nils-herrmann/clean_scirepeval huggingface dataset:
Families of Supermanifolds: Splitting Types and Obstruction Maps.

In this article we study the notion of supermanifolds families, starting from Green's general classification of supermanifolds. The topics studied divide this article into two distinct parts, labelled I and II respectively. Part I concerns the splitting type of a supermanifold and our attempt to construct variations thereof. In Part II we look at a particular class of families, referred to as `$gtm$-families'. We are concerned with the notion of a `secondary obstruction theory', which is apparent in any $gtm$-family of supermanifolds over a (connected and Stein) non-reduced, superspace base.
Generative Model-Based Ischemic Stroke Lesion Segmentation

CT perfusion (CTP) has been used to triage ischemic stroke patients in the early stage, because of its speed, availability, and lack of contraindications. Perfusion parameters including cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time (MTT) and time of peak (Tmax) could also be computed from CTP data. However, CTP data or the perfusion parameters, are ambiguous to locate the infarct core or tissue at risk (penumbra), which is normally confirmed by the follow-up Diffusion Weighted Imaging (DWI) or perfusion diffusion mismatch. In this paper, we propose a novel generative modelbased segmentation framework composed of an extractor, a generator and a segmentor for ischemic stroke lesion segmentation. First, an extractor is used to directly extract the representative feature images from the CTP feature images. Second, a generator is used to generate the clinical relevant DWI images using the output from the extractor and perfusion parameters. Finally, the segmentor is used to precisely segment the ischemic stroke lesion using the generated DWI from the generator. Meanwhile, a novel pixel-region loss function, generalized dice combined with weighted cross entropy, is used to handle data unbalance problem which is commonly encountered in medical image segmentation. All networks are trained end-to-end from scratch using the 2018 Ischemic Stroke Lesion Segmentation Challenge (ISLES) dataset and our method won the first place in the 2018 ischemic stroke lesions segmentation challenge in the test stage.
Query-efficient Meta Attack to Deep Neural Networks

Black-box attack methods aim to infer suitable attack patterns to targeted DNN models by only using output feedback of the models and the corresponding input queries. However, due to lack of prior and inefficiency in leveraging the query and feedback information, existing methods are mostly query-intensive for obtaining effective attack patterns. In this work, we propose a meta attack approach that is capable of attacking a targeted model with much fewer queries. Its high queryefficiency stems from effective utilization of meta learning approaches in learning generalizable prior abstraction from the previously observed attack patterns and exploiting such prior to help infer attack patterns from only a few queries and outputs. Extensive experiments on MNIST, CIFAR10 and tiny-Imagenet demonstrate that our meta-attack method can remarkably reduce the number of model queries without sacrificing the attack performance. Besides, the obtained meta attacker is not restricted to a particular model but can be used easily with a fast adaptive ability to attack a variety of models.The code of our work is available at this https URL.
SparseSense: Human Activity Recognition from Highly Sparse Sensor Data-streams Using Set-based Neural Networks

Batteryless or so called passive wearables are providing new and innovative methods for human activity recognition (HAR), especially in healthcare applications for older people. Passive sensors are low cost, lightweight, unobtrusive and desirably disposable; attractive attributes for healthcare applications in hospitals and nursing homes. Despite the compelling propositions for sensing applications, the data streams from these sensors are characterised by high sparsity---the time intervals between sensor readings are irregular while the number of readings per unit time are often limited. In this paper, we rigorously explore the problem of learning activity recognition models from temporally sparse data. We describe how to learn directly from sparse data using a deep learning paradigm in an end-to-end manner. We demonstrate significant classification performance improvements on real-world passive sensor datasets from older people over the state-of-the-art deep learning human activity recognition models. Further, we provide insights into the model's behaviour through complementary experiments on a benchmark dataset and visualisation of the learned activity feature spaces.
Ease-of-Teaching and Language Structure from Emergent Communication

Artificial agents have been shown to learn to communicate when needed to complete a cooperative task. Some level of language structure (e.g., compositionality) has been found in the learned communication protocols. This observed structure is often the result of specific environmental pressures during training. By introducing new agents periodically to replace old ones, sequentially and within a population, we explore such a new pressure -- ease of teaching -- and show its impact on the structure of the resulting language.
Indirect interactions influence contact network structure and diffusion dynamics

