nils-herrmann/clean_scirepeval huggingface dataset:
Explainable Anatomical Shape Analysis Through Deep Hierarchical Generative Models

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer’s disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating high-throughput analysis of normal anatomy and pathology in large-scale studies of volumetric imaging.
On Reducing Negative Jacobian Determinant of the Deformation Predicted by Deep Registration Networks

Image registration is a fundamental step in medical image analysis. Ideally, the transformation that registers one image to another should be a diffeomorphism that is both invertible and smooth. Traditional methods like geodesic shooting approach the problem via differential geometry, with theoretical guarantees that the resulting transformation will be smooth and invertible. Most previous research using unsupervised deep neural networks for registration have used a local smoothness constraint (typically, a spatial variation loss) to address the smoothness issue. These networks usually produce non-invertible transformations with ``folding'' in multiple voxel locations, indicated by a negative determinant of the Jacobian matrix of the transformation. While using a loss function that specifically penalizes the folding is a straightforward solution, this usually requires carefully tuning the regularization strength, especially when there are also other losses. In this paper we address this problem from a different angle, by investigating possible training mechanisms that will help the network avoid negative Jacobians and produce smoother deformations. We contribute two independent ideas in this direction. Both ideas greatly reduce the number of folding locations in the predicted deformation, without making changes to the hyperparameters or the architecture used in the existing baseline registration network.
A 1d convolutional network for leaf and time series classification

In this paper, a 1d convolutional neural network is designed for classification tasks of plant leaves. This network based classifier is analyzed in two directions. In the forward direction, the proposed network can be used in two ways: a classifier and an automatic feature extractor. As a classifier, it takes the simple centroid contour distance curve as the single feature and achieves comparable performance with state-of-art methods that usually require multiple extracted features. As a feature extractor, it produces nearly linear separable features, hence can be used together with other classifiers such as support vector machines to provide better performance. The proposed network adopts simple 1d input and is generally applicable for other tasks such as classifying one dimensional time series in an end-to-end fashion without changes. Experiments on some benchmark datasets show this architecture can provide classification accuracies that are comparable or higher than some existing methods. In the backward direction, methods like gradient-weighted class activation mapping and maximum activation map of neurons in the classification layer with respect to inputs are performed to help investigate and further validate that hidden signatures helping trigger the trained classifier's specific decisions can be human interpretable. Code for the paper is available at this https URL.
Latent geometry and dynamics of proximity networks

Proximity networks are time-varying graphs representing the closeness among humans moving in a physical space. Their properties have been extensively studied in the past decade as they critically affect the behavior of spreading phenomena and the performance of routing algorithms. Yet the mechanisms responsible for their observed characteristics remain elusive. Here we show that many of the observed properties of proximity networks emerge naturally and simultaneously in a simple latent space network model, called dynamic-S^{1}. The dynamic-S^{1} does not model node mobility directly but captures the connectivity in each snapshot-each snapshot in the model is a realization of the S^{1} model of traditional complex networks, which is isomorphic to hyperbolic geometric graphs. By forgoing the motion component the model facilitates mathematical analysis, allowing us to prove the contact, intercontact, and weight distributions. We show that these distributions are power laws in the thermodynamic limit with exponents lying within the ranges observed in real systems. Interestingly, we find that network temperature plays a central role in network dynamics, dictating the exponents of these distributions, the time-aggregated agent degrees, and the formation of unique and recurrent components. Further, we show that paradigmatic epidemic and rumor-spreading processes perform similarly in real and modeled networks. The dynamic-S^{1} or extensions of it may apply to other types of time-varying networks and constitute the basis of maximum likelihood estimation methods that infer the node coordinates and their evolution in the latent spaces of real systems.
Programming with Timespans in Interactive Visualizations

Modern interactive visualizations are akin to distributed systems, where user interactions, background data processing, remote requests, and streaming data read and modify the interface at the same time. This concurrency is crucial to provide an interactive user experience---forbidding it can cripple responsiveness. However, it is notoriously challenging to program distributed systems, and concurrency can easily lead to ambiguous or confusing interface behaviors. In this paper, we present DIEL, a declarative programming model to help developers reason about and reconcile concurrency-related issues. Using DIEL, developers no longer need to procedurally describe how the interface should update based on different input events, but rather declaratively specify what the state of the interface should be as queries over event history. We show that resolving conflicts from concurrent processes in real-world interactive visualizations can be done in a few lines of DIEL code.
Learning to Identify Patients at Risk of Uncontrolled Hypertension Using Electronic Health Records Data

