Miracle-dz/UniFAR-FTUs huggingface dataset:
Energy Efficiency Features of the Intel Skylake-SP Processor and Their Impact on Performance

The overwhelming majority of High Performance Computing (HPC) systems and server infrastructure uses Intel x86 processors. This makes an architectural analysis of these processors relevant for a wide audience of administrators and performance engineers. In this paper, we describe the effects of hardware controlled energy efficiency features for the Intel Skylake-SP processor. Due to the prolonged micro-architecture cycles, which extend the previous Tick-Tock scheme by Intel, our findings will also be relevant for succeeding architectures. The findings of this paper include the following: C-state latencies increased significantly over the Haswell-EP processor generation. The mechanism that controls the uncore frequency has a latency of approximately 10ms and it is not possible to truly fix the uncore frequency to a specific level. The out-of-order throttling for workloads using 512 bit wide vectors also occurs at low processor frequencies. Data has a significant impact on processor power consumption which causes a large error in energy models relying only on instructions.
Fast and Robust Rank Aggregation against Model Misspecification

In rank aggregation (RA), a collection of preferences from different users are summarized into a total order under the assumption of homogeneity of users. Model misspecification in RA arises since the homogeneity assumption fails to be satisfied in the complex real-world situation. Existing robust RAs usually resort to an augmentation of the ranking model to account for additional noises, where the collected preferences can be treated as a noisy perturbation of idealized preferences. Since the majority of robust RAs rely on certain perturbation assumptions, they cannot generalize well to agnostic noise-corrupted preferences in the real world. In this paper, we propose CoarsenRank, which possesses robustness against model misspecification. Specifically, the properties of our CoarsenRank are summarized as follows: (1) CoarsenRank is designed for mild model misspecification, which assumes there exist the ideal preferences (consistent with model assumption) that locates in a neighborhood of the actual preferences. (2) CoarsenRank then performs regular RAs over a neighborhood of the preferences instead of the original dataset directly. Therefore, CoarsenRank enjoys robustness against model misspecification within a neighborhood. (3) The neighborhood of the dataset is defined via their empirical data distributions. Further, we put an exponential prior on the unknown size of the neighborhood, and derive a much-simplified posterior formula for CoarsenRank under particular divergence measures. (4) CoarsenRank is further instantiated to Coarsened Thurstone, Coarsened Bradly-Terry, and Coarsened Plackett-Luce with three popular probability ranking models. Meanwhile, tractable optimization strategies are introduced with regards to each instantiation respectively. In the end, we apply CoarsenRank on four real-world datasets.
Flat2Layout: Flat Representation for Estimating Layout of General Room Types

This paper proposes a new approach, Flat2Layout, for estimating general indoor room layout from a single-view RGB image whereas existing methods can only produce layout topologies captured from the box-shaped room. The proposed flat representation encodes the layout information into row vectors which are treated as the training target of the deep model. A dynamic programming based postprocessing is employed to decode the estimated flat output from the deep model into the final room layout. Flat2Layout achieves state-of-the-art performance on existing room layout benchmark. This paper also constructs a benchmark for validating the performance on general layout topologies, where Flat2Layout achieves good performance on general room types. Flat2Layout is applicable on more scenario for layout estimation and would have an impact on applications of Scene Modeling, Robotics, and Augmented Reality.
The $N$-stars network evolution model

A new network evolution model is introduced in this paper. The model is based on co-operations of $N$ units. The units are the nodes of the network and the co-operations are indicated by directed links. At each evolution step $N$ units co-operate which formally means that they form a directed $N$-star subgraph. At each step either a new unit joins to the network and it co-operates with $N-1$ old units or $N$ old units co-operate. During the evolution both preferential attachment and uniform choice are applied. Asymptotic power law distributions are obtained both for the in-degrees and the out-degrees.
Revision in Continuous Space: Fine-Grained Control of Text Style Transfer

Typical methods for unsupervised text style transfer often rely on two key ingredients: 1) seeking for the disentanglement of the content and the attributes, and 2) troublesome adversarial learning. In this paper, we show that neither of these components is indispensable. We propose a new framework without them and instead consists of three key components: a variational auto-encoder (VAE), some attribute predictors (one for each attribute), and a content predictor. The VAE and the two types of predictors enable us to perform gradient-based optimization in the continuous space, which is mapped from sentences in a discrete space, to find the representation of a target sentence with the desired attributes and preserved content. Moreover, the proposed method can, for the first time, simultaneously manipulate multiple fine-grained attributes, such as sentence length and the presence of specific words, in synergy when performing text style transfer tasks. Extensive experimental studies on three popular text style transfer tasks show that the proposed method significantly outperforms five state-of-the-art methods.2
Understanding Perceptions and Attitudes in Breast Cancer Discussions on Twitter