Interaction patterns at the individual level influence the behaviour of diffusion over contact networks. Most of the current diffusion models only consider direct interactions, capable of transferring infectious items among individuals, to build transmission networks of diffusion. However, delayed indirect interactions, where a susceptible individual interacts with infectious items after the infected individual has left the interaction space, can also cause transmission events. We define a diffusion model called the same place different time transmission (SPDT)-based diffusion that considers transmission links for these indirect interactions. Our SPDT model changes the network dynamics where the connectivity among individuals varies with the decay rates of link infectivity. We investigate SPDT diffusion behaviours by simulating airborne disease spreading on data-driven contact networks. The SPDT model significantly increases diffusion dynamics with a high rate of disease transmission. By making the underlying connectivity denser and stronger due to the inclusion of indirect transmissions, SPDT models are more realistic than same place same time transmission (SPST)-based models for the study of various airborne disease outbreaks. Importantly, we also find that the diffusion dynamics including indirect links are not reproducible by the current SPST models based on direct links, even if both SPDT and SPST networks assume the same underlying connectivity. This is because the transmission dynamics of indirect links are different from those of direct links. These outcomes highlight the importance of the indirect links for predicting outbreaks of airborne diseases.
The Effects of Finite Distance on the Gravitational Deflection Angle of Light

In order to clarify the effects of the finite distance from a lens object to a light source and a receiver, the gravitational deflection of light has been recently reexamined by using the Gauss–Bonnet (GB) theorem in differential geometry (Ishihara et al. 2016). The purpose of the present paper is to give a short review of a series of works initiated by the above paper. First, we provide the definition of the gravitational deflection angle of light for the finite-distance source and receiver in a static, spherically symmetric and asymptotically flat spacetime. We discuss the geometrical invariance of the definition by using the GB theorem. The present definition is used to discuss finite-distance effects on the light deflection in Schwarzschild spacetime for both the cases of weak deflection and strong deflection. Next, we extend the definition to stationary and axisymmetric spacetimes. We compute finite-distance effects on the deflection angle of light for Kerr black holes and rotating Teo wormholes. Our results are consistent with the previous works if we take the infinite-distance limit. We briefly mention also the finite-distance effects on the light deflection by Sagittarius A * .
Handling Inter-Annotator Agreement for Automated Skin Lesion Segmentation

In this work, we explore the issue of the inter-annotator agreement for training and evaluating automated segmentation of skin lesions. We explore what different degrees of agreement represent, and how they affect different use cases for segmentation. We also evaluate how conditioning the ground truths using different (but very simple) algorithms may help to enhance agreement and may be appropriate for some use cases. The segmentation of skin lesions is a cornerstone task for automated skin lesion analysis, useful both as an end-result to locate/detect the lesions and as an ancillary task for lesion classification. Lesion segmentation, however, is a very challenging task, due not only to the challenge of image segmentation itself but also to the difficulty in obtaining properly annotated data. Detecting accurately the borders of lesions is challenging even for trained humans, since, for many lesions, those borders are fuzzy and ill-defined. Using lesions and annotations from the ISIC Archive, we estimate inter-annotator agreement for skin-lesion segmentation and propose several simple procedures that may help to improve inter-annotator agreement if used to condition the ground truths.
Sparse Parallel Training for Hierarchical Dirichlet Process Topic Models

Nonparametric extensions of topic models such as Latent Dirichlet Allocation, including Hierarchical Dirichlet Process (HDP), are often studied in natural language processing. Training these models generally requires use of serial algorithms, which limits scalability to large data sets and complicates acceleration via use of parallel and distributed systems. Most current approaches to scalable training of such models either don't converge to the correct target, or are not data-parallel. Moreover, these approaches generally do not utilize all available sources of sparsity found in natural language - an important way to make computation efficient. Based upon a representation of certain conditional distributions within an HDP, we propose a doubly sparse data-parallel sampler for the HDP topic model that addresses these issues. We benchmark our method on a well-known corpora (PubMed) with 8m documents and 768m tokens, using a single multi-core machine in under three days.
OnionNet: a Multiple-Layer Intermolecular-Contact-Based Convolutional Neural Network for Protein–Ligand Binding Affinity Prediction

Computational drug discovery provides an efficient tool for helping large-scale lead molecule screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities toward a target, a protein in general. The accuracies of current scoring functions that are used to predict the binding affinity are not satisfactory enough. Thus, machine learning or deep learning based methods have been developed recently to improve the scoring functions. In this study, a deep convolutional neural network model (called OnionNet) is introduced; its features are based on rotation-free element-pair-specific contacts between ligands and protein atoms, and the contacts are further grouped into different distance ranges to cover both the local and nonlocal interaction information between the ligand and the protein. The prediction power of the model is evaluated and compared with other scoring functions using the comparative assessment of scoring functions (CASF-2013) benchmark and the v2016 core set of the PDBbind database. The robustness of the model is further explored by predicting the binding affinities of the complexes generated from docking simulations instead of experimentally determined PDB structures.
Extreme Points Derived Confidence Map as a Cue For Class-Agnostic Segmentation Using Deep Neural Network

