OpenRaiser/Intern-Atlas huggingface dataset:
Reflections on kernelizing and computing unrooted agreement forests
Venue: arXiv cs.DS 2021
Year: 2021

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary phylogenetic trees. This problem is better-known in the literature as the maximum agreement forest problem, where the goal is to partition the two trees into a minimum number of common, non-overlapping subtrees. We have implemented two well-known reduction rules, the subtree and chain reduction, and five more recent, theoretically stronger reduction rules, and compare the reduction achieved with and without the stronger rules. We find that the new rules yield smaller reduced instances and thus have clear practical added value. In many cases they also cause the TBR distance to decrease in a controlled fashion. Next, we compare the achieved reduction to the known worst-case theoretical bounds of 15k-9 and 11k-9 respectively, on the number of leaves of the two reduced trees, where k is the TBR distance, observing in both cases a far larger reduction in practice. As a by-product of our experimental framework we obtain a number of new insights into the actual computation of TBR distance. We find, for example, that very strong lower bounds on TBR distance can be obtained efficiently by randomly sampling certain carefully constructed partitions of the leaf labels, and identify instances which seem particularly challenging to solve exactly. The reduction rules have been implemented within our new solver Tubro which combines kernelization with an Integer Linear Programming (ILP) approach. Tubro also incorporates a number of additional features, such as a cluster reduction and a practical upper-bounding heuristic, and it can leverage combinatorial insights emerging from the proofs of correctness of the reduction rules to simplify the ILP.
One-Shot Learning with Triplet Loss for Vegetation Classification Tasks
Venue: arXiv cs.CV 2021
Year: 2021

Triplet loss function is one of the options that can significantly improve the accuracy of the One-shot Learning tasks. Starting from 2015, many projects use Siamese networks and this kind of loss for face recognition and object classification. In our research, we focused on two tasks related to vegetation. The first one is plant disease detection on 25 classes of five crops (grape, cotton, wheat, cucumbers, and corn). This task is motivated because harvest losses due to diseases is a serious problem for both large farming structures and rural families. The second task is the identification of moss species (5 classes). Mosses are natural bioaccumulators of pollutants; therefore, they are used in environmental monitoring programs. The identification of moss species is an important step in the sample preprocessing. In both tasks, we used self-collected image databases. We tried several deep learning architectures and approaches. Our Siamese network architecture with a triplet loss function and MobileNetV2 as a base network showed the most impressive results in both above-mentioned tasks. The average accuracy for plant disease detection amounted to over 97.8% and 97.6% for moss species classification.
Automatic self-contained calibration of an industrial dual-arm robot with cameras using self-contact, planar constraints, and self-observation
Venue: arXiv cs.RO 2021
Year: 2021

We present a robot kinematic calibration method that combines complementary calibration approaches: self-contact, planar constraints, and self-observation. We analyze the estimation of the end effector parameters, joint offsets of the manipulators, and calibration of the complete kinematic chain (DH parameters). The results are compared with ground truth measurements provided by a laser tracker. Our main findings are: (1) When applying the complementary calibration approaches in isolation, the self-contact approach yields the best and most stable results. (2) All combinations of more than one approach were always superior to using any single approach in terms of calibration errors and the observability of the estimated parameters. Combining more approaches delivers robot parameters that better generalize to the workspace parts not used for the calibration. (3) Sequential calibration, i.e. calibrating cameras first and then robot kinematics, is more effective than simultaneous calibration of all parameters. In real experiments, we employ two industrial manipulators mounted on a common base. The manipulators are equipped with force/torque sensors at their wrists, with two cameras attached to the robot base, and with special end effectors with fiducial markers. We collect a new comprehensive dataset for robot kinematic calibration and make it publicly available. The dataset and its analysis provide quantitative and qualitative insights that go beyond the specific manipulators used in this work and apply to self-contained robot kinematic calibration in general.
Growth rates of modern science: A latent piecewise growth curve approach to model publication numbers from established and new literature databases
Venue: arXiv cs.DL 2021
Year: 2021