Hypertension is a major risk factor for stroke, cardiovascular disease, and end-stage renal disease, and its prevalence is expected to rise dramatically. Effective hypertension management is thus critical. A particular priority is decreasing the incidence of uncontrolled hypertension. Early identification of patients at risk for uncontrolled hypertension would allow targeted use of personalized, proactive treatments. We develop machine learning models (logistic regression and recurrent neural networks) to stratify patients with respect to the risk of exhibiting uncontrolled hypertension within the coming three-month period. We trained and tested models using EHR data from 14,407 and 3,009 patients, respectively. The best model achieved an AUROC of 0.719, outperforming the simple, competitive baseline of relying prediction based on the last BP measure alone (0.634). Perhaps surprisingly, recurrent neural networks did not outperform a simple logistic regression for this task, suggesting that linear models should be included as strong baselines for predictive tasks using EHR.
Data integration for high-resolution, continental-scale estimation of air pollution concentrations

Air pollution constitutes the highest environmental risk factor in relation to heath. In order to provide the evidence required for health impact analyses, to inform policy and to develop potential mitigation strategies comprehensive information is required on the state of air pollution. Information on air pollution traditionally comes from ground monitoring (GM) networks but these may not be able to provide sufficient coverage and may need to be supplemented with information from other sources (e.g. chemical transport models; CTMs). However, these may only be available on grids and may not capture micro-scale features that may be important in assessing air quality in areas of high population. We develop a model that allows calibration between multiple data sources available at different levels of support by allowing the coefficients of calibration equations to vary over space and time, enabling downscaling where the data is sufficient to support it. The model is used to produce high-resolution (1km $\times$ 1km) estimates of NO$_2$ and PM$_{2.5}$ across Western Europe for 2010-2016. Concentrations of both pollutants are decreasing during this period, however there remain large populations exposed to levels exceeding the WHO Air Quality Guidelines and thus air pollution remains a serious threat to health.
Parallel performance of molecular dynamics trajectory analysis

The performance of biomolecular molecular dynamics simulations has steadily increased on modern high‐performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations is becoming a bottleneck. To close this gap, we studied the performance of trajectory analysis with message passing interface (MPI) parallelization and the Python MDAnalysis library on three different Extreme Science and Engineering Discovery Environment (XSEDE) supercomputers where trajectories were read from a Lustre parallel file system. Strong scaling performance was impeded by stragglers, MPI processes that were slower than the typical process. Stragglers were less prevalent for compute‐bound workloads, thus pointing to file reading as a bottleneck for scaling. However, a more complicated picture emerged in which both the computation and the data ingestion exhibited close to ideal strong scaling behavior whereas stragglers were primarily caused by either large MPI communication costs or long times to open the single shared trajectory file. We improved overall strong scaling performance by either subfiling (splitting the trajectory into separate files) or MPI‐IO with parallel HDF5 trajectory files. The parallel HDF5 approach resulted in near ideal strong scaling on up to 384 cores (16 nodes), thus reducing trajectory analysis times by two orders of magnitude compared with the serial approach.
Robustness Guarantees for Deep Neural Networks on Videos

The widespread adoption of deep learning models places demands on their robustness. In this paper, we consider the robustness of deep neural networks on videos, which comprise both the spatial features of individual frames extracted by a convolutional neural network and the temporal dynamics between adjacent frames captured by a recurrent neural network. To measure robustness, we study the maximum safe radius problem, which computes the minimum distance from the optical flow sequence obtained from a given input to that of an adversarial example in the neighbourhood of the input. We demonstrate that, under the assumption of Lipschitz continuity, the problem can be approximated using finite optimisation via discretising the optical flow space, and the approximation has provable guarantees. We then show that the finite optimisation problem can be solved by utilising a two-player turn-based game in a cooperative setting, where the first player selects the optical flows and the second player determines the dimensions to be manipulated in the chosen flow. We employ an anytime approach to solve the game, in the sense of approximating the value of the game by monotonically improving its upper and lower bounds. We exploit a gradient-based search algorithm to compute the upper bounds, and the admissible A* algorithm to update the lower bounds. Finally, we evaluate our framework on the UCF101 video dataset.
Learning Effective Loss Functions Efficiently