To automate the process of segmenting an anatomy of interest, we can learn a model from previously annotated data. The learning-based approach uses annotations to train a model that tries to emulate the expert labeling on a new data set. While tremendous progress has been made using such approaches, labeling of medical images remains a time-consuming and expensive task. In this paper, we evaluate the utility of extreme points in learning to segment. Specifically, we propose a novel approach to compute a confidence map from extreme points that quantitatively encodes the priors derived from extreme points. We use the confidence map as a cue to train a deep neural network based on ResNet-101 and PSP module to develop a class-agnostic segmentation model that outperforms state-of-the-art method that employs extreme points as a cue. Further, we evaluate a realistic use-case by using our model to generate training data for supervised learning (U-Net) and observed that U-Net performs comparably when trained with either the generated data or the ground truth data. These findings suggest that models trained using cues can be used to generate reliable training data.
On $3$-dimensional foliated dynamical systems and Hilbert type reciprocity law

We show some fundamental results concerning $3$-dimensional foliated dynamical systems (FDS$^3$ for short) introduced by Deninger. Firstly, we give a decomposition theorem for an FDS$^3$, which yields a classification of FDS$^3$'s. Secondly, for each type of the classification, we construct concrete examples of FDS$^3$'s. Finally, by using the integration theory for smooth Deligne cohomology, we introduce geometric analogues of local symbols and show a Hilbert type reciprocity law for an FDS$^3$. Our results answer the question posed by Deninger.
Uncertainty-guided Continual Learning with Bayesian Neural Networks

Continual learning aims to learn new tasks without forgetting previously learned ones. This is especially challenging when one cannot access data from previous tasks and when the model has a fixed capacity. Current regularization-based continual learning algorithms need an external representation and extra computation to measure the parameters' \textit{importance}. In contrast, we propose Uncertainty-guided Continual Bayesian Neural Networks (UCB), where the learning rate adapts according to the uncertainty defined in the probability distribution of the weights in networks. Uncertainty is a natural way to identify \textit{what to remember} and \textit{what to change} as we continually learn, and thus mitigate catastrophic forgetting. We also show a variant of our model, which uses uncertainty for weight pruning and retains task performance after pruning by saving binary masks per tasks. We evaluate our UCB approach extensively on diverse object classification datasets with short and long sequences of tasks and report superior or on-par performance compared to existing approaches. Additionally, we show that our model does not necessarily need task information at test time, i.e. it does not presume knowledge of which task a sample belongs to.
One-shot Information Extraction from Document Images using Neuro-Deductive Program Synthesis

Our interest in this paper is in meeting a rapidly growing industrial demand for information extraction from images of documents such as invoices, bills, receipts etc. In practice users are able to provide a very small number of example images labeled with the information that needs to be extracted. We adopt a novel two-level neuro-deductive, approach where (a) we use pre-trained deep neural networks to populate a relational database with facts about each document-image; and (b) we use a form of deductive reasoning, related to meta-interpretive learning of transition systems to learn extraction programs: Given task-specific transitions defined using the entities and relations identified by the neural detectors and a small number of instances (usually 1, sometimes 2) of images and the desired outputs, a resource-bounded meta-interpreter constructs proofs for the instance(s) via logical deduction; a set of logic programs that extract each desired entity is easily synthesized from such proofs. In most cases a single training example together with a noisy-clone of itself suffices to learn a program-set that generalizes well on test documents, at which time the value of each entity is determined by a majority vote across its program-set. We demonstrate our two-level neuro-deductive approach on publicly available datasets ("Patent" and "Doctor's Bills") and also describe its use in a real-life industrial problem.
Amortized Inference of Variational Bounds for Learning Noisy-OR

Classical approaches for approximate inference depend on cleverly designed variational distributions and bounds. Modern approaches employ amortized variational inference, which uses a neural network to approximate any posterior without leveraging the structures of the generative models. In this paper, we propose Amortized Conjugate Posterior (ACP), a hybrid approach taking advantages of both types of approaches. Specifically, we use the classical methods to derive specific forms of posterior distributions and then learn the variational parameters using amortized inference. We study the effectiveness of the proposed approach on the noisy-or model and compare to both the classical and the modern approaches for approximate inference and parameter learning. Our results show that the proposed method outperforms or are at par with other approaches.
Shift-of-Perspective Identification within Legal Cases

