nils-herrmann/clean_scirepeval huggingface dataset:
Boosting the Rule-Out Accuracy of Deep Disease Detection Using Class Weight Modifiers

In many screening applications, the primary goal of a radiologist or assisting artificial intelligence is to rule out certain findings. The classifiers built for such applications are often trained on large datasets that derive labels from clinical notes written for patients. While the quality of the positive findings described in these notes is often reliable, lack of the mention of a finding does not always rule out the presence of it. This happens because radiologists comment on the patient in the context of the exam, for example focusing on trauma as opposed to chronic disease at emergency rooms. However, this disease finding ambiguity can affect the performance of algorithms. Hence it is critical to model the ambiguity during training. We propose a scheme to apply reasonable class weight modifiers to our loss function for the no mention cases during training. We experiment with two different deep neural network architectures and show that the proposed method results in a large improvement in the performance of the classifiers, specially on negated findings. The baseline performance of a custom-made dilated block network proposed in this paper shows an improvement in comparison with baseline DenseNet-201, while both architectures benefit from the new proposed loss function weighting scheme. Over 200,000 chest X-ray images and three highly common diseases, along with their negated counterparts, are included in this study.
Unsupervised Ensemble Classification with Dependent Data

Ensemble learning, the machine learning paradigm where multiple algorithms are combined, has exhibited promising perfomance in a variety of tasks. The present work focuses on unsupervised ensemble classification. The term unsupervised refers to the ensemble combiner who has no knowledge of the ground-truth labels that each classifier has been trained on. While most prior works on unsupervised ensemble classification are designed for independent and identically distributed (i.i.d.) data, the present work introduces an unsupervised scheme for learning from ensembles of classifiers in the presence of data dependencies. Two types of data dependencies are considered: sequential data and networked data whose dependencies are captured by a graph. Moment matching and Expectation Maximization algorithms are developed for the aforementioned cases, and their performance is evaluated on synthetic and real datasets.
Collective Mobile Sequential Recommendation: A Recommender System for Multiple Taxicabs

Mobile sequential recommendation was originally designed to find a promising route for a single taxicab. Directly applying it for multiple taxicabs may cause an excessive overlap of recommended routes. The multi-taxicab recommendation problem is challenging and has been less studied. In this paper, we first formalize a collective mobile sequential recommendation problem based on a classic mathematical model, which characterizes time-varying influence among competing taxicabs. Next, we propose a new evaluation metric for a collection of taxicab routes aimed to minimize the sum of potential travel time. We then develop an efficient algorithm to calculate the metric and design a greedy recommendation method to approximate the solution. Finally, numerical experiments show the superiority of our methods. In trace-driven simulation, the set of routes recommended by our method significantly outperforms those obtained by conventional methods.
A Halo Merger Tree Generation and Evaluation Framework

Semi-analytic models are best suited to compare galaxy formation and evolution theories with observations. These models rely heavily on halo merger trees, and their realistic features (i.e., no drastic changes on halo mass or jumps on physical locations). Our aim is to provide a new framework for halo merger tree generation that takes advantage of the results of large volume simulations, with a modest computational cost. We treat halo merger tree construction as a matrix generation problem, and propose a Generative Adversarial Network that learns to generate realistic halo merger trees. We evaluate our proposal on merger trees from the EAGLE simulation suite, and show the quality of the generated trees.
A Bandit Approach to Posterior Dialog Orchestration Under a Budget

Building multi-domain AI agents is a challenging task and an open problem in the area of AI. Within the domain of dialog, the ability to orchestrate multiple independently trained dialog agents, or skills, to create a unified system is of particular significance. In this work, we study the task of online posterior dialog orchestration, where we define posterior orchestration as the task of selecting a subset of skills which most appropriately answer a user input using features extracted from both the user input and the individual skills. To account for the various costs associated with extracting skill features, we consider online posterior orchestration under a skill execution budget. We formalize this setting as Context Attentive Bandit with Observations (CABO), a variant of context attentive bandits, and evaluate it on simulated non-conversational and proprietary conversational datasets.
Models of Continuous-Time Networks with Tie Decay, Diffusion, and Convection