We consider the problem of learning a loss function which, when minimized over a training dataset, yields a model that approximately minimizes a validation error metric. Though learning an optimal loss function is NP-hard, we present an anytime algorithm that is asymptotically optimal in the worst case, and is provably efficient in an idealized "easy" case. Experimentally, we show that this algorithm can be used to tune loss function hyperparameters orders of magnitude faster than state-of-the-art alternatives. We also show that our algorithm can be used to learn novel and effective loss functions on-the-fly during training.
Adaptive Sequential Experiments with Unknown Information Flows

When information is limited, online recommendation services aim to strike a balance between maximizing immediate payoffs based on available information, and acquiring new information that is essential for maximizing future payoffs. This trade-off is captured by the multi-armed bandit (MAB) framework that has been studied and applied for designing sequential experiments when at each time epoch a single observation is collected on the action that was selected at that epoch. However, in many cases, additional information may become available between decision epochs. We introduce a generalized MAB formulation in which auxiliary information may appear arbitrarily over time. By obtaining matching lower and upper bounds, we characterize the minimax complexity of this family of problems as a function of the information arrival process, and study how salient characteristics of this process impact policy design and achievable performance. 
We establish that while Thompson sampling and UCB policies leverage additional information naturally, other policies, such as epsilon-greedy, do not exhibit such robustness. We introduce a virtual time indexes method for dynamically controlling the exploration rate of policies, and apply it for designing epsilon-greedy-type policies that, without any prior knowledge on the information arrival process, attain the best performance (in terms of regret rate) that is achievable when the information arrival process is a priori known. We use data from a large media site to empirically analyze the value that may be captured in practice by leveraging auxiliary information flows for content recommendations. We further apply our method to a contextual bandit framework that allows for personalized recommendations using idiosyncratic consumer characteristics.
SetGAN: Improving the stability and diversity of generative models through a permutation invariant architecture

Generative adversarial networks (GANs) have proven effective in modeling distributions of high-dimensional data. However, their training instability is a well-known hindrance to convergence, which results in practical challenges in their applications to novel data. Furthermore, even when convergence is reached, GANs can be affected by mode collapse, a phenomenon for which the generator learns to model only a small part of the target distribution, disregarding the vast majority of the data manifold or distribution. This paper addresses these challenges by introducing SetGAN, an adversarial architecture that processes sets of generated and real samples, and discriminates between the origins of these sets (i.e., training versus generated data) in a flexible, permutation invariant manner. We also propose a new metric to quantitatively evaluate GANs that does not require previous knowledge of the application, apart from the data itself. Using the new metric, in conjunction with the state-of-the-art evaluation methods, we show that the proposed architecture, when compared with GAN variants stemming from similar strategies, produces more accurate models of the input data in a way that is also less sensitive to hyperparameter settings.
An Intrinsic Geometrical Approach for Statistical Process Control of Surface and Manifold Data

We present a new method for statistical process control (SPC) of a discrete part manufacturing system based on intrinsic geometrical properties of the parts, estimated from three-dimensional sensor data. An intrinsic method has the computational advantage of avoiding the difficult part registration problem, necessary in previous SPC approaches of three-dimensional geometrical data, but inadequate if noncontact sensors are used. The approach estimates the spectrum of the Laplace–Beltrami (LB) operator of the scanned parts and uses a multivariate nonparametric control chart for online process control. Our proposal brings SPC closer to computer vision and computer graphics methods aimed to detect large differences in shape (but not in size). However, the SPC problem differs in that small changes in either shape or size of the parts need to be detected, keeping a controllable false alarm rate and without completely filtering noise. An online or “Phase II” method and a scheme for starting up in the absence of prior data (“Phase I”) are presented. Comparison with earlier approaches that require registration shows the LB spectrum method to be more sensitive to rapidly detect small changes in shape and size, including the practical case when the sequence of part datasets is in the form of large, unequal size meshes. A post-alarm diagnostic method to investigate the location of defects on the surface of a part is also presented. While we focus in this article on surface (triangulation) data, the methods can also be applied to point cloud and voxel metrology data.
Learning Markov Models Via Low-Rank Optimization

