OpenRaiser/Intern-Atlas huggingface dataset:
Counterfactual Explanation with Multi-Agent Reinforcement Learning for Drug Target Prediction
Venue: arXiv cs.AI 2021
Year: 2021

Motivation: Many high-performance DTA models have been proposed, but they are mostly black-box and thus lack human interpretability. Explainable AI (XAI) can make DTA models more trustworthy, and can also enable scientists to distill biological knowledge from the models. Counterfactual explanation is one popular approach to explaining the behaviour of a deep neural network, which works by systematically answering the question "How would the model output change if the inputs were changed in this way?". Most counterfactual explanation methods only operate on single input data. It remains an open problem how to extend counterfactual-based XAI methods to DTA models, which have two inputs, one for drug and one for target, that also happen to be discrete in nature. Methods: We propose a multi-agent reinforcement learning framework, Multi-Agent Counterfactual Drug target binding Affinity (MACDA), to generate counterfactual explanations for the drug-protein complex. Our proposed framework provides human-interpretable counterfactual instances while optimizing both the input drug and target for counterfactual generation at the same time. Results: We benchmark the proposed MACDA framework using the Davis dataset and find that our framework produces more parsimonious explanations with no loss in explanation validity, as measured by encoding similarity and QED. We then present a case study involving ABL1 and Nilotinib to demonstrate how MACDA can explain the behaviour of a DTA model in the underlying substructure interaction between inputs in its prediction, revealing mechanisms that align with prior domain knowledge.
Industrial Machine Tool Component Surface Defect Dataset
Venue: arXiv cs.CV 2021
Year: 2021

Using machine learning (ML) techniques in general and deep learning techniques in specific needs a certain amount of data often not available in large quantities in technical domains. The manual inspection of machine tool components and the manual end-of-line check of products are labor-intensive tasks in industrial applications that companies often want to automate. To automate classification processes and develop reliable and robust machine learning-based classification and wear prognostics models, one needs real-world datasets to train and test the models. The dataset is available under https://doi.org/10.5445/IR/1000129520.
Finnish Paraphrase Corpus
Venue: arXiv cs.CL 2021
Year: 2021

In this paper, we introduce the first fully manually annotated paraphrase corpus for Finnish containing 53,572 paraphrase pairs harvested from alternative subtitles and news headings. Out of all paraphrase pairs in our corpus 98% are manually classified to be paraphrases at least in their given context, if not in all contexts. Additionally, we establish a manual candidate selection method and demonstrate its feasibility in high quality paraphrase selection in terms of both cost and quality.
W2WNet: a two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality
Venue: arXiv cs.CV 2021
Year: 2021

Convolutional Neural Networks (CNNs) are supposed to be fed with only high-quality annotated datasets. Nonetheless, in many real-world scenarios, such high quality is very hard to obtain, and datasets may be affected by any sort of image degradation and mislabelling issues. This negatively impacts the performance of standard CNNs, both during the training and the inference phase. To address this issue we propose Wise2WipedNet (W2WNet), a new two-module Convolutional Neural Network, where a Wise module exploits Bayesian inference to identify and discard spurious images during the training, and a Wiped module takes care of the final classification while broadcasting information on the prediction confidence at inference time. The goodness of our solution is demonstrated on a number of public benchmarks addressing different image classification tasks, as well as on a real-world case study on histological image analysis. Overall, our experiments demonstrate that W2WNet is able to identify image degradation and mislabelling issues both at training and at inference time, with a positive impact on the final classification accuracy.
Behavior coordination for self-adaptive robots using constraint-based configuration
Venue: arXiv cs.RO 2021
Year: 2021

Autonomous robots may be able to adapt their behavior in response to changes in the environment. This is useful, for example, to efficiently handle limited resources or to respond appropriately to unexpected events such as faults. The architecture of a self-adaptive robot is complex because it should include automatic mechanisms to dynamically configure the elements that control robot behaviors. To facilitate the construction of this type of architectures, it is useful to have general solutions in the form of software tools that may be applicable to different robotic systems. This paper presents an original algorithm to dynamically configure the control architecture, which is applicable to the development of self-adaptive autonomous robots. This algorithm uses a constraint-based configuration approach to decide which basic robot behaviors should be activated in response to both reactive and deliberative events. The algorithm uses specific search heuristics and initialization procedures to achieve the performance required by robotic systems. The solution has been implemented as a software development tool called Behavior Coordinator CBC (Constraint-Based Configuration), which is based on ROS and open source, available to the general public. This tool has been successfully used for building multiple applications of autonomous aerial robots.
Towards Accommodating Real-time Jobs on HPC Platforms
Venue: arXiv cs.DC 2021
Year: 2021

