nils-herrmann/clean_scirepeval huggingface dataset:
Encoding High-Level Visual Attributes in Capsules for Explainable Medical Diagnoses

Deep neural networks are often called black-boxes due to their difficult-to-interpret decisions. This is characteristic of a deeper trend in machine learning, where predictive performance typically comes at the cost of interpretability. In some domains, such as image-based diagnostic tasks, understanding the reasons behind machine generated predictions is vital in assessing trust. In this study, we introduce novel designs of capsule networks to provide explainable diagnoses. Our proposed deep explainable capsule architecture, called DX-Caps, can encode high-level visual attributes within the vectors of capsules in order to simultaneously produce malignancy predictions for lung cancer as well as approximations of six visuallyinterpretable attributes, used by radiologists to explain their predictions. To reduce parameter and memory burden of this deeper network, we introduce a new capsuleaverage pooling function. With this simple, but fundamental addition, capsule networks can be designed in a deeper fashion than was possible before. Our overall approach can be characterized as multi-task learning; we learn to approximate the six high-level visual attributes of a lung nodule within the vectors of our uniquely constructed deep capsule network, while simultaneously segmenting the nodule and predicting its malignancy potential (diagnosis). Tested on over 1000 CT scans, our experimental results show that our proposed algorithm can approximate the visual attributes of lung nodules far better than a deep multi-path dense 3D CNN . The proposed network also achieves higher diagnostic accuracy than a baseline explainable capsule network X-Caps and CapsNet  when applied to this task for the first time as well. To the best of our knowledge, this is the first study to investigate capsule networks for visual attribute prediction in general, and explainable medical image diagnosis in particular.
The Urban Observatory: A Multi-Modal Imaging Platform for the Study of Dynamics in Complex Urban Systems

We describe an “Urban Observatory” facility designed for the study of complex urban systems via persistent, synoptic, and granular imaging of dynamical processes in cities. An initial deployment of the facility has been demonstrated in New York City and consists of a suite of imaging systems—both broadband and hyperspectral—sensitive to wavelengths from the visible (∼400 nm) to the infrared (∼13 micron) operating at cadences of ∼0.01–30 Hz (characteristically ∼0.1 Hz). Much like an astronomical survey, the facility generates a large imaging catalog from which we have extracted observables (e.g., time-dependent brightnesses, spectra, temperatures, chemical species, etc.), collecting them in a parallel source catalog. We have demonstrated that, in addition to the urban science of cities as systems, these data are applicable to a myriad of domain-specific scientific inquiries related to urban functioning including energy consumption and end use, environmental impacts of cities, and patterns of life and public health. We show that an Urban Observatory facility of this type has the potential to improve both a city’s operations and the quality of life of its inhabitants.
Gaussians on Riemannian Manifolds: Applications for Robot Learning and Adaptive Control

This article presents an overview of robot learning and adaptive control applications that can benefit from a joint use of Riemannian geometry and probabilistic representations. The roles of Riemannian manifolds, geodesics, and parallel transport in robotics are discussed, and several forms of manifolds already employed in robotics are explained. A varied range of techniques employing Gaussian distributions on Riemannian manifolds is then introduced, and two example applications are presented, involving the control of a prosthetic hand from surface electromyography (sEMG) data and the teleoperation of a bimanual underwater robot.
Unsupervised Image Regression for Heterogeneous Change Detection

Change detection (CD) in heterogeneous multitemporal satellite images is an emerging and challenging topic in remote sensing. In particular, one of the main challenges is to tackle the problem in an unsupervised manner. In this paper, we propose an unsupervised framework for bitemporal heterogeneous CD based on the comparison of affinity matrices and image regression. First, our method quantifies the similarity of affinity matrices computed from colocated image patches in the two images. This is done to automatically identify pixels that are likely to be unchanged. With the identified pixels as pseudotraining data, we learn a transformation to map the first image to the domain of the other image and vice versa. Four regression methods are selected to carry out the transformation: Gaussian process regression, support vector regression, random forest regression (RFR), and a recently proposed kernel regression method called homogeneous pixel transformation. To evaluate the potentials and limitations of our framework and also the benefits and disadvantages of each regression method, we perform experiments on two real data sets. The results indicate that the comparison of the affinity matrices can already be considered a CD method by itself. However, image regression is shown to improve the results obtained by the previous step alone and produces accurate CD maps despite of the heterogeneity of the multitemporal input data. Notably, the RFR approach excels by achieving similar accuracy as the other methods, but with a significantly lower computational cost and with fast and robust tuning of hyperparameters.
Adjusting Rate of Spread Factors through Derivative-Free Optimization: A New Methodology to Improve the Performance of Forest Fire Simulators

