OpenRaiser/Intern-Atlas huggingface dataset:
Improving scalability and reliability of MPI-agnostic transparent checkpointing for production workloads at NERSC
Venue: arXiv cs.DC 2021
Year: 2021

Checkpoint/restart (C/R) provides fault-tolerant computing capability, enables long running applications, and provides scheduling flexibility for computing centers to support diverse workloads with different priority. It is therefore vital to get transparent C/R capability working at NERSC. MANA, by Garg et. al., is a transparent checkpointing tool that has been selected due to its MPI-agnostic and network-agnostic approach. However, originally written as a proof-of-concept code, MANA was not ready to use with NERSC's diverse production workloads, which are dominated by MPI and hybrid MPI+OpenMP applications. In this talk, we present ongoing work at NERSC to enable MANA for NERSC's production workloads, including fixing bugs that were exposed by the top applications at NERSC, adding new features to address system changes, evaluating C/R overhead at scale, etc. The lessons learned from making MANA production-ready for HPC applications will be useful for C/R tool developers, supercomputing centers and HPC end-users alike.
Efficient Intrusion Detection Using Evidence Theory
Venue: arXiv cs.LG 2021
Year: 2021

Intrusion Detection Systems (IDS) are now an essential element when it comes to securing computers and networks. Despite the huge research efforts done in the field, handling sources' reliability remains an open issue. To address this problem, this paper proposes a novel contextual discounting method based on sources' reliability and their distinguishing ability between normal and abnormal behavior. Dempster-Shafer theory, a general framework for reasoning under uncertainty, is used to construct an evidential classifier. The NSL-KDD dataset, a significantly revised and improved version of the existing KDDCUP'99 dataset, provides the basis for assessing the performance of our new detection approach. While giving comparable results on the KDDTest+ dataset, our approach outperformed some other state-of-the-art methods on the KDDTest-21 dataset which is more challenging.
Does Code Review Promote Conformance? A Study of OpenStack Patches
Venue: arXiv cs.SE 2021
Year: 2021

Code Review plays a crucial role in software quality, by allowing reviewers to discuss and critique any new patches before they can be successfully integrated into the project code. Yet, it is unsure the extent to which coding pattern changes (i.e., repetitive code) from when a patch is first submitted and when the decision is made (i.e., during the review process). In this study, we revisit coding patterns in code reviews, aiming to analyze whether or not the coding pattern changes during the review process. Comparing prior submitted patches, we measure differences in coding pattern between pre-review~(i.e., patch before the review) and post-review~(i.e., patch after a review) from 27,736 reviewed OpenStack patches. Results show that patches after review, tend to conform to similar coding patterns of accepted patches, compared to when they were first submitted. We also find that accepted patches do have similar coding patterns to prior accepted patches. Our study reveals insights into the review process, supporting the potential for automated tool support for newcomers and lays the groundwork for work into understanding conformance and how it makes for an efficient code review process.
Deep learning of material transport in complex neurite networks
Venue: arXiv cs.CE 2021
Year: 2021

Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for modeling the material transport process via solving partial differential equations (PDEs), they require long computation time and huge computation resources to ensure accurate geometry representation and solution, thus limit their biomedical application. Here we present a graph neural network (GNN)-based deep learning model to learn the IGA-based material transport simulation and provide fast material concentration prediction within neurite networks of any topology. Given input boundary conditions and geometry configurations, the well-trained model can predict the dynamical concentration change during the transport process with an average error less than 10% and 120~330 times faster compared to IGA simulations. The effectiveness of the proposed model is demonstrated within several complex neurite networks.
dNNsolve: an efficient NN-based PDE solver
Venue: arXiv cs.LG 2021
Year: 2021

Neural Networks (NNs) can be used to solve Ordinary and Partial Differential Equations (ODEs and PDEs) by redefining the question as an optimization problem. The objective function to be optimized is the sum of the squares of the PDE to be solved and of the initial/boundary conditions. A feed forward NN is trained to minimise this loss function evaluated on a set of collocation points sampled from the domain where the problem is defined. A compact and smooth solution, that only depends on the weights of the trained NN, is then obtained. This approach is often referred to as PINN, from Physics Informed Neural Network~\cite{raissi2017physics_1, raissi2017physics_2}. Despite the success of the PINN approach in solving various classes of PDEs, an implementation of this idea that is capable of solving a large class of ODEs and PDEs with good accuracy and without the need to finely tune the hyperparameters of the network, is not available yet. In this paper, we introduce a new implementation of this concept - called dNNsolve - that makes use of dual Neural Networks to solve ODEs/PDEs. These include: i) sine and sigmoidal activation functions, that provide a more efficient basis to capture both secular and periodic patterns in the solutions; ii) a newly designed architecture, that makes it easy for the the NN to approximate the solution using the basis functions mentioned above. We show that dNNsolve is capable of solving a broad range of ODEs/PDEs in 1, 2 and 3 spacetime dimensions, without the need of hyperparameter fine-tuning.
System Component-Level Self-Adaptations for Security via Bayesian Games
Venue: arXiv cs.AI 2021
Year: 2021