Growth of science is a prevalent issue in science of science studies. In recent years, two new bibliographic databases have been introduced which can be used to study growth processes in science from centuries back: Dimensions from Digital Science and Microsoft Academic. In this study, we used publication data from these new databases and added publication data from two established databases (Web of Science from Clarivate Analytics and Scopus from Elsevier) to investigate scientific growth processes from the beginning of the modern science system until today. We estimated regression models that included simultaneously the publication counts from the four databases. The results of the unrestricted growth of science calculations show that the overall growth rate amounts to 4.10% with a doubling time of 17.3 years. As the comparison of various segmented regression models in the current study revealed, the model with five segments fits the publication data best. We demonstrated that these segments with different growth rates can be interpreted very well, since they are related to either phases of economic (e.g., industrialization) and / or political developments (e.g., Second World War). In this study, we additionally analyzed scientific growth in two broad fields (Physical and Technical Sciences as well as Life Sciences) and the relationship of scientific and economic growth in UK. The comparison between the two fields revealed only slight differences. The comparison of the British economic and scientific growth rates showed that the economic growth rate is slightly lower than the scientific growth rate.
Digital rock reconstruction with user-defined properties using conditional generative adversarial networks
Venue: arXiv cs.CV 2021
Year: 2021

Uncertainty is ubiquitous with flow in subsurface rocks because of their inherent heterogeneity and lack of in-situ measurements. To complete uncertainty analysis in a multi-scale manner, it is a prerequisite to provide sufficient rock samples. Even though the advent of digital rock technology offers opportunities to reproduce rocks, it still cannot be utilized to provide massive samples due to its high cost, thus leading to the development of diversified mathematical methods. Among them, two-point statistics (TPS) and multi-point statistics (MPS) are commonly utilized, which feature incorporating low-order and high-order statistical information, respectively. Recently, generative adversarial networks (GANs) are becoming increasingly popular since they can reproduce training images with excellent visual and consequent geologic realism. However, standard GANs can only incorporate information from data, while leaving no interface for user-defined properties, and thus may limit the representativeness of reconstructed samples. In this study, we propose conditional GANs for digital rock reconstruction, aiming to reproduce samples not only similar to the real training data, but also satisfying user-specified properties. In fact, the proposed framework can realize the targets of MPS and TPS simultaneously by incorporating high-order information directly from rock images with the GANs scheme, while preserving low-order counterparts through conditioning. We conduct three reconstruction experiments, and the results demonstrate that rock type, rock porosity, and correlation length can be successfully conditioned to affect the reconstructed rock images. Furthermore, in contrast to existing GANs, the proposed conditioning enables learning of multiple rock types simultaneously, and thus invisibly saves computational cost.
Application-aware Congestion Mitigation for High-Performance Computing Systems
Venue: arXiv cs.DC 2021
Year: 2021

High-performance computing (HPC) systems frequently experience congestion leading to significant application performance variation. However, the impact of congestion on application runtime differs from application to application depending on their network characteristics (such as bandwidth and latency requirements). We leverage this insight to develop Netscope, an automated ML-driven framework that considers those network characteristics to dynamically mitigate congestion. We evaluate Netscope on four Cray Aries systems, including a production supercomputer on real scientific applications. Netscope has a lower training cost and accurately estimates the impact of congestion on application runtime with a correlation between 0.7and 0.9 for common scientific applications. Moreover, we find that Netscope reduces tail runtime variability by up to 14.9 times while improving median system utility by 12%.
A review of on-device fully neural end-to-end automatic speech recognition algorithms
Venue: arXiv cs.LG 2021
Year: 2021

In this paper, we review various end-to-end automatic speech recognition algorithms and their optimization techniques for on-device applications. Conventional speech recognition systems comprise a large number of discrete components such as an acoustic model, a language model, a pronunciation model, a text-normalizer, an inverse-text normalizer, a decoder based on a Weighted Finite State Transducer (WFST), and so on. To obtain sufficiently high speech recognition accuracy with such conventional speech recognition systems, a very large language model (up to 100 GB) is usually needed. Hence, the corresponding WFST size becomes enormous, which prohibits their on-device implementation. Recently, fully neural network end-to-end speech recognition algorithms have been proposed. Examples include speech recognition systems based on Connectionist Temporal Classification (CTC), Recurrent Neural Network Transducer (RNN-T), Attention-based Encoder-Decoder models (AED), Monotonic Chunk-wise Attention (MoChA), transformer-based speech recognition systems, and so on. These fully neural network-based systems require much smaller memory footprints compared to conventional algorithms, therefore their on-device implementation has become feasible. In this paper, we review such end-to-end speech recognition models. We extensively discuss their structures, performance, and advantages compared to conventional algorithms.
Traditional IR rivals neural models on the MS MARCO Document Ranking Leaderboard
Venue: arXiv cs.CL 2021
Year: 2021