In practical applications, it is common that wildfire simulators do not correctly predict the evolution of the fire scar. Usually, this is caused due to multiple factors including inaccuracy in the input data such as land cover classification, moisture, improperly represented local winds, cumulative errors in the fire growth simulation model, high level of discontinuity/heterogeneity within the landscape, among many others. Therefore in practice, it is necessary to adjust the propagation of the fire to obtain better results, either to support suppression activities or to improve the performance of the simulator considering new default parameters for future events, best representing the current fire spread growth phenomenon. In this article, we address this problem through a new methodology using Derivative-Free Optimization (DFO) algorithms for adjusting the Rate of Spread (ROS) factors in a fire simulation growth model called Cell2Fire. To achieve this, we solve an error minimization optimization problem that captures the difference between the simulated and observed fire, which involves the evaluation of the simulator output in each iteration as part of a DFO framework, allowing us to find the best possible factors for each fuel present on the landscape. Numerical results for different objective functions are shown and discussed, including a performance comparison of alternative DFO algorithms.
Mutual-Information Regularization in Markov Decision Processes and Actor-Critic Learning

Cumulative entropy regularization introduces a regulatory signal to the reinforcement learning (RL) problem that encourages policies with high-entropy actions, which is equivalent to enforcing small deviations from a uniform reference marginal policy. This has been shown to improve exploration and robustness, and it tackles the value overestimation problem. It also leads to a significant performance increase in tabular and high-dimensional settings, as demonstrated via algorithms such as soft Q-learning (SQL) and soft actor-critic (SAC). Cumulative entropy regularization has been extended to optimize over the reference marginal policy instead of keeping it fixed, yielding a regularization that minimizes the mutual information between states and actions. While this has been initially proposed for Markov Decision Processes (MDPs) in tabular settings, it was recently shown that a similar principle leads to significant improvements over vanilla SQL in RL for high-dimensional domains with discrete actions and function approximators. 
Here, we follow the motivation of mutual-information regularization from an inference perspective and theoretically analyze the corresponding Bellman operator. Inspired by this Bellman operator, we devise a novel mutual-information regularized actor-critic learning (MIRACLE) algorithm for continuous action spaces that optimizes over the reference marginal policy. We empirically validate MIRACLE in the Mujoco robotics simulator, where we demonstrate that it can compete with contemporary RL methods. Most notably, it can improve over the model-free state-of-the-art SAC algorithm which implicitly assumes a fixed reference policy.
Deterministic parallel fixpoint computation

Abstract interpretation is a general framework for expressing static program analyses. It reduces the problem of extracting properties of a program to computing an approximation of the least fixpoint of a system of equations. The de facto approach for computing this approximation uses a sequential algorithm based on weak topological order (WTO). This paper presents a deterministic parallel algorithm for fixpoint computation by introducing the notion of weak partial order (WPO). We present an algorithm for constructing a WPO in almost-linear time. Finally, we describe Pikos, our deterministic parallel abstract interpreter, which extends the sequential abstract interpreter IKOS. We evaluate the performance and scalability of Pikos on a suite of 1017 C programs. When using 4 cores, Pikos achieves an average speedup of 2.06x over IKOS, with a maximum speedup of 3.63x. When using 16 cores, Pikos achieves a maximum speedup of 10.97x.
Quantitative Programming by Examples

Programming-by-Example (PBE) systems synthesize an intended program in some (relatively constrained) domain-specific language from a small number of input-output examples provided by the user. In this paper, we motivate and define the problem of quantitative PBE (qPBE) that relates to synthesizing an intended program over an underlying (real world) programming language that also minimizes a given quantitative cost function. We present a modular approach for solving qPBE that consists of three phases: intent disambiguation, global search, and local search. On two concrete objectives, namely program performance and size, our qPBE procedure achieves $1.53 X$ and $1.26 X$ improvement respectively over the baseline FlashFill PBE system, averaged over $701$ benchmarks. Our detailed experiments validate the design of our procedure and show the value of combining global and local search for qPBE.
Analysis of Regression Tree Fitting Algorithms in Learning to Rank

In learning to rank area, industry-level applications have been dominated by gradient boosting framework, which fits a tree using least square error principle. While in classification area, another tree fitting principle, weighted least square error, has been widely used, such as LogitBoost and its variants. However, there is a lack of analysis on the relationship between the two principles in the scenario of learning to rank. We propose a new principle named least objective loss based error that enables us to analyze the issue above as well as several important learning to rank models. We also implement two typical and strong systems and conduct our experiments in two real-world datasets. Experimental results show that our proposed method brings moderate improvements over least square error principle.
Learning Bayesian Posteriors with Neural Networks for Gravitational-Wave Inference.