Among American women, the rate of breast cancer is only second to lung cancer. An estimated 12.4% women will develop breast cancer over the course of their lifetime. The widespread use of social media across the socio-economic spectrum offers unparalleled ways to facilitate information sharing, in particular as it pertains to health. Social media is also used by many healthcare stakeholders, ranging from government agencies to healthcare industry, to disseminate health information and to engage patients. The purpose of this study is to investigate people's perceptions and attitudes related to breast cancer, especially those that are related to physical activities, on Twitter. To achieve this, we first identified and collected tweets related to breast cancer; and then used topic modeling and sentiment analysis techniques to understand discussion themes and quantify Twitter users' perceptions and emotions with respect tobreast cancer to answer 5 research questions.
Deep Learning for Bug-Localization in Student Programs

Providing feedback is an integral part of teaching. Most open online courses on programming make use of automated grading systems to support programming assignments and give real-time feedback. These systems usually rely on test results to quantify the programs' functional correctness. They return failing tests to the students as feedback. However, students may find it difficult to debug their programs if they receive no hints about where the bug is and how to fix it. In this work, we present the first deep learning based technique that can localize bugs in a faulty program w.r. t. a failing test, without even running the program. At the heart of our technique is a novel tree convolutional neural network which is trained to predict whether a program passes or fails a given test. To localize the bugs, we analyze the trained network using a state-of-the-art neural prediction attribution technique and see which lines of the programs make it predict the test outcomes. Our experiments show that the proposed technique is generally more accurate than two state-of-the-art program-spectrum based and one syntactic difference based bug-localization baselines.
Hijacking Malaria Simulators with Probabilistic Programming

Epidemiology simulations have become a fundamental tool in the fight against the epidemics of various infectious diseases like AIDS and malaria. However, the complicated and stochastic nature of these simulators can mean their output is difficult to interpret, which reduces their usefulness to policymakers. In this paper, we introduce an approach that allows one to treat a large class of population-based epidemiology simulators as probabilistic generative models. This is achieved by hijacking the internal random number generator calls, through the use of a universal probabilistic programming system (PPS). In contrast to other methods, our approach can be easily retrofitted to simulators written in popular industrial programming frameworks. We demonstrate that our method can be used for interpretable introspection and inference, thus shedding light on black-box simulators. This reinstates much-needed trust between policymakers and evidence-based methods.
Targeted Attacks on Deep Reinforcement Learning Agents through Adversarial Observations

This paper deals with adversarial attacks on perceptions of neural network policies in the Reinforcement Learning (RL) context. While previous approaches perform untargeted attacks on the state of the agent, we propose a method to perform targeted attacks to lure an agent into consistently following a desired policy. We place ourselves in a realistic setting, where attacks are performed on observations of the environment rather than the internal state of the agent and develop constant attacks instead of per-observation ones. We illustrate our method by attacking deep RL agents playing Atari games and show that universal additive masks can be applied not only to degrade performance but to take control of an agent.
Bayesian Inference for Polya Inverse Gamma Models.

Probability density functions that include the gamma function are widely used in statistics and machine learning. The normalizing constants of gamma, inverse gamma, beta, and Dirichlet distributions all include model parameters as arguments in the gamma function; however, the gamma function does not naturally admit a conjugate prior distribution in a Bayesian analysis, and statistical inference of these parameters is a significant challenge. In this paper, we construct the Polya-inverse Gamma (P-IG) distribution as an infinite convolution of Generalized inverse Gaussian (GIG) distributions, and we represent the reciprocal gamma function as a scale mixture of normal distributions. As a result, the P-IG distribution yields an efficient data augmentation strategy for fully Bayesian inference on model parameters in gamma, inverse gamma, beta, and Dirichlet distributions. To illustrate the applied utility of our data augmentation strategy, we infer the proportion of overdose deaths in the United States attributed to different opioid and prescription drugs with a Dirichlet allocation model.
A I ] 2 8 M ay 2 01 9 Guarantees for Sound Abstractions for Generalized Planning ( Extended Paper )