Increasing data volumes in scientific experiments necessitate the use of high-performance computing (HPC) resources for data analysis. In many scientific fields, the data generated from scientific instruments and supercomputer simulations must be analyzed rapidly. In fact, the requirement for quasi-instant feedback is growing. Scientists want to use results from one experiment to guide the selection of the next or even to improve the course of a single experiment. Current HPC systems are typically batch-scheduled under policies in which an arriving job is run immediately only if enough resources are available; otherwise, it is queued. It is hard for these systems to support real-time jobs. Real-time jobs, in order to meet their requirements, should sometimes have to preempt batch jobs and/or be scheduled ahead of batch jobs that were submitted earlier. Accommodating real-time jobs may negatively impact system utilization also, especially when preemption/restart of batch jobs is involved. We first explore several existing scheduling strategies to make real-time jobs more likely to be scheduled in due time. We then rigorously formulate the problem as a mixed-integer linear programming for offline scheduling and develop novel scheduling heuristics for online scheduling. We perform simulation studies using trace logs of Mira, the IBM BG/Q system at Argonne National Laboratory, to quantify the impact of real-time jobs on batch job performance for various percentages of real-time jobs in the workload. We present new insights gained from grouping jobs into different categories based on runtime and the number of nodes used and studying the performance of each category. Our results show that with 10% real-time job percentages, just-in-time checkpointing combined with our heuristic can improve the slowdowns of real-time jobs by 35% while limiting the increase of the slowdowns of batch jobs to 10%.
Learning Polar Encodings for Arbitrary-Oriented Ship Detection in SAR Images
Venue: arXiv cs.CV 2021
Year: 2021

Common horizontal bounding box (HBB)-based methods are not capable of accurately locating slender ship targets with arbitrary orientations in synthetic aperture radar (SAR) images. Therefore, in recent years, methods based on oriented bounding box (OBB) have gradually received attention from researchers. However, most of the recently proposed deep learning-based methods for OBB detection encounter the boundary discontinuity problem in angle or key point regression. In order to alleviate this problem, researchers propose to introduce some manually set parameters or extra network branches for distinguishing the boundary cases, which make training more diffcult and lead to performance degradation. In this paper, in order to solve the boundary discontinuity problem in OBB regression, we propose to detect SAR ships by learning polar encodings. The encoding scheme uses a group of vectors pointing from the center of the ship target to the boundary points to represent an OBB. The boundary discontinuity problem is avoided by training and inference directly according to the polar encodings. In addition, we propose an Intersect over Union (IOU) -weighted regression loss, which further guides the training of polar encodings through the IOU metric and improves the detection performance. Experiments on the Rotating SAR Ship Detection Dataset (RSSDD) show that the proposed method can achieve better detection performance over other comparison algorithms and other OBB encoding schemes, demonstrating the effectiveness of our method.
End-Effector Stabilization of a 10-DOF Mobile Manipulator using Nonlinear Model Predictive Control
Venue: arXiv cs.RO 2021
Year: 2021

Motion control of mobile manipulators (a robotic arm mounted on a mobile base) can be challenging for complex tasks such as material and package handling. In this paper, a task-space stabilization controller based on Nonlinear Model Predictive Control (NMPC) is designed and implemented to a 10 Degrees of Freedom (DOF) mobile manipulator which consists of a 7-DOF robotic arm and a 3-DOF mobile base. The system model is based on kinematic models where the end-effector orientation is parameterized directly by a rotation matrix. The state and control constraints as well as singularity constraints are explicitly included in the NMPC formulation. The controller is tested using real-time simulations, which demonstrate high positioning accuracy with tractable computational cost.
Exploiting the Unique Expression for Improved Sentiment Analysis in Software Engineering Text
Venue: arXiv cs.SE 2021
Year: 2021

Sentiment analysis on software engineering (SE) texts has been widely used in the SE research, such as evaluating app reviews or analyzing developers sentiments in commit messages. To better support the use of automated sentiment analysis for SE tasks, researchers built an SE-domain-specified sentiment dictionary to further improve the accuracy of the results. Unfortunately, recent work reported that current mainstream tools for sentiment analysis still cannot provide reliable results when analyzing the sentiments in SE texts. We suggest that the reason for this situation is because the way of expressing sentiments in SE texts is largely different from the way in social network or movie comments. In this paper, we propose to improve sentiment analysis in SE texts by using sentence structures, a different perspective from building a domain dictionary. Specifically, we use sentence structures to first identify whether the author is expressing her sentiment in a given clause of an SE text, and to further adjust the calculation of sentiments which are confirmed in the clause. An empirical evaluation based on four different datasets shows that our approach can outperform two dictionary-based baseline approaches, and is more generalizable compared to a learning-based baseline approach.
PureGaze: Purifying Gaze Feature for Generalizable Gaze Estimation
Venue: arXiv cs.CV 2021
Year: 2021