The study of temporal networks in discrete time has yielded numerous insights into time-dependent networked systems in a wide variety of applications. However, for many complex systems, it is useful to develop continuous-time models of networks and to compare them to associated discrete models. In this paper, we study several continuous-time network models and examine discrete approximations of them both numerically and analytically. To consider continuous-time networks, we associate each edge in a graph with a time-dependent tie strength that can take continuous non-negative values and decays in time after the most recent interaction. We investigate how the moments of the tie strength evolve with time in several models, and we explore-both numerically and analytically-criteria for the emergence of a giant connected component in some of these models. We also briefly examine the effects of the interaction patterns of continuous-time networks on the contagion dynamics of a susceptible-infected-recovered model of an infectious disease.
Learning Set-equivariant Functions with SWARM Mappings

In this work we propose a new neural network architecture that efficiently implements and learns general purpose set-equivariant functions. Such a function $f$ maps a set of entities $x=\left\{ x_{1},\ldots,x_{n}\right\} $ from one domain to a set of same cardinality $y=f\left(x\right)=\left\{ y_{1},\ldots,y_{n}\right\} $ in another domain regardless of the ordering of the entities. The architecture is based on a gated recurrent network which is iteratively applied to all entities individually and at the same time syncs with the progression of the whole population. In reminiscence to this pattern, which can be frequently observable in nature, we call our approach SWARM mapping. Set-equivariant and generally permutation invariant functions are important building blocks for many state of the art machine learning approaches. Even in application where the permutation invariance is not of primary interest, as to be seen in the recent success of attention based transformer models (Vaswani et. al. 2017). Accordingly, we demonstrate the power and usefulness of SWARM mappings in different applications. We compare the performance of our approach with another recently proposed set-equivariant function, the SetTransformer (Lee this http URL. 2018) and we demonstrate that transformer solely based on SWARM layers gives state of the art results.
RLTM: An Efficient Neural IR Framework for Long Documents

Deep neural networks have achieved significant improvements in information retrieval (IR). However, most existing models are computational costly and can not efficiently scale to long documents. This paper proposes a novel End-to-End neural ranking framework called Reinforced Long Text Matching (RLTM) which matches a query with long documents efficiently and effectively. The core idea behind the framework can be analogous to the human judgment process which firstly locates the relevance parts quickly from the whole document and then matches these parts with the query carefully to obtain the final label. Firstly, we select relevant sentences from the long documents by a coarse and efficient matching model. Secondly, we generate a relevance score by a more sophisticated matching model based on the sentence selected. The whole model is trained jointly with reinforcement learning in a pairwise manner by maximizing the expected score gaps between positive and negative examples. Experimental results demonstrate that RLTM has greatly improved the efficiency and effectiveness of the states-of-the-art models.
Multichannel scattering theory for Toeplitz operators with piecewise continuous symbols

Self-adjoint Toeplitz operators have purely absolutely continuous spectrum. For Toeplitz operators $T$ with piecewise continuous symbols, we suggest a further spectral classification determined by propagation properties of the operator $T$, that is, by the behavior of $\exp(-iTt) f$ for $t\to\pm\infty$. It turns out that the spectrum is naturally partitioned into three disjoint subsets: thick, thin and mixed spectra. On the thick spectrum, the propagation properties are modeled by the continuous part of the symbol, whereas on the thin spectrum, the model operator is determined by the jumps of the symbol. On the mixed spectrum, these two types of the asymptotic evolution of $\exp(-iTt) f$ coexist. This classification is justified in the framework of scattering theory. We prove the existence of wave operators that relate the model operators with the Toeplitz operator $T$. The ranges of these wave operators are pairwise orthogonal, and their orthogonal sum exhausts the whole space, i.e., the set of these wave operators is asymptotically complete.
Link prediction in real-world multiplex networks via layer reconstruction method

Networks are invaluable tools to study real biological, social and technological complex systems in which connected elements form a purposeful phenomenon. A higher resolution image of these systems shows that the connection types do not confine to one but to a variety of types. Multiplex networks encode this complexity with a set of nodes which are connected in different layers via different types of links. A large body of research on link prediction problem is devoted to finding missing links in single-layer (simplex) networks. In recent years, the problem of link prediction in multiplex networks has gained the attention of researchers from different scientific communities. Although most of these studies suggest that prediction performance can be enhanced by using the information contained in different layers of the network, the exact source of this enhancement remains obscure. Here, it is shown that similarity w.r.t. structural features (eigenvectors) is a major source of enhancements for link prediction task in multiplex networks using the proposed layer reconstruction method and experiments on real-world multiplex networks from different disciplines. Moreover, we characterize how low values of similarity w.r.t. structural features result in cases where improving prediction performance is substantially hard.
End-to-End ASR for Code-switched Hindi-English Speech