Security attacks present unique challenges to self-adaptive system design due to the adversarial nature of the environment. However, modeling the system as a single player, as done in prior works in security domain, is insufficient for the system under partial compromise and for the design of fine-grained defensive strategies where the rest of the system with autonomy can cooperate to mitigate the impact of attacks. To deal with such issues, we propose a new self-adaptive framework incorporating Bayesian game and model the defender (i.e., the system) at the granularity of components in system architecture. The system architecture model is translated into a Bayesian multi-player game, where each component is modeled as an independent player while security attacks are encoded as variant types for the components. The defensive strategy for the system is dynamically computed by solving the pure equilibrium to achieve the best possible system utility, improving the resiliency of the system against security attacks.
Self-Adaptive Microservice-based Systems -- Landscape and Research Opportunities
Venue: arXiv cs.SE 2021
Year: 2021

Microservices have become popular in the past few years, attracting the interest of both academia and industry. Despite of its benefits, this new architectural style still poses important challenges, such as resilience, performance and evolution. Self-adaptation techniques have been applied recently as an alternative to solve or mitigate those problems. However, due to the range of quality attributes that affect microservice architectures, many different self-adaptation strategies can be used. Thus, to understand the state-of-the-art of the use of self-adaptation techniques and mechanisms in microservice-based systems, this work conducted a systematic mapping, in which 21 primary studies were analyzed considering qualitative and quantitative research questions. The results show that most studies focus on the Monitor phase (28.57%) of the adaptation control loop, address the self-healing property (23.81%), apply a reactive adaptation strategy (80.95%) in the system infrastructure level (47.62%) and use a centralized approach (38.10%). From those, it was possible to propose some research directions to fill existing gaps.
Multi-task learning for virtual flow metering
Venue: arXiv cs.LG 2021
Year: 2021

Virtual flow metering (VFM) is a cost-effective and non-intrusive technology for inferring multiphase flow rates in petroleum assets. Inferences about flow rates are fundamental to decision support systems that operators extensively rely on. Data-driven VFM, where mechanistic models are replaced with machine learning models, has recently gained attention due to its promise of lower maintenance costs. While excellent performances in small sample studies have been reported in the literature, there is still considerable doubt about the robustness of data-driven VFM. In this paper, we propose a new multi-task learning (MTL) architecture for data-driven VFM. Our method differs from previous methods in that it enables learning across oil and gas wells. We study the method by modeling 55 wells from four petroleum assets and compare the results with two single-task baseline models. Our findings show that MTL improves robustness over single-task methods, without sacrificing performance. MTL yields a 25-50% error reduction on average for the assets where single-task architectures are struggling.
The Complexity of Checking Partial Total Positivity
Venue: arXiv cs.CC 2021
Year: 2021

We prove that checking if a partial matrix is partial totally positive is co-NP-complete. This contrasts with checking a conventional matrix for total positivity, for which we provide a cubic time algorithm. Checking partial sign regularity with any signature, including partial total nonnegativity, is also co-NP-complete. Finally, we prove that checking partial total positivity in a partial matrix with logarithmically many unspecified entries may be done in polynomial time.
Fairness and Transparency in Recommendation: The Users' Perspective
Venue: arXiv cs.IR 2021
Year: 2021

Though recommender systems are defined by personalization, recent work has shown the importance of additional, beyond-accuracy objectives, such as fairness. Because users often expect their recommendations to be purely personalized, these new algorithmic objectives must be communicated transparently in a fairness-aware recommender system. While explanation has a long history in recommender systems research, there has been little work that attempts to explain systems that use a fairness objective. Even though the previous work in other branches of AI has explored the use of explanations as a tool to increase fairness, this work has not been focused on recommendation. Here, we consider user perspectives of fairness-aware recommender systems and techniques for enhancing their transparency. We describe the results of an exploratory interview study that investigates user perceptions of fairness, recommender systems, and fairness-aware objectives. We propose three features -- informed by the needs of our participants -- that could improve user understanding of and trust in fairness-aware recommender systems.
Skeleton Aware Multi-modal Sign Language Recognition
Venue: arXiv cs.CV 2021
Year: 2021