Gaze estimation methods learn eye gaze from facial features. However, among rich information in the facial image, real gaze-relevant features only correspond to subtle changes in eye region, while other gaze-irrelevant features like illumination, personal appearance and even facial expression may affect the learning in an unexpected way. This is a major reason why existing methods show significant performance degradation in cross-domain/dataset evaluation. In this paper, we tackle the cross-domain problem in gaze estimation. Different from common domain adaption methods, we propose a domain generalization method to improve the cross-domain performance without touching target samples. The domain generalization is realized by gaze feature purification. We eliminate gaze-irrelevant factors such as illumination and identity to improve the cross-domain performance. We design a plug-and-play self-adversarial framework for the gaze feature purification. The framework enhances not only our baseline but also existing gaze estimation methods directly and significantly. To the best of our knowledge, we are the first to propose domain generalization methods in gaze estimation. Our method achieves not only state-of-the-art performance among typical gaze estimation methods but also competitive results among domain adaption methods. The code is released in https://github.com/yihuacheng/PureGaze.
Multimode piezoelectric shunt damping of thin plates with arrays of separately shunted patches, method, and experimental validation
Venue: arXiv cs.CG 2021
Year: 2021

Two-dimensional thin plates are widely used in many applications. Shunt damping is a promising way for the attenuation of vibration of these electromechanical systems. It enables a compact vibration damping method without adding significant mass and volumetric occupancy. Analyzing the dynamics of such electromechanical systems requires precise modeling tools that properly consider the coupling between the piezoelectric elements and the host structure. Although the concept of shunt damping has been studied extensively in the literature, most of the studies do not provide a formulation for modeling the multiple piezoelectric patches that are scattered on the host structure and shunted separately. This paper presents a methodology and a formulation for separately shunted piezoelectric patches for achieving higher performance on vibration attenuation. The Rayleigh-Ritz method is used for performing modal analysis and obtaining the frequency response functions of the electro-mechanical system. The developed model includes mass and stiffness contribution of the piezoelectric patches as well as the electromechanical coupling effect. In this study, the piezoelectric patches are shunted via separate electrical circuits and compared with the ones those are shunted via interconnected electrical circuits. For verification, system-level finite element simulations are performed in ANSYS software and compared with the analytical model results. An experimental setup is also built to validate the performance of the separately shunted piezoelectric patches. The effectiveness of the method is investigated for a broader range of frequencies and it was shown that separately shunted piezoelectric patches are more effective compared to connected for a wide range of frequencies.
Transfer Learning for Piano Sustain-Pedal Detection
Venue: arXiv cs.SD 2021
Year: 2021

Detecting piano pedalling techniques in polyphonic music remains a challenging task in music information retrieval. While other piano-related tasks, such as pitch estimation and onset detection, have seen improvement through applying deep learning methods, little work has been done to develop deep learning models to detect playing techniques. In this paper, we propose a transfer learning approach for the detection of sustain-pedal techniques, which are commonly used by pianists to enrich the sound. In the source task, a convolutional neural network (CNN) is trained for learning spectral and temporal contexts when the sustain pedal is pressed using a large dataset generated by a physical modelling virtual instrument. The CNN is designed and experimented through exploiting the knowledge of piano acoustics and physics. This can achieve an accuracy score of 0.98 in the validation results. In the target task, the knowledge learned from the synthesised data can be transferred to detect the sustain pedal in acoustic piano recordings. A concatenated feature vector using the activations of the trained convolutional layers is extracted from the recordings and classified into frame-wise pedal press or release. We demonstrate the effectiveness of our method in acoustic piano recordings of Chopin's music. From the cross-validation results, the proposed transfer learning method achieves an average F-measure of 0.89 and an overall performance of 0.84 obtained using the micro-averaged F-measure. These results outperform applying the pre-trained CNN model directly or the model with a fine-tuned last layer.
Pole-like Objects Mapping and Long-Term Robot Localization in Dynamic Urban Scenarios
Venue: arXiv cs.RO 2021
Year: 2021

