OpenRaiser/Intern-Atlas huggingface dataset:
A comprehensive study on the prediction reliability of graph neural networks for virtual screening
Venue: arXiv cs.LG 2020
Year: 2020

Prediction models based on deep neural networks are increasingly gaining attention for fast and accurate virtual screening systems. For decision makings in virtual screening, researchers find it useful to interpret an output of classification system as probability, since such interpretation allows them to filter out more desirable compounds. However, probabilistic interpretation cannot be correct for models that hold over-parameterization problems or inappropriate regularizations, leading to unreliable prediction and decision making. In this regard, we concern the reliability of neural prediction models on molecular properties, especially when models are trained with sparse data points and imbalanced distributions. This work aims to propose guidelines for training reliable models, we thus provide methodological details and ablation studies on the following train principles. We investigate the effects of model architectures, regularization methods, and loss functions on the prediction performance and reliability of classification results. Moreover, we evaluate prediction reliability of models on virtual screening scenario. Our result highlights that correct choice of regularization and inference methods is evidently important to achieve high success rate, especially in data imbalanced situation. All experiments were performed under a single unified model implementation to alleviate external randomness in model training and to enable precise comparison of results.
Building Computationally Efficient and Well-Generalizing Person Re-Identification Models with Metric Learning
Venue: arXiv cs.CV 2020
Year: 2020

This work considers the problem of domain shift in person re-identification.Being trained on one dataset, a re-identification model usually performs much worse on unseen data. Partially this gap is caused by the relatively small scale of person re-identification datasets (compared to face recognition ones, for instance), but it is also related to training objectives. We propose to use the metric learning objective, namely AM-Softmax loss, and some additional training practices to build well-generalizing, yet, computationally efficient models. We use recently proposed Omni-Scale Network (OSNet) architecture combined with several training tricks and architecture adjustments to obtain state-of-the art results in cross-domain generalization problem on a large-scale MSMT17 dataset in three setups: MSMT17-all->DukeMTMC, MSMT17-train->Market1501 and MSMT17-all->Market1501.
iNALU: Improved Neural Arithmetic Logic Unit
Venue: arXiv cs.NE 2020
Year: 2020

Neural networks have to capture mathematical relationships in order to learn various tasks. They approximate these relations implicitly and therefore often do not generalize well. The recently proposed Neural Arithmetic Logic Unit (NALU) is a novel neural architecture which is able to explicitly represent the mathematical relationships by the units of the network to learn operations such as summation, subtraction or multiplication. Although NALUs have been shown to perform well on various downstream tasks, an in-depth analysis reveals practical shortcomings by design, such as the inability to multiply or divide negative input values or training stability issues for deeper networks. We address these issues and propose an improved model architecture. We evaluate our model empirically in various settings from learning basic arithmetic operations to more complex functions. Our experiments indicate that our model solves stability issues and outperforms the original NALU model in means of arithmetic precision and convergence.
Chemotaxis and Quorum Sensing inspired Device Interaction supporting Social Networking
Venue: arXiv cs.CY 2020
Year: 2020

Conference and social events provides an opportunity for people to interact and develop formal contacts with various groups of individuals. In this paper, we propose an efficient interaction mechanism in a pervasive computing environment that provide recommendation to users of suitable locations within a conference or expo hall to meet and interact with individuals of similar interests. The proposed solution is based on evaluation of context information to deduce each user's interests as well as bioinspired self-organisation mechanism to direct users towards appropriate locations.Simulation results have also been provided to validate our proposed solution.
Designing Tools for Semi-Automated Detection of Machine Learning Biases: An Interview Study
Venue: arXiv cs.CY 2020
Year: 2020

Machine learning models often make predictions that bias against certain subgroups of input data. When undetected, machine learning biases can constitute significant financial and ethical implications. Semi-automated tools that involve humans in the loop could facilitate bias detection. Yet, little is known about the considerations involved in their design. In this paper, we report on an interview study with 11 machine learning practitioners for investigating the needs surrounding semi-automated bias detection tools. Based on the findings, we highlight four considerations in designing to guide system designers who aim to create future tools for bias detection.
Identifying Disinformation Websites Using Infrastructure Features
Venue: arXiv cs.CY 2020
Year: 2020