Sign language is commonly used by deaf or speech impaired people to communicate but requires significant effort to master. Sign Language Recognition (SLR) aims to bridge the gap between sign language users and others by recognizing signs from given videos. It is an essential yet challenging task since sign language is performed with the fast and complex movement of hand gestures, body posture, and even facial expressions. Recently, skeleton-based action recognition attracts increasing attention due to the independence between the subject and background variation. However, skeleton-based SLR is still under exploration due to the lack of annotations on hand keypoints. Some efforts have been made to use hand detectors with pose estimators to extract hand key points and learn to recognize sign language via Neural Networks, but none of them outperforms RGB-based methods. To this end, we propose a novel Skeleton Aware Multi-modal SLR framework (SAM-SLR) to take advantage of multi-modal information towards a higher recognition rate. Specifically, we propose a Sign Language Graph Convolution Network (SL-GCN) to model the embedded dynamics and a novel Separable Spatial-Temporal Convolution Network (SSTCN) to exploit skeleton features. RGB and depth modalities are also incorporated and assembled into our framework to provide global information that is complementary to the skeleton-based methods SL-GCN and SSTCN. As a result, SAM-SLR achieves the highest performance in both RGB (98.42\%) and RGB-D (98.53\%) tracks in 2021 Looking at People Large Scale Signer Independent Isolated SLR Challenge. Our code is available at https://github.com/jackyjsy/CVPR21Chal-SLR
Adversarial YOLO: Defense Human Detection Patch Attacks via Detecting Adversarial Patches
Venue: arXiv cs.CV 2021
Year: 2021

The security of object detection systems has attracted increasing attention, especially when facing adversarial patch attacks. Since patch attacks change the pixels in a restricted area on objects, they are easy to implement in the physical world, especially for attacking human detection systems. The existing defenses against patch attacks are mostly applied for image classification problems and have difficulty resisting human detection attacks. Towards this critical issue, we propose an efficient and effective plug-in defense component on the YOLO detection system, which we name Ad-YOLO. The main idea is to add a patch class on the YOLO architecture, which has a negligible inference increment. Thus, Ad-YOLO is expected to directly detect both the objects of interest and adversarial patches. To the best of our knowledge, our approach is the first defense strategy against human detection attacks. We investigate Ad-YOLO's performance on the YOLOv2 baseline. To improve the ability of Ad-YOLO to detect variety patches, we first use an adversarial training process to develop a patch dataset based on the Inria dataset, which we name Inria-Patch. Then, we train Ad-YOLO by a combination of Pascal VOC, Inria, and Inria-Patch datasets. With a slight drop of $0.70\%$ mAP on VOC 2007 test set, Ad-YOLO achieves $80.31\%$ AP of persons, which highly outperforms $33.93\%$ AP for YOLOv2 when facing white-box patch attacks. Furthermore, compared with YOLOv2, the results facing a physical-world attack are also included to demonstrate Ad-YOLO's excellent generalization ability.
A New Autoregressive Neural Network Model with Command Compensation for Imitation Learning Based on Bilateral Control
Venue: arXiv cs.RO 2021
Year: 2021

In the near future, robots are expected to work with humans or operate alone and may replace human workers in various fields such as homes and factories. In a previous study, we proposed bilateral control-based imitation learning that enables robots to utilize force information and operate almost simultaneously with an expert's demonstration. In addition, we recently proposed an autoregressive neural network model (SM2SM) for bilateral control-based imitation learning to obtain long-term inferences. In the SM2SM model, both master and slave states must be input, but the master states are obtained from the previous outputs of the SM2SM model, resulting in destabilized estimation under large environmental variations. Hence, a new autoregressive neural network model (S2SM) is proposed in this study. This model requires only the slave state as input and its outputs are the next slave and master states, thereby improving the task success rates. In addition, a new feedback controller that utilizes the error between the responses and estimates of the slave is proposed, which shows better reproducibility.
Distributed Deep Learning Using Volunteer Computing-Like Paradigm
Venue: arXiv cs.DC 2021
Year: 2021

Use of Deep Learning (DL) in commercial applications such as image classification, sentiment analysis and speech recognition is increasing. When training DL models with large number of parameters and/or large datasets, cost and speed of training can become prohibitive. Distributed DL training solutions that split a training job into subtasks and execute them over multiple nodes can decrease training time. However, the cost of current solutions, built predominantly for cluster computing systems, can still be an issue. In contrast to cluster computing systems, Volunteer Computing (VC) systems can lower the cost of computing, but applications running on VC systems have to handle fault tolerance, variable network latency and heterogeneity of compute nodes, and the current solutions are not designed to do so. We design a distributed solution that can run DL training on a VC system by using a data parallel approach. We implement a novel asynchronous SGD scheme called VC-ASGD suited for VC systems. In contrast to traditional VC systems that lower cost by using untrustworthy volunteer devices, we lower cost by leveraging preemptible computing instances on commercial cloud platforms. By using preemptible instances that require applications to be fault tolerant, we lower cost by 70-90% and improve data security.
Two tales of science technology linkage: Patent in-text versus front-page references
Venue: arXiv cs.DL 2021
Year: 2021