Taming high-dimensional Markov models In “Learning Markov models via low-rank optimization”, Z. Zhu, X. Li, M. Wang, and A. Zhang focus on learning a high-dimensional Markov model with low-dimensional latent structure from a single trajectory of states. To overcome the curse of high dimensions, the authors propose to equip the standard MLE (maximum-likelihood estimation) with either nuclear norm regularization or rank constraint. They show that both approaches can estimate the full transition matrix accurately using a trajectory of length that is merely proportional to the number of states. To solve the rank-constrained MLE, which is a nonconvex problem, the authors develop a new DC (difference) programming algorithm. Finally, they apply the proposed methods to analyze taxi trips on the Manhattan island and partition the island based on the destination preference of customers; this partition can help balance supply and demand of taxi service and optimize the allocation of traffic resources.
Cellular State Transformations using Generative Adversarial Networks

We introduce a novel method to unite deep learning with biology by which generative adversarial networks (GANs) generate transcriptome perturbations and reveal condition-defining gene expression patterns. We find that a generator conditioned to perturb any input gene expression profile simulates a realistic transition between source and target RNA expression states. The perturbed samples follow a similar distribution to original samples from the dataset, also suggesting these are biologically meaningful perturbations. Finally, we show that it is possible to identify the genes most positively and negatively perturbed by the generator and that the enriched biological function of the perturbed genes are realistic. We call the framework the Transcriptome State Perturbation Generator (TSPG), which is open source software available at this https URL.
Competing Neural Networks for Robust Control of Nonlinear Systems

The output of physical systems is often accessible by measurements such as the 3D position of a robotic arm actuated by many actuators or the speckle patterns formed by shining the spot of a laser pointer on a wall. The selection of the input of such a system (actuators and the shape of the laser spot respectively) to obtain a desired output is difficult because it is an ill-posed problem i.e. there are multiple inputs yielding the same output. In this paper, we propose an approach that provides a robust solution to this dilemma for any physical system. We show that it is possible to find the appropriate input of a system that results in a desired output, despite the input-output relation being nonlinear and\or with incomplete measurements of the systems variables. We showcase our approach using an extremely ill-posed problem in imaging. We demonstrate the projection of arbitrary shapes through a multimode fiber (MMF) when a sample of intensity-only measurements are taken at the output. We show image projection fidelity as high as ~90 %, which is on par with the gold standard methods which characterize the system fully by phase and amplitude measurements. The generality as well as simplicity of the proposed approach provides a new way of target-oriented control in real-world applications.
Fast Convolutive Nonnegative Matrix Factorization Through Coordinate and Block Coordinate Updates

Identifying recurring patterns in high-dimensional time series data is an important problem in many scientific domains. A popular model to achieve this is convolutive nonnegative matrix factorization (CNMF), which extends classic nonnegative matrix factorization (NMF) to extract short-lived temporal motifs from a long time series. Prior work has typically fit this model by multiplicative parameter updates---an approach widely considered to be suboptimal for NMF, especially in large-scale data applications. Here, we describe how to extend two popular and computationally scalable NMF algorithms---Hierarchical Alternating Least Squares (HALS) and Alternatining Nonnegative Least Squares (ANLS)---for the CNMF model. Both methods demonstrate performance advantages over multiplicative updates on large-scale synthetic and real world data.
Approximate Inference in Structured Instances with Noisy Categorical Observations

We study the problem of recovering the latent ground truth labeling of a structured instance with categorical random variables in the presence of noisy observations. We present a new approximate algorithm for graphs with categorical variables that achieves low Hamming error in the presence of noisy vertex and edge observations. Our main result shows a logarithmic dependency of the Hamming error to the number of categories of the random variables. Our approach draws connections to correlation clustering with a fixed number of clusters. Our results generalize the works of Globerson et al. (2015) and Foster et al. (2018), who study the hardness of structured prediction under binary labels, to the case of categorical labels.
Time-changed Lévy processes and option pricing: a critical comment

Carr and Wu (2004), henceforth CW, developed a framework that encompasses almost all of the continuous-time models proposed in the option pricing literature. Their framework hinges on the stopping time property of the time changes. By ana- lyzing the measurability of the time changes with respect to the underlying filtration, we show that many asset price models using correlated time changes fail to satisfy this assumption.