We seek to achieve the holy grail of Bayesian inference for gravitational-wave astronomy: using deep-learning techniques to instantly produce the posterior p(θ|D) for the source parameters θ, given the detector data D. To do so, we train a deep neural network to take as input a signal + noise dataset (drawn from the astrophysical source-parameter prior and the sampling distribution of detector noise), and to output a parametrized approximation of the corresponding posterior. We rely on a compact representation of the data based on reduced-order modeling, which we generate efficiently using a separate neural-network waveform interpolant [A. J. K. Chua, C. R. Galley, and M. Vallisneri,  (2019)PRLTAO0031-900710.1103/PhysRevLett.122.211101]. Our scheme has broad relevance to gravitational-wave applications such as low-latency parameter estimation and characterizing the science returns of future experiments.
Detecting Architectural Erosion using Runtime Verification

The architecture of a system captures important design decisions for the system. Over time, changes in a system's implementation may lead to violations of specific design decisions. This problem is common in industry and known as architectural erosion. Since it may have severe consequences on the quality of a system, research has focused on the development of tools and techniques to address the presented problem. As of today, most of the approaches to detect architectural erosion employ static analysis techniques. While these techniques are well-suited for the analysis of static architectures, they reach their limit when it comes to dynamic architectures. Thus, in this paper, we propose an alternative approach based on runtime verification. To this end, we propose a systematic way to translate a formal specification of architectural constraints to monitors, which can be used to detect violations of these constraints. The approach is implemented in Eclipse/EMF, demonstrated through a running example, and evaluated using two case studies.
DyANE: Dynamics-aware node embedding for temporal networks

Low-dimensional vector representations of network nodes have proven successful to feed graph data to machine learning algorithms and to improve performance across diverse tasks. Most of the embedding techniques, however, have been developed with the goal of achieving dense, low-dimensional encoding of network structure and patterns. Here, we present a node embedding technique aimed at providing low-dimensional feature vectors that are informative of dynamical processes occurring over temporal networks-rather than of the network structure itself-with the goal of enabling prediction tasks related to the evolution and outcome of these processes. We achieve this by using a modified supra-adjacency representation of temporal networks and building on standard embedding techniques for static graphs based on random-walks. We show that the resulting embedding vectors are useful for prediction tasks related to paradigmatic dynamical processes, namely epidemic spreading over empirical temporal networks. In particular, we illustrate the performance of our approach for the prediction of nodes' epidemic states in a single instance of the spreading process. We show how framing this task as a supervised multi-label classification task on the embedding vectors allows us to estimate the temporal evolution of the entire system from a partial sampling of nodes at random times, with potential impact for nowcasting infectious disease dynamics.
Finite Depth and Width Corrections to the Neural Tangent Kernel

We prove the precise scaling, at finite depth and width, for the mean and variance of the neural tangent kernel (NTK) in a randomly initialized ReLU network. The standard deviation is exponential in the ratio of network depth to width. Thus, even in the limit of infinite overparameterization, the NTK is not deterministic if depth and width simultaneously tend to infinity. Moreover, we prove that for such deep and wide networks, the NTK has a non-trivial evolution during training by showing that the mean of its first SGD update is also exponential in the ratio of network depth to width. This is sharp contrast to the regime where depth is fixed and network width is very large. Our results suggest that, unlike relatively shallow and wide networks, deep and wide ReLU networks are capable of learning data-dependent features even in the so-called lazy training regime.
Center-Extraction-Based Three Dimensional Nuclei Instance Segmentation of Fluorescence Microscopy Images

Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of nuclei using convolutional neural networks (CNNs) is described. In particular, since creating labeled volumes manually for training purposes is not practical due to the size and complexity of the 3D data sets, the paper describes a method for generating synthetic microscopy volumes based on a spatially constrained cycle-consistent adversarial network. The proposed method is tested on multiple real microscopy data sets and outperforms other commonly used segmentation techniques.
FoodTracker: A Real-time Food Detection Mobile Application by Deep Convolutional Neural Networks

We present a mobile application made to recognize food items of multi-object meal from a single image in real-time, and then return the nutrition facts with components and approximate amounts. Our work is organized in two parts. First, we build a deep convolutional neural network merging with YOLO, a state-of-the-art detection strategy, to achieve simultaneous multi-object recognition and localization with nearly 80% mean average precision. Second, we adapt our model into a mobile application with extending function for nutrition analysis. After inferring and decoding the model output in the app side, we present detection results that include bounding box position and class label in either real-time or local mode. Our model is well-suited for mobile devices with negligible inference time and small memory requirements with a deep learning algorithm.
Towards Generalizable Forgery Detection with Locality-aware AutoEncoder