There is recurrent debate about how useful science is for technological development, but we know little about what kinds of science are more useful for technology. This paper fills this gap in the literature by exploring how the value of a patent (as measured by patent forward citations and the stock market response to the issuing of the patent) depends on the characteristics of the scientific papers that it builds on, specifically, basicness, interdisciplinarity, novelty, and scientific citations. Using a dataset of 33,337 USPTO biotech utility patents and their 860,879 in-text references to Web of Science journal articles, we find (1) a positive effect of the number of referenced scientific papers, (2) an inverted U-shaped effect of basicness, (3) an insignificant effect of interdisciplinarity, (4) a discontinuous and nonlinear effect of novelty, and (5) a positive effect of scientific citations for patent market value but an insignificant effect on patent citations. In addition, in-text referenced papers have a higher chance of being listed on the front-page of the same patent when they are moderately basic, less interdisciplinary, less novel, and more highly cited. Accordingly, using front-page reference yields substantially different results than using in-text references.
Wait-free approximate agreement on graphs
Venue: arXiv cs.DC 2021
Year: 2021

Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a vertex of the graph as input and, if non-faulty, must output a vertex such that - all the outputs are within distance 1 of one another, and - each output value lies on a shortest path between two input values. From prior work, it is known that there is no wait-free algorithm among $n \ge 3$ processes for this problem on any cycle of length $c \ge 4$, by reduction from 2-set agreement (Castañeda et al., 2018). In this work, we investigate the solvability and complexity of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length $c \ge 4$, via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on on these graphs is unsolvable. Furthermore, we show that combinatorial arguments, used by both existing proofs, are necessary, by showing that the impossibility of a wait-free algorithm in the nonuniform iterated snapshot model cannot be proved via an extension-based proof. On the positive side, we present a wait-free algorithm for a class of graphs that properly contains the class of chordal graphs.
Generating Interpretable Counterfactual Explanations By Implicit Minimisation of Epistemic and Aleatoric Uncertainties
Venue: arXiv cs.LG 2021
Year: 2021

Counterfactual explanations (CEs) are a practical tool for demonstrating why machine learning classifiers make particular decisions. For CEs to be useful, it is important that they are easy for users to interpret. Existing methods for generating interpretable CEs rely on auxiliary generative models, which may not be suitable for complex datasets, and incur engineering overhead. We introduce a simple and fast method for generating interpretable CEs in a white-box setting without an auxiliary model, by using the predictive uncertainty of the classifier. Our experiments show that our proposed algorithm generates more interpretable CEs, according to IM1 scores, than existing methods. Additionally, our approach allows us to estimate the uncertainty of a CE, which may be important in safety-critical applications, such as those in the medical domain.
Coordinate Constructions in English Enhanced Universal Dependencies: Analysis and Computational Modeling
Venue: arXiv cs.CL 2021
Year: 2021

In this paper, we address the representation of coordinate constructions in Enhanced Universal Dependencies (UD), where relevant dependency links are propagated from conjunction heads to other conjuncts. English treebanks for enhanced UD have been created from gold basic dependencies using a heuristic rule-based converter, which propagates only core arguments. With the aim of determining which set of links should be propagated from a semantic perspective, we create a large-scale dataset of manually edited syntax graphs. We identify several systematic errors in the original data, and propose to also propagate adjuncts. We observe high inter-annotator agreement for this semantic annotation task. Using our new manually verified dataset, we perform the first principled comparison of rule-based and (partially novel) machine-learning based methods for conjunction propagation for English. We show that learning propagation rules is more effective than hand-designing heuristic rules. When using automatic parses, our neural graph-parser based edge predictor outperforms the currently predominant pipelinesusing a basic-layer tree parser plus converters.
Fast Development of ASR in African Languages using Self Supervised Speech Representation Learning
Venue: arXiv cs.SD 2021
Year: 2021

This paper describes the results of an informal collaboration launched during the African Master of Machine Intelligence (AMMI) in June 2020. After a series of lectures and labs on speech data collection using mobile applications and on self-supervised representation learning from speech, a small group of students and the lecturer continued working on automatic speech recognition (ASR) project for three languages: Wolof, Ga, and Somali. This paper describes how data was collected and ASR systems developed with a small amount (1h) of transcribed speech as training data. In these low resource conditions, pre-training a model on large amounts of raw speech was fundamental for the efficiency of ASR systems developed.