End-to-end (E2E) models have been explored for large speech corpora and have been found to match or outperform traditional pipeline-based systems in some languages. However, most prior work on end-to-end models use speech corpora exceeding hundreds or thousands of hours. In this study, we explore end-to-end models for code-switched Hindi-English language with less than 50 hours of data. We utilize two specific measures to improve network performance in the low-resource setting, namely multi-task learning (MTL) and balancing the corpus to deal with the inherent class imbalance problem i.e. the skewed frequency distribution over graphemes. We compare the results of the proposed approaches with traditional, cascaded ASR systems. While the lack of data adversely affects the performance of end-to-end models, we see promising improvements with MTL and balancing the corpus.
Alchemy: A Quantum Chemistry Dataset for Benchmarking AI Models

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website \footnote{this https URL}. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.
Semitractability of optimal stopping problems via a weighted stochastic mesh algorithm

In this paper, we propose a Weighted Stochastic Mesh (WSM) algorithm for approximating the value of discrete‐ and continuous‐time optimal stopping problems. In this context, we consider tractability of such problems via a useful notion of semitractability and the introduction of a tractability index for a particular numerical solution algorithm. It is shown that in the discrete‐time case the WSM algorithm leads to semitractability of the corresponding optimal stopping problem in the sense that its complexity is bounded in order by ε−4logd+2(1/ε) with d being the dimension of the underlying Markov chain. Furthermore, we study the WSM approach in the context of continuous‐time optimal stopping problems and derive the corresponding complexity bounds. Although we cannot prove semitractability in this case, our bounds turn out to be the tightest ones among the complexity bounds known in the literature. We illustrate our theoretical findings by a numerical example.
Classifying Types.

The study of homotopy theoretic phenomena in the language of type theory is sometimes loosely called `synthetic homotopy theory'. Homotopy theory in type theory is only one of the many aspects of homotopy type theory, which also includes the study of the set theoretic semantics (models of homotopy type theory and univalence in a meta-theory of sets or categories), type theoretic semantics (internal models of homotopy type theory), and computational semantics, as well as the study of various questions in the internal language of homotopy type theory which are not necessarily motivated by homotopy theory, or questions related to the development of formalized libraries of mathematics based on homotopy type theory. This thesis concerns the development of synthetic homotopy theory.
Fisher and Kernel Fisher Discriminant Analysis: Tutorial

This is a detailed tutorial paper which explains the Fisher discriminant Analysis (FDA) and kernel FDA. We start with projection and reconstruction. Then, one- and multi-dimensional FDA subspaces are covered. Scatters in two- and then multi-classes are explained in FDA. Then, we discuss on the rank of the scatters and the dimensionality of the subspace. A real-life example is also provided for interpreting FDA. Then, possible singularity of the scatter is discussed to introduce robust FDA. PCA and FDA directions are also compared. We also prove that FDA and linear discriminant analysis are equivalent. Fisher forest is also introduced as an ensemble of fisher subspaces useful for handling data with different features and dimensionality. Afterwards, kernel FDA is explained for both one- and multi-dimensional subspaces with both two- and multi-classes. Finally, some simulations are performed on AT&T face dataset to illustrate FDA and compare it with PCA.
Retrieving Sequential Information for Non-Autoregressive Neural Machine Translation

Non-Autoregressive Transformer (NAT) aims to accelerate the Transformer model through discarding the autoregressive mechanism and generating target words independently, which fails to exploit the target sequential information. Over-translation and under-translation errors often occur for the above reason, especially in the long sentence translation scenario. In this paper, we propose two approaches to retrieve the target sequential information for NAT to enhance its translation ability while preserving the fast-decoding property. Firstly, we propose a sequence-level training method based on a novel reinforcement algorithm for NAT (Reinforce-NAT) to reduce the variance and stabilize the training procedure. Secondly, we propose an innovative Transformer decoder named FS-decoder to fuse the target sequential information into the top layer of the decoder. Experimental results on three translation tasks show that the Reinforce-NAT surpasses the baseline NAT system by a significant margin on BLEU without decelerating the decoding speed and the FS-decoder achieves comparable translation performance to the autoregressive Transformer with considerable speedup.
Deep learning approach to describe and classify fungi microscopic images