Platforms have struggled to keep pace with the spread of disinformation. Current responses like user reports, manual analysis, and third-party fact checking are slow and difficult to scale, and as a result, disinformation can spread unchecked for some time after being created. Automation is essential for enabling platforms to respond rapidly to disinformation. In this work, we explore a new direction for automated detection of disinformation websites: infrastructure features. Our hypothesis is that while disinformation websites may be perceptually similar to authentic news websites, there may also be significant non-perceptual differences in the domain registrations, TLS/SSL certificates, and web hosting configurations. Infrastructure features are particularly valuable for detecting disinformation websites because they are available before content goes live and reaches readers, enabling early detection. We demonstrate the feasibility of our approach on a large corpus of labeled website snapshots. We also present results from a preliminary real-time deployment, successfully discovering disinformation websites while highlighting unexplored challenges for automated disinformation detection.
Data-driven surrogate modelling and benchmarking for process equipment
Venue: arXiv cs.CE 2020
Year: 2020

In chemical process engineering, surrogate models of complex systems are often necessary for tasks of domain exploration, sensitivity analysis of the design parameters, and optimization. A suite of computational fluid dynamics (CFD) simulations geared toward chemical process equipment modeling has been developed and validated with experimental results from the literature. Various regression-based active learning strategies are explored with these CFD simulators in-the-loop under the constraints of a limited function evaluation budget. Specifically, five different sampling strategies and five regression techniques are compared, considering a set of four test cases of industrial significance and varying complexity. Gaussian process regression was observed to have a consistently good performance for these applications. The present quantitative study outlines the pros and cons of the different available techniques and highlights the best practices for their adoption. The test cases and tools are available with an open-source license to ensure reproducibility and engage the wider research community in contributing to both the CFD models and developing and benchmarking new improved algorithms tailored to this field.
An Experimental Evaluation of Robustness and Precision for Long-term LiDAR-based Localization in Highly Changing Environments
Venue: arXiv cs.RO 2020
Year: 2020

One of the hardest challenges to face in the development of a non GPS-based localization system for autonomous vehicles is the changes of the environment. LiDAR-based systems typically try to match the last measurements obtained with a previously recorded map of the area. If the existing map is not updated along time, there is a good chance that the measures will not match the environment well enough, causing the vehicle to lose track of its location. In this paper, we present and analyze experimental results regarding the robustness and precision of a map-matching based localization system over a certain period of time in the following three cases: (1) without any update of the initial map, (2) updating the map as the vehicle moves and (3) with map updates that take into account surrounding structures labeled as "fixed" which are treated differently. The environment of the tests is a busy parking area, which ensures drastic changes from one day to the next. The precision is obtained by comparing the positions computed using the map with the ones provided by a Real-Time Kinematic GPS system. The experimental results reveal a positioning error of about 6cm which remains stable even after 23 days when using fixed structures on the working area.
Tensor Graph Convolutional Networks for Multi-relational and Robust Learning
Venue: arXiv cs.LG 2020
Year: 2020

The era of "data deluge" has sparked renewed interest in graph-based learning methods and their widespread applications ranging from sociology and biology to transportation and communications. In this context of graph-aware methods, the present paper introduces a tensor-graph convolutional network (TGCN) for scalable semi-supervised learning (SSL) from data associated with a collection of graphs, that are represented by a tensor. Key aspects of the novel TGCN architecture are the dynamic adaptation to different relations in the tensor graph via learnable weights, and the consideration of graph-based regularizers to promote smoothness and alleviate over-parameterization. The ultimate goal is to design a powerful learning architecture able to: discover complex and highly nonlinear data associations, combine (and select) multiple types of relations, scale gracefully with the graph size, and remain robust to perturbations on the graph edges. The proposed architecture is relevant not only in applications where the nodes are naturally involved in different relations (e.g., a multi-relational graph capturing family, friendship and work relations in a social network), but also in robust learning setups where the graph entails a certain level of uncertainty, and the different tensor slabs correspond to different versions (realizations) of the nominal graph. Numerical tests showcase that the proposed architecture achieves markedly improved performance relative to standard GCNs, copes with state-of-the-art adversarial attacks, and leads to remarkable SSL performance over protein-to-protein interaction networks.
Store-Collect in the Presence of Continuous Churn with Application to Snapshots and Lattice Agreement
Venue: arXiv cs.DC 2020
Year: 2020

We present an algorithm for implementing a store-collect object in an asynchronous crash-prone message-passing dynamic system, where nodes continually enter and leave. The algorithm is very simple and efficient, requiring just one round trip for a store operation and two for a collect. We then show the versatility of the store-collect object for implementing churn-tolerant versions of useful data structures, while shielding the user from the complications of the underlying churn. In particular, we present elegant and efficient implementations of atomic snapshot and generalized lattice agreement objects that use store-collect.
When is Ontology-Mediated Querying Efficient?
Venue: arXiv cs.DB 2020
Year: 2020