Generalized planning is about finding plans that solve collections of planning instances, often infinite collections, rather than single instances. Recently it has been shown how to reduce the planning problem for generalized planning to the planning problem for a qualitative numerical problem; the latter being a reformulation that simultaneously captures all the instances in the collection. An important thread of research thus consists in finding such reformulations, or abstractions, automatically. A recent proposal learns the abstractions inductively from a finite and small sample of transitions from instances in the collection. However, as in all inductive processes, the learned abstraction is not guaranteed to be correct for the whole collection. In this work we address this limitation by performing an analysis of the abstraction with respect to the collection, and show how to obtain formal guarantees for generalization. These guarantees, in the form of first-order formulas, may be used to 1) define subcollections of instances on which the abstraction is guaranteed to be sound, 2) obtain necessary conditions for generalization under certain assumptions, and 3) do automated synthesis of complex invariants for planning problems. Our framework is general, it can be extended or combined with other approaches, and it has applications that go beyond generalized planning.
Segmentation of blood vessels in retinal fundus images

In recent years, several automatic segmentation methods have been proposed for blood vessels in retinal fundus images, ranging from using cheap and fast trainable filters to complicated neural networks and even deep learning. One example of a filted-based segmentation method is B-COSFIRE. In this approach the image filter is trained with example prototype patterns, to which the filter becomes selective by finding points in a Difference of Gaussian response on circles around the center with large intensity variation. In this paper we discuss and evaluate several of these vessel segmentation methods. We take a closer look at B-COSFIRE and study the performance of B-COSFIRE on the recently published IOSTAR dataset by experiments and we examine how the parameter values affect the performance. In the experiment we manage to reach a segmentation accuracy of 0.9419. Based on our findings we discuss when B-COSFIRE is the preferred method to use and in which circumstances it could be beneficial to use a more (computationally) complex segmentation method. We also shortly discuss areas beyond blood vessel segmentation where these methods can be used to segment elongated structures, such as rivers in satellite images or nerves of a leaf.
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.

A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N. ; Feller, S. E. ; Pastor, R. W. ; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than that of the overall rotational diffusion of ubiquitin and whose effects would not be apparent in experimentally derived order parameters. A coupled analysis of internal and overall motion yields simulated order parameters substantially closer to the experimentally determined values than is the case for a conventional analysis of internal motion alone. Improved agreement between simulation and experiment also is encouraging from the viewpoint of assessing the accuracy of long MD simulations.
An Effective Multiresolution Hierarchical Granular Representation Based Classifier Using General Fuzzy Min-Max Neural Network

Motivated by the practical demands for simplification of data toward being consistent with human thinking and problem-solving, as well as tolerance of uncertainty, information granules are becoming important entities in data processing at different levels of data abstraction. This article proposes a method to construct classifiers from multiresolution hierarchical granular representations using hyperbox fuzzy sets. The proposed approach forms a series of granular inferences hierarchically through many levels of abstraction. An attractive characteristic of our classifier is that it can maintain a high accuracy in comparison to other fuzzy min-max models at a low degree of granularity based on reusing the knowledge learned from lower levels of abstraction. In addition, our approach can reduce the data size significantly as well as handle the uncertainty and incompleteness associated with data in real-world applications. The construction process of the classifier consists of two phases. The first phase is to formulate the model at the greatest level of granularity, while the later stage aims to reduce the complexity of the constructed model and deduce it from data at higher abstraction levels. Experimental analyses conducted comprehensively on both synthetic and real datasets indicated the efficiency of our method in terms of training time and predictive performance in comparison to other types of fuzzy min-max neural networks and common machine learning algorithms.
ATTACK2VEC: Leveraging Temporal Word Embeddings to Understand the Evolution of Cyberattacks

Despite the fact that cyberattacks are constantly growing in complexity, the research community still lacks effective tools to easily monitor and understand them. In particular, there is a need for techniques that are able to not only track how prominently certain malicious actions, such as the exploitation of specific vulnerabilities, are exploited in the wild, but also (and more importantly) how these malicious actions factor in as attack steps in more complex cyberattacks. In this paper we present ATTACK2VEC, a system that uses temporal word embeddings to model how attack steps are exploited in the wild, and track how they evolve. We test ATTACK2VEC on a dataset of billions of security events collected from the customers of a commercial Intrusion Prevention System over a period of two years, and show that our approach is effective in monitoring the emergence of new attack strategies in the wild and in flagging which attack steps are often used together by attackers (e.g., vulnerabilities that are frequently exploited together). ATTACK2VEC provides a useful tool for researchers and practitioners to better understand cyberattacks and their evolution, and use this knowledge to improve situational awareness and develop proactive defenses.
Spin-orbit coupling affecting the evolution of transverse spin