With advancements of deep learning techniques, it is now possible to generate super-realistic fake images and videos. These manipulated forgeries could reach mass audience and result in adverse impacts on our society. Although lots of efforts have been devoted to detect forgeries, their performance drops significantly on previously unseen but related manipulations and the detection generalization capability remains a problem. To bridge this gap, in this paper we propose Locality-aware AutoEncoder (LAE), which combines fine-grained representation learning and enforcing locality in a unified framework. In the training process, we use pixel-wise mask to regularize local interpretation of LAE to enforce the model to learn intrinsic representation from the forgery region, instead of capturing artifacts in the training set and learning spurious correlations to perform detection. We further propose an active learning framework to select the challenging candidates for labeling, to reduce the annotation efforts to regularize interpretations. Experimental results indicate that LAE indeed could focus on the forgery regions to make decisions. The results further show that LAE achieves superior generalization performance compared to state-of-the-arts on forgeries generated by alternative manipulation methods.
Multiple Partitions Aligned Clustering

Multi-view clustering is an important yet challenging task due to the difficulty of integrating the information from multiple representations. Most existing multi-view clustering methods explore the heterogeneous information in the space where the data points lie. Such common practice may cause significant information loss because of unavoidable noise or inconsistency among views. Since different views admit the same cluster structure, the natural space should be all partitions. Orthogonal to existing techniques, in this paper, we propose to leverage the multi-view information by fusing partitions. Specifically, we align each partition to form a consensus cluster indicator matrix through a distinct rotation matrix. Moreover, a weight is assigned for each view to account for the clustering capacity differences of views. Finally, the basic partitions, weights, and consensus clustering are jointly learned in a unified framework. We demonstrate the effectiveness of our approach on several real datasets, where significant improvement is found over other state-of-the-art multi-view clustering methods.
On educating machines

Machine education is an emerging research field that focuses on the problem which is inverse to machine learning. To date, the literature on educating machines is still in its infancy. A fairly low number of methodology and method papers are scattered throughout various formal and informal publication avenues, mainly because the field is not yet well coalesced (with no well established discussion forums or investigation pathways), but also due to the breadth of its potential ramifications and research directions. In this study we bring together the existing literature and organise the discussion into a small number of research directions (out of many) which are to date sufficiently explored to form a minimal critical mass that can push the machine education concept further towards a standalone research field status.
Part-Guided Attention Learning for Vehicle Re-Identification

Vehicle re-identification (Re-ID) often requires one to recognize the fine-grained visual differences between vehicles. Besides the holistic appearance of vehicles which is easily affected by the viewpoint variation and distortion, vehicle parts also provide crucial cues to differentiate near-identical vehicles. Motivated by these observations, we introduce a Part-Guided Attention Network (PGAN) to pinpoint the prominent part regions and effectively combine the global and part information for discriminative feature learning. PGAN first detects the locations of different part components and salient regions regardless of the vehicle identity, which serve as the bottom-up attention to narrow down the possible searching regions. To estimate the importance of detected parts, we propose a Part Attention Module (PAM) to adaptively locate the most discriminative regions with high-attention weights and suppress the distraction of irrelevant parts with relatively low weights. The PAM is guided by the Re-ID loss and therefore provides top-down attention that enables attention to be calculated at the level of car parts and other salient regions. Finally, we aggregate the global appearance and part features to improve the feature performance further. The PGAN combines part-guided bottom-up and top-down attention, global and part visual features in an end-to-end framework. Extensive experiments demonstrate that the proposed method achieves new state-of-the-art vehicle Re-ID performance on four large-scale benchmark datasets.
Evaluating and Boosting Uncertainty Quantification in Classification

Emergence of artificial intelligence techniques in biomedical applications urges the researchers to pay more attention on the uncertainty quantification (UQ) in machine-assisted medical decision making. For classification tasks, prior studies on UQ are difficult to compare with each other, due to the lack of a unified quantitative evaluation metric. Considering that well-performing UQ models ought to know when the classification models act incorrectly, we design a new evaluation metric, area under Confidence-Classification Characteristic curves (AUCCC), to quantitatively evaluate the performance of the UQ models. AUCCC is threshold-free, robust to perturbation, and insensitive to the classification performance. We evaluate several UQ methods (e.g., max softmax output) with AUCCC to validate its effectiveness. Furthermore, a simple scheme, named Uncertainty Distillation (UDist), is developed to boost the UQ performance, where a confidence model is distilling the confidence estimated by deep ensembles. The proposed method is easy to implement; it consistently outperforms strong baselines on natural and medical image datasets in our experiments.