Preliminary diagnosis of fungal infections can rely on microscopic examination. However, in many cases, it does not allow unambiguous identification of the species due to their visual similarity. Therefore, it is usually necessary to use additional biochemical tests. That involves additional costs and extends the identification process up to 10 days. Such a delay in the implementation of targeted therapy may be grave in consequence as the mortality rate for immunosuppressed patients is high. In this paper, we apply a machine learning approach based on deep neural networks and bag-of-words to classify microscopic images of various fungi species. Our approach makes the last stage of biochemical identification redundant, shortening the identification process by 2-3 days, and reducing the cost of the diagnosis.
Computer Vision with a Single (Robust) Classifier

We show that the basic classification framework alone can be used to tackle some of the most challenging computer vision tasks. In contrast to other state-of-the-art approaches, the toolkit we develop is rather minimal: it uses a single, off-the-shelf classifier for all these tasks. The crux of our approach is that we train this classifier to be adversarially robust. It turns out that adversarial robustness is precisely what we need to directly manipulate salient features of the input. Overall, our findings demonstrate the utility of robustness in the broader machine learning
The phase diagram of approximation rates for deep neural networks

We explore the phase diagram of approximation rates for deep neural networks. The phase diagram describes theoretically optimal accuracy-complexity relations and their qualitative properties. Our contribution is three-fold. First, we generalize the existing result on the existence of deep discontinuous phase in ReLU networks to functional classes of arbitrary positive smoothness, and identify the boundary between the feasible and infeasible rates. Second, we demonstrate that standard fully-connected architectures of a fixed width independent of smoothness can adapt to smoothness and achieve almost optimal rates. Finally, we discuss how the phase diagram can change in the case of non-ReLU activation functions. In particular, we prove that using both sine and ReLU activations theoretically leads to very fast, nearly exponential approximation rates, thanks to the emerging capability of the network to implement efficient lookup operations.
A neurally plausible model learns successor representations in partially observable environments

Animals need to devise strategies to maximize returns while interacting with their environment based on incoming noisy sensory observations. Task-relevant states, such as the agent's location within an environment or the presence of a predator, are often not directly observable but must be inferred using available sensory information. Successor representations (SR) have been proposed as a middle-ground between model-based and model-free reinforcement learning strategies, allowing for fast value computation and rapid adaptation to changes in the reward function or goal locations. Indeed, recent studies suggest that features of neural responses are consistent with the SR framework. However, it is not clear how such representations might be learned and computed in partially observed, noisy environments. Here, we introduce a neurally plausible model using distributional successor features, which builds on the distributed distributional code for the representation and computation of uncertainty, and which allows for efficient value function computation in partially observed environments via the successor representation. We show that distributional successor features can support reinforcement learning in noisy environments in which direct learning of successful policies is infeasible.
Cation dependent electroosmotic flow in glass nanopores

We present our findings on the changes to electroosmotic flow outside glass nanopores with respect to the choice of Group 1 cation species. In contrast with standard electrokinetic theory, flow reversal was observed for all salts under a negative driving voltage. Moving down Group 1 resulted in weaker flow when the driving voltage was negative, in line with the reduction in the zeta potential on the glass surface going down the periodic table. No trend emerged with a positive driving voltage, however for Cs, flow was uniquely found to be in reverse. These results are explained by the interplay between the flow inside the nanopore and flow along the outer walls in the vicinity of the nanopore.
Defending Against Adversarial Examples with K-Nearest Neighbor

Robustness is an increasingly important property of machine learning models as they become more and more prevalent. We propose a defense against adversarial examples based on a k-nearest neighbor (kNN) on the intermediate activation of neural networks. Our scheme surpasses state-of-the-art defenses on MNIST and CIFAR-10 against l2-perturbation by a significant margin. With our models, the mean perturbation norm required to fool our MNIST model is 3.07 and 2.30 on CIFAR-10. Additionally, we propose a simple certifiable lower bound on the l2-norm of the adversarial perturbation using a more specific version of our scheme, a 1-NN on representations learned by a Lipschitz network. Our model provides a nontrivial average lower bound of the perturbation norm, comparable to other schemes on MNIST with similar clean accuracy.