We investigate the evolution of transverse spin in tightly focused circularly polarized beams of light, where spin-orbit coupling causes a local rotation of the polarization ellipses upon propagation through the focal volume. The effect can be explained as a relative Gouy-phase shift between the circularly polarized transverse field and the longitudinal field carrying orbital angular momentum. The corresponding rotation of the electric transverse spin density is observed experimentally by utilizing a recently developed reconstruction scheme, which relies on transverse-spin-dependent directional scattering of a nano-probe.
Smooth Shells: Multi-Scale Shape Registration With Functional Maps

We propose a novel 3D shape correspondence method based on the iterative alignment of so-called smooth shells. Smooth shells define a series of coarse-to-fine shape approximations designed to work well with multiscale algorithms. The main idea is to first align rough approximations of the geometry and then add more and more details to refine the correspondence. We fuse classical shape registration with Functional Maps by embedding the input shapes into an intrinsic-extrinsic product space. Moreover, we disambiguate intrinsic symmetries by applying a surrogate based Markov chain Monte Carlo initialization. Our method naturally handles various types of noise that commonly occur in real scans, like non-isometry or incompatible meshing. Finally, we demonstrate state-of-the-art quantitative results on several datasets and show that our pipeline produces smoother, more realistic results than other automatic matching methods in real world applications.
CURIOUS: Intrinsically Motivated Modular Multi-Goal Reinforcement Learning

In open-ended environments, autonomous learning agents must set their own goals and build their own curriculum through an intrinsically motivated exploration. They may consider a large diversity of goals, aiming to discover what is controllable in their environments, and what is not. Because some goals might prove easy and some impossible, agents must actively select which goal to practice at any moment, to maximize their overall mastery on the set of learnable goals. This paper proposes CURIOUS, an algorithm that leverages 1) a modular Universal Value Function Approximator with hindsight learning to achieve a diversity of goals of different kinds within a unique policy and 2) an automated curriculum learning mechanism that biases the attention of the agent towards goals maximizing the absolute learning progress. Agents focus sequentially on goals of increasing complexity, and focus back on goals that are being forgotten. Experiments conducted in a new modular-goal robotic environment show the resulting developmental self-organization of a learning curriculum, and demonstrate properties of robustness to distracting goals, forgetting and changes in body properties.
Transferable and extensible machine learning derived atomic charges for modeling metal-organic frameworks

In most cases, calculations of properties of metal-organic frameworks (MOFs) based on classical force fields (FFs) are the most suitable in terms of the ratio between accuracy and computational cost, especially in efforts to screen a large number of structures. Such calculations require an initial partial charge assignment to describe the Coulomb contribution. In this study, we would like to present a machine-learning algorithm for MOF partial charge prediction and its verification on experimental data using the FF approach. Proposed ML method offers the accuracy of reference DFT calculations at a fraction of the computational cost with linear scalability.
Pharmacokinetics and metabolism of the dipeptidyl peptidase IV inhibitor carmegliptin in rats, dogs, and monkeys

The pharmacokinetics and excretion of carmegliptin, a novel dipeptidyl peptidase IV inhibitor, were examined in rats, dogs, and cynomolgus monkeys. Carmegliptin exhibited a moderate clearance, extensive tissue distribution, and a variable oral bioavailability of 28–174%. Due to saturation of intestinal active secretion, the area under the plasma concentration–time curve (AUC) in dogs and monkeys increased in a more than dose-proportional manner over an oral dose range of 2.5–10 mg/kg. Following oral administration of [14C]carmegliptin at 3 mg/kg, > 94% of the radioactive dose was recovered in 72-h post-dose from Wistar rats and Beagle dogs. Virtually, the entire administered radioactive dose was excreted unchanged in urine, intestinal lumen, and bile. Approximately 36%, 29%, and 19% of the dose were excreted by respective routes. Consistently, in vitro, carmegliptin was highly resistant to hepatic metabolism in all species tested. Based on in vitro studies, carmegliptin is a good substrate for Mdr1/MDR1. Breast cancer resistance protein (Bcrp) is not expected to be involved in the transport of carmegliptin since in vitro carmegliptin was not significantly transported by this transporter. The very high extravascular distribution of carmegliptin in the intestinal tissues, as demonstrated in Wistar rats and Beagle dogs, could play a significant role in its therapeutic effect.