This short document describes a traditional IR system that achieved MRR@100 equal to 0.298 on the MS MARCO Document Ranking leaderboard (on 2020-12-06). Although inferior to most BERT-based models, it outperformed several neural runs (as well as all non-neural ones), including two submissions that used a large pretrained Transformer model for re-ranking. We provide software and data to reproduce our results.
Event-based Motion Segmentation with Spatio-Temporal Graph Cuts
Venue: arXiv cs.CV 2021
Year: 2021

Identifying independently moving objects is an essential task for dynamic scene understanding. However, traditional cameras used in dynamic scenes may suffer from motion blur or exposure artifacts due to their sampling principle. By contrast, event-based cameras are novel bio-inspired sensors that offer advantages to overcome such limitations. They report pixelwise intensity changes asynchronously, which enables them to acquire visual information at exactly the same rate as the scene dynamics. We develop a method to identify independently moving objects acquired with an event-based camera, i.e., to solve the event-based motion segmentation problem. We cast the problem as an energy minimization one involving the fitting of multiple motion models. We jointly solve two subproblems, namely event cluster assignment (labeling) and motion model fitting, in an iterative manner by exploiting the structure of the input event data in the form of a spatio-temporal graph. Experiments on available datasets demonstrate the versatility of the method in scenes with different motion patterns and number of moving objects. The evaluation shows state-of-the-art results without having to predetermine the number of expected moving objects. We release the software and dataset under an open source licence to foster research in the emerging topic of event-based motion segmentation.
Container Orchestration on HPC Systems
Venue: arXiv cs.DC 2021
Year: 2021

Containerisation demonstrates its efficiency in application deployment in cloud computing. Containers can encapsulate complex programs with their dependencies in isolated environments, hence are being adopted in HPC clusters. HPC workload managers lack micro-services support and deeply integrated container management, as opposed to container orchestrators (e.g. Kubernetes). We introduce Torque-Operator (a plugin) which serves as a bridge between HPC workload managers and container Orchestrators.
Costs to Consider in Adopting NLP for Your Business
Venue: arXiv cs.CL 2021
Year: 2021

Recent advances in Natural Language Processing (NLP) have largely pushed deep transformer-based models as the go-to state-of-the-art technique without much regard to the production and utilization cost. Companies planning to adopt these methods into their business face difficulties because of the lack of machine, data, and human resources to build them. We compare both the performance and the cost of classical learning algorithms to the latest ones in common sequence and text labeling tasks. In our industrial datasets, we find that classical models often perform on par with deep neural ones despite the lower cost. We show the trade-off between performance gain and the cost across the models to give more insights for AI-pivoting business. Further, we call for more research into low-cost models, especially for under-resourced languages.
Edge (of the Earth) Replication: Optimizing Content Delivery in Large LEO Satellite Communication Networks
Venue: arXiv cs.DC 2021
Year: 2021

Large low earth orbit (LEO) satellite networks such as SpaceX's Starlink constellation promise to deliver low-latency, high-bandwidth Internet access with global coverage. As an alternative to terrestrial fiber as a global Internet backbone, they could potentially serve billions of Internet-connected devices. Currently, operators of CDNs exploit the hierarchical topology of the Internet to place points-of-presence near users, yet this approach is no longer possible when the topology changes to a single, wide-area, converged access and backhaul network. In this paper, we explore the opportunities of points-of-presence for CDNs within the satellite network itself, as it could provide better access latency for users while reducing operational costs for the satellite Internet service providers. We propose four strategies for selecting points-of-presence in satellite constellations that we evaluate through extensive simulation. In one case, we find that replicating web content within satellites can reduce bandwidth use in the constellation by 93% over an approach without replication in the network, while storing just 0.01% of all content in individual satellites.
Secure Degrees-of-Freedom of the MIMO X Channel with Delayed CSIT
Venue: arXiv cs.IT 2021
Year: 2021

