows processing any quantitative datasets, regardless the experimental design (nature and hierarchy of replicates, number of conditions, etc.), it is easy-to-use and it can be embedded in any bioinformatics pipeline via the CRAN [14]. ” is replaced with: “CP4P allows processing any quantitative datasets, regardless the experimental design (nature and hierarchy of replicates, number of conditions, etc.), it is easy-to-use and it can be embedded in any bioinformatics pipeline via CRAN (http://cran.r-project.org/web/packages/ cp4p). ” In addition, all first and last names in the References were originally switched and should appear as follows:
VITRO OF Melanoxylon brauna SCHOTT. MORPHOGENESIS: RESPONSIVENESS OF EXPLANTS TO PERMANENT AND TEMPORARY IMMERSION GROWTH REGULATORS

Melanoxylon brauna is propagated by seeds, however, low yield, pest attack and short viability are problems in seedling production. In vitro cultivation is an alternative for large-scale seedling production, but studies with this species are scarce. The aim of the work was to analyze the in vitro morphogenesis of braúna. Explants after induction of growth regulators. Three experiments were performed: I. In vitro bud proliferation of juvenile explants at different BAP concentrations. Was analyzed the number and length of shoots (mm); bud explants-1 (%); calogenesis (%) and direct and indirect organogenesis budding-1 (%). II. In vitro rhizogenesis of shoots with different types and auxin concentrations. III. In vitro rhizogenesis of under temporary immersion of shoots at different IBA concentrations. It was analyzed in experiment I and II: calogenesis (%); rhizogenesis (%); number, length (mm) and root dry mass (mg) the shoots. The nodal segment with two axillary buds was the most responsive explant regardless of the use of BAP. The stem apex with the use of BAP (2.5-3.5 mg.L-1) was the most responsive in the proliferation of shoots. Tested concentrations of auxins IBA, NAA and 2,4-D were not sufficient for in vitro rhizogenesis. The average of the maximum technical efficiencies of the variables used to analyze rhizogenic process suggests the treatment of the shoots base by temporary immersion in the IBA at an approximate concentration of 2,500 mg.L1 and planting on the vermiculite substrate. v.26 n.1 2020