In ontology-mediated querying, description logic (DL) ontologies are used to enrich incomplete data with domain knowledge which results in more complete answers to queries. However, the evaluation of ontology-mediated queries (OMQs) over relational databases is computationally hard. This raises the question when OMQ evaluation is efficient, in the sense of being tractable in combined complexity or fixed-parameter tractable. We study this question for a range of ontology-mediated query languages based on several important and widely-used DLs, using unions of conjunctive queries as the actual queries. For the DL ELHI extended with the bottom concept, we provide a characterization of the classes of OMQs that are fixed-parameter tractable. For its fragment EL extended with domain and range restrictions and the bottom concept (which restricts the use of inverse roles), we provide a characterization of the classes of OMQs that are tractable in combined complexity. Both results are in terms of equivalence to OMQs of bounded tree width and rest on a reasonable assumption from parameterized complexity theory. They are similar in spirit to Grohe's seminal characterization of the tractable classes of conjunctive queries over relational databases. We further study the complexity of the meta problem of deciding whether a given OMQ is equivalent to an OMQ of bounded tree width, providing several completeness results that range from NP to 2ExpTime, depending on the DL used. We also consider the DL-Lite family of DLs, including members that admit functional roles.
Enhancing the Monte Carlo Tree Search Algorithm for Video Game Testing
Venue: arXiv cs.AI 2020
Year: 2020

In this paper, we study the effects of several Monte Carlo Tree Search (MCTS) modifications for video game testing. Although MCTS modifications are highly studied in game playing, their impacts on finding bugs are blank. We focused on bug finding in our previous study where we introduced synthetic and human-like test goals and we used these test goals in Sarsa and MCTS agents to find bugs. In this study, we extend the MCTS agent with several modifications for game testing purposes. Furthermore, we present a novel tree reuse strategy. We experiment with these modifications by testing them on three testbed games, four levels each, that contain 45 bugs in total. We use the General Video Game Artificial Intelligence (GVG-AI) framework to create the testbed games and collect 427 human tester trajectories using the GVG-AI framework. We analyze the proposed modifications in three parts: we evaluate their effects on bug finding performances of agents, we measure their success under two different computational budgets, and we assess their effects on human-likeness of the human-like agent. Our results show that MCTS modifications improve the bug finding performance of the agents.
Overview of the TREC 2019 deep learning track
Venue: arXiv cs.IR 2020
Year: 2020

The Deep Learning Track is a new track for TREC 2019, with the goal of studying ad hoc ranking in a large data regime. It is the first track with large human-labeled training sets, introducing two sets corresponding to two tasks, each with rigorous TREC-style blind evaluation and reusable test sets. The document retrieval task has a corpus of 3.2 million documents with 367 thousand training queries, for which we generate a reusable test set of 43 queries. The passage retrieval task has a corpus of 8.8 million passages with 503 thousand training queries, for which we generate a reusable test set of 43 queries. This year 15 groups submitted a total of 75 runs, using various combinations of deep learning, transfer learning and traditional IR ranking methods. Deep learning runs significantly outperformed traditional IR runs. Possible explanations for this result are that we introduced large training data and we included deep models trained on such data in our judging pools, whereas some past studies did not have such training data or pooling.
Breast Cancer Detection Using Convolutional Neural Networks
Venue: arXiv cs.CV 2020
Year: 2020

Breast cancer is prevalent in Ethiopia that accounts 34% among women cancer patients. The diagnosis technique in Ethiopia is manual which was proven to be tedious, subjective, and challenging. Deep learning techniques are revolutionizing the field of medical image analysis and hence in this study, we proposed Convolutional Neural Networks (CNNs) for breast mass detection so as to minimize the overheads of manual analysis. CNN architecture is designed for the feature extraction stage and adapted both the Region Proposal Network (RPN) and Region of Interest (ROI) portion of the faster R-CNN for the automated breast mass abnormality detection. Our model detects mass region and classifies them into benign or malignant abnormality in mammogram(MG) images at once. For the proposed model, MG images were collected from different hospitals, locally.The images were passed through different preprocessing stages such as gaussian filter, median filter, bilateral filters and extracted the region of the breast from the background of the MG image. The performance of the model on test dataset is found to be: detection accuracy 91.86%, sensitivity of 94.67% and AUC-ROC of 92.2%.
Big Code != Big Vocabulary: Open-Vocabulary Models for Source Code
Venue: arXiv cs.SE 2020
Year: 2020