Arguments, counter-arguments, facts, and evidence obtained via documents related to previous court cases are of essential need for legal professionals. Therefore, the process of automatic information extraction from documents containing legal opinions related to court cases can be considered to be of significant importance. This study is focused on the identification of sentences in legal opinion texts which convey different perspectives on a certain topic or entity. We combined several approaches based on semantic analysis, open information extraction, and sentiment analysis to achieve our objective. Then, our methodology was evaluated with the help of human judges. The outcomes of the evaluation demonstrate that our system is successful in detecting situations where two sentences deliver different opinions on the same topic or entity. The proposed methodology can be used to facilitate other information extraction tasks related to the legal domain. One such task is the automated detection of counter arguments for a given argument. Another is the identification of opponent parties in a court case.
Quantum strips in higher dimensions

We consider the Dirichlet Laplacian in unbounded strips on ruled surfaces in any space dimension. We locate the essential spectrum under the condition that the strip is asymptotically flat. If the Gauss curvature of the strip equals zero, we establish the existence of discrete spectrum under the condition that the curve along which the strip is built is not a geodesic. On the other hand, if it is a geodesic and the Gauss curvature is not identically equal to zero, we prove the existence of Hardy-type inequalities. We also derive an effective operator for thin strips, which enables one to replace the spectral problem for the Laplace-Beltrami operator on the two-dimensional surface by a one-dimensional Schroedinger operator whose potential is expressed in terms of curvatures. 
In the appendix, we establish a purely geometric fact about the existence of relatively parallel adapted frames for any curve under minimal regularity hypotheses.
Validating fast-ion wall-load IR analysis-methods against W7-X NBI empty-torus experiment

The first neutral beam injection (NBI) experiments in Wendelstein 7-X (W7-X) stellarator were conducted in the summer of 2018. The NBI system is used to heat the magnetically confined plasma by neutralising an accelerated hydrogen ion beam and directing it into the plasma, where the resulting energetic ions release their energy to heat the plasma. The modelling of the NBI fast ion experiments has commenced, including estimation of the shine-through and the orbit-losses. The stellarator has a wide-angle infra red (IR) imaging system to monitor the machine plasma facing component surface temperatures. This work validates the NBI model “Beamlet Based NBI (BBNBI)” and the newly written synthetic IR camera model. The validation is accomplished by comparing the measured and the synthetic IR camera measurements of an experiment where the NBI was injected into the vacuum vessel without a plasma. A good qualitative and quantitative match was found. This agreement is further supported by spectroscopic and calibration measurements of the NBI and and IR camera systems.
Complete Dictionary Learning via 𝓁4-Norm Maximization over the Orthogonal Group

This paper considers the fundamental problem of learning a complete (orthogonal) dictionary from samples of sparsely generated signals. Most existing methods solve the dictionary (and sparse representations) based on heuristic algorithms, usually without theoretical guarantees for either optimality or complexity. The recent $\ell^1$-minimization based methods do provide such guarantees but the associated algorithms recover the dictionary one column at a time. In this work, we propose a new formulation that maximizes the $\ell^4$-norm over the orthogonal group, to learn the entire dictionary. We prove that under a random data model, with nearly minimum sample complexity, the global optima of the $\ell^4$ norm are very close to signed permutations of the ground truth. Inspired by this observation, we give a conceptually simple and yet effective algorithm based on `matching, stretching, and projection' (MSP). The algorithm provably converges locally at a superlinear (cubic) rate and cost per iteration is merely an SVD. In addition to strong theoretical guarantees, experiments show that the new algorithm is significantly more efficient and effective than existing methods, including KSVD and $\ell^1$-based methods. Preliminary experimental results on real images clearly demonstrate advantages of so learned dictionary over classic PCA bases.
Primal-Dual Block Frank-Wolfe

We propose a variant of the Frank-Wolfe algorithm for solving a class of sparse/low-rank optimization problems. Our formulation includes Elastic Net, regularized SVMs and phase retrieval as special cases. The proposed Primal-Dual Block Frank-Wolfe algorithm reduces the per-iteration cost while maintaining linear convergence rate. The per iteration cost of our method depends on the structural complexity of the solution (i.e. sparsity/low-rank) instead of the ambient dimension. We empirically show that our algorithm outperforms the state-of-the-art methods on (multi-class) classification tasks.
Should Adversarial Attacks Use Pixel p-Norm?

Adversarial attacks aim to confound machine learning systems, while remaining virtually imperceptible to humans. Attacks on image classification systems are typically gauged in terms of $p$-norm distortions in the pixel feature space. We perform a behavioral study, demonstrating that the pixel $p$-norm for any $0\le p \le \infty$, and several alternative measures including earth mover's distance, structural similarity index, and deep net embedding, do not fit human perception. Our result has the potential to improve the understanding of adversarial attack and defense strategies.