Localization on 3D data is a challenging task for unmanned vehicles, especially in long-term dynamic urban scenarios. Due to the generality and long-term stability, the pole-like objects are very suitable as landmarks for unmanned vehicle localization in time-varing scenarios. In this paper, a long-term LiDAR-only localization algorithm based on semantic cluster map is proposed. At first, the Convolutional Neural Network(CNN) is used to infer the semantics of LiDAR point clouds. Combined with the point cloud segmentation, the long-term static objects pole/trunk in the scene are extracted and registered into a semantic cluster map. When the unmanned vehicle re-enters the environment again, the relocalization is completed by matching the clusters of the local map with the clusters of the global map. Furthermore, the continuous matching between the local and global maps stably outputs the global pose at 2Hz to correct the drift of the 3D LiDAR odometry. The proposed approach realizes localization in the long-term scenarios without maintaining the high-precision point cloud map. The experimental results on our campus dataset demonstrate that the proposed approach performs better in localization accuracy compared with the current state-of-the-art methods. The source of this paper is available at: http://www.github.com/HITSZ-NRSL/long-term-localization.
FastMoE: A Fast Mixture-of-Expert Training System
Venue: arXiv cs.LG 2021
Year: 2021

Mixture-of-Expert (MoE) presents a strong potential in enlarging the size of language model to trillions of parameters. However, training trillion-scale MoE requires algorithm and system co-design for a well-tuned high performance distributed training system. Unfortunately, the only existing platform that meets the requirements strongly depends on Google's hardware (TPU) and software (Mesh Tensorflow) stack, and is not open and available to the public, especially GPU and PyTorch communities. In this paper, we present FastMoE, a distributed MoE training system based on PyTorch with common accelerators. The system provides a hierarchical interface for both flexible model design and easy adaption to different applications, such as Transformer-XL and Megatron-LM. Different from direct implementation of MoE models using PyTorch, the training speed is highly optimized in FastMoE by sophisticated high-performance acceleration skills. The system supports placing different experts on multiple GPUs across multiple nodes, enabling enlarging the number of experts linearly against the number of GPUs. The source of FastMoE is available at https://github.com/laekov/fastmoe under Apache-2 license.
Model Independent Error Bound Estimation for Conformance Checking Approximation
Venue: arXiv cs.SE 2021
Year: 2021

Conformance checking techniques allow us to quantify the correspondence of a process's execution, captured in event data, w.r.t., a reference process model. In this context, alignments have proven to be useful for calculating conformance statistics. However, for extensive event data and complex process models, the computation time of alignments is considerably high, hampering their practical use. Simultaneously, it suffices to approximate either alignments or their corresponding conformance value(s) for many applications. Recent work has shown that using subsets of the process model behavior leads to accurate conformance approximations. The accuracy of such an approximation heavily depends on the selected subset of model behavior. Thus, in this paper, we show that we can derive a priori error bounds for conformance checking approximation based on arbitrary activity sequences, independently of the given process model. Such error bounds subsequently let us select the most relevant subset of process model behavior for the alignment approximation. Experiments confirm that conformance approximation accuracy improves when using the proposed error bound approximation to guide the selection of relevant subsets of process model behavior.
I Know What You Would Like to Drink: Benefits and Detriments of Sharing Personal Info with a Bartender Robot
Venue: arXiv cs.RO 2021
Year: 2021

This paper introduces benefits and detriments of a robot bartender that is capable of adapting the interaction with human users according to their preferences in drinks, music, and hobbies. We believe that a personalised experience during a human-robot interaction increases the human user's engagement with the robot and that such information will be used by the robot during the interaction. However, this implies that the users need to share several personal information with the robot. In this paper, we introduce the research topic and our approach to evaluate people's perceptions and consideration of their privacy with a robot. We present a within-subject study in which participants interacted twice with a robot that firstly had not any previous info about the users, and, then, having a knowledge of their preferences. We observed that less than 60\% of the participants were not concerned about sharing personal information with the robot.
Bag of Tricks for Node Classification with Graph Neural Networks
Venue: arXiv cs.LG 2021
Year: 2021

Over the past few years, graph neural networks (GNN) and label propagation-based methods have made significant progress in addressing node classification tasks on graphs. However, in addition to their reliance on elaborate architectures and algorithms, there are several key technical details that are frequently overlooked, and yet nonetheless can play a vital role in achieving satisfactory performance. In this paper, we first summarize a series of existing tricks-of-the-trade, and then propose several new ones related to label usage, loss function formulation, and model design that can significantly improve various GNN architectures. We empirically evaluate their impact on final node classification accuracy by conducting ablation studies and demonstrate consistently-improved performance, often to an extent that outweighs the gains from more dramatic changes in the underlying GNN architecture. Notably, many of the top-ranked models on the Open Graph Benchmark (OGB) leaderboard and KDDCUP 2021 Large-Scale Challenge MAG240M-LSC benefit from these techniques we initiated.