Statistical language modeling techniques have successfully been applied to large source code corpora, yielding a variety of new software development tools, such as tools for code suggestion, improving readability, and API migration. A major issue with these techniques is that code introduces new vocabulary at a far higher rate than natural language, as new identifier names proliferate. Both large vocabularies and out-of-vocabulary issues severely affect Neural Language Models (NLMs) of source code, degrading their performance and rendering them unable to scale. In this paper, we address this issue by: 1) studying how various modelling choices impact the resulting vocabulary on a large-scale corpus of 13,362 projects; 2) presenting an open vocabulary source code NLM that can scale to such a corpus, 100 times larger than in previous work; and 3) showing that such models outperform the state of the art on three distinct code corpora (Java, C, Python). To our knowledge, these are the largest NLMs for code that have been reported. All datasets, code, and trained models used in this work are publicly available.
The value of randomized strategies in distributionally robust risk averse network interdiction games
Venue: arXiv cs.GT 2020
Year: 2020

Conditional Value at Risk (CVaR) is widely used to account for the preferences of a risk-averse agent in the extreme loss scenarios. To study the effectiveness of randomization in interdiction games with an interdictor that is both risk and ambiguity averse, we introduce a distributionally robust network interdiction game where the interdictor randomizes over the feasible interdiction plans in order to minimize the worst-case CVaR of the flow with respect to both the unknown distribution of the capacity of the arcs and his mixed strategy over interdicted arcs. The flow player, on the contrary, maximizes the total flow in the network. By using the budgeted uncertainty set, we control the degree of conservatism in the model and reformulate the interdictor's non-linear problem as a bi-convex optimization problem. For solving this problem to any given optimality level, we devise a spatial branch and bound algorithm that uses the McCormick inequalities and reduced reformulation linearization technique (RRLT) to obtain convex relaxation of the problem. We also develop a column generation algorithm to identify the optimal support of the convex relaxation which is then used in the coordinate descent algorithm to determine the upper bounds. The efficiency and convergence of the spatial branch and bound algorithm is established in the numerical experiments. Further, our numerical experiments show that randomized strategies can have significantly better in-sample and out-of-sample performance than optimal deterministic ones.
Getting to 99% Accuracy in Interactive Segmentation
Venue: arXiv cs.CV 2020
Year: 2020

Interactive object cutout tools are the cornerstone of the image editing workflow. Recent deep-learning based interactive segmentation algorithms have made significant progress in handling complex images and rough binary selections can typically be obtained with just a few clicks. Yet, deep learning techniques tend to plateau once this rough selection has been reached. In this work, we interpret this plateau as the inability of current algorithms to sufficiently leverage each user interaction and also as the limitations of current training/testing datasets. We propose a novel interactive architecture and a novel training scheme that are both tailored to better exploit the user workflow. We also show that significant improvements can be further gained by introducing a synthetic training dataset that is specifically designed for complex object boundaries. Comprehensive experiments support our approach, and our network achieves state of the art performance.
Co-Optimizing Performance and Memory FootprintVia Integrated CPU/GPU Memory Management, anImplementation on Autonomous Driving Platform
Venue: arXiv cs.DC 2020
Year: 2020

Cutting-edge embedded system applications, such as self-driving cars and unmanned drone software, are reliant on integrated CPU/GPU platforms for their DNNs-driven workload, such as perception and other highly parallel components. In this work, we set out to explore the hidden performance implication of GPU memory management methods of integrated CPU/GPU architecture. Through a series of experiments on micro-benchmarks and real-world workloads, we find that the performance under different memory management methods may vary according to application characteristics. Based on this observation, we develop a performance model that can predict system overhead for each memory management method based on application characteristics. Guided by the performance model, we further propose a runtime scheduler. By conducting per-task memory management policy switching and kernel overlapping, the scheduler can significantly relieve the system memory pressure and reduce the multitasking co-run response time. We have implemented and extensively evaluated our system prototype on the NVIDIA Jetson TX2, Drive PX2, and Xavier AGX platforms, using both Rodinia benchmark suite and two real-world case studies of drone software and autonomous driving software.
BrazilDAM: A Benchmark dataset for Tailings Dam Detection
Venue: arXiv cs.CV 2020
Year: 2020

In this work we present BrazilDAM, a novel public dataset based on Sentinel-2 and Landsat-8 satellite images covering all tailings dams cataloged by the Brazilian National Mining Agency (ANM). The dataset was built using georeferenced images from 769 dams, recorded between 2016 and 2019. The time series were processed in order to produce cloud free images. The dams contain mining waste from different ore categories and have highly varying shapes, areas and volumes, making BrazilDAM particularly interesting and challenging to be used in machine learning benchmarks. The original catalog contains, besides the dam coordinates, information about: the main ore, constructive method, risk category, and associated potential damage. To evaluate BrazilDAM's predictive potential we performed classification essays using state-of-the-art deep Convolutional Neural Network (CNNs). In the experiments, we achieved an average classification accuracy of 94.11% in tailing dam binary classification task. In addition, others four setups of experiments were made using the complementary information from the original catalog, exhaustively exploiting the capacity of the proposed dataset.