In this paper, we study the secure degrees-of-freedom (SDoF) characterization for the multiple-input multiple-output (MIMO) X channel with confidential messages and delayed CSIT. In particular, we propose a transmission scheme, which can be regarded as a generalization of the state-of-the-art scheme without security and with delayed CSIT. The key of this generalization is performing the security analysis, by which we derive the optimal duration of the artificial noise transmission phase. As a result, we derive the sum-SDoF lower bound. Furthermore, we reveal that if the number of receive antennas, denoted by N, is fixed, the minimum number of transmit antennas achieving the maximum of the lower bound is $\frac{7+\sqrt{33}}{8}N$.
Improved StyleGAN Embedding: Where are the Good Latents?
Venue: arXiv cs.CV 2021
Year: 2021

StyleGAN is able to produce photorealistic images that are almost indistinguishable from real photos. The reverse problem of finding an embedding for a given image poses a challenge. Embeddings that reconstruct an image well are not always robust to editing operations. In this paper, we address the problem of finding an embedding that both reconstructs images and also supports image editing tasks. First, we introduce a new normalized space to analyze the diversity and the quality of the reconstructed latent codes. This space can help answer the question of where good latent codes are located in latent space. Second, we propose an improved embedding algorithm using a novel regularization method based on our analysis. Finally, we analyze the quality of different embedding algorithms. We compare our results with the current state-of-the-art methods and achieve a better trade-off between reconstruction quality and editing quality.
You Are What You Tweet: Profiling Users by Past Tweets to Improve Hate Speech Detection
Venue: arXiv cs.CL 2021
Year: 2021

Hate speech detection research has predominantly focused on purely content-based methods, without exploiting any additional context. We briefly critique pros and cons of this task formulation. We then investigate profiling users by their past utterances as an informative prior to better predict whether new utterances constitute hate speech. To evaluate this, we augment three Twitter hate speech datasets with additional timeline data, then embed this additional context into a strong baseline model. Promising results suggest merit for further investigation, though analysis is complicated by differences in annotation schemes and processes, as well as Twitter API limitations and data sharing policies.
Realizing the Promise of Automated Exposure Notification (AEN) Technology to Control the Spread of COVID-19: Recommendations for Smartphone App Deployment, Use, and Iterative Assessment
Venue: arXiv cs.CY 2021
Year: 2021

By using modern cryptographic techniques, privacy-preserving Automated Exposure Notification (AEN) technologies offer the promise of mitigating disease spread by automatically recording contacts between people over the incubation period while maintaining individual data privacy. Today, public health departments in States and other countries around the world are deploying AEN systems at a rapid pace. Though many organizations conducted research prior to deploying apps, experience around the world shows that contact-tracing apps are installed and used at relatively low levels. This whitepaper is intended to provide usable information for States who are considering the deployment of an AEN system, as well as to guide ongoing improvements for States that have already deployed. We outline the human factors considerations related to employing AEN systems with the ultimate goal of controlling the spread of COVID-19, including the GAEN consortium Exposure Notifications (EN) Express tool. We will also provide a practical design and implementation guide for States and others designing and deploying AEN systems, as well as a set of recommendations for assessing deployment of contact tracing apps and targeting areas of concern to improve efficacy of use during and after initial deployment. As a case study, we consider the commercial app deployed by the state of Pennsylvania (PA) and the ongoing efforts to drive user adoption there.
Shape My Face: Registering 3D Face Scans by Surface-to-Surface Translation
Venue: arXiv cs.CV 2021
Year: 2021

Standard registration algorithms need to be independently applied to each surface to register, following careful pre-processing and hand-tuning. Recently, learning-based approaches have emerged that reduce the registration of new scans to running inference with a previously-trained model. In this paper, we cast the registration task as a surface-to-surface translation problem, and design a model to reliably capture the latent geometric information directly from raw 3D face scans. We introduce Shape-My-Face (SMF), a powerful encoder-decoder architecture based on an improved point cloud encoder, a novel visual attention mechanism, graph convolutional decoders with skip connections, and a specialized mouth model that we smoothly integrate with the mesh convolutions. Compared to the previous state-of-the-art learning algorithms for non-rigid registration of face scans, SMF only requires the raw data to be rigidly aligned (with scaling) with a pre-defined face template. Additionally, our model provides topologically-sound meshes with minimal supervision, offers faster training time, has orders of magnitude fewer trainable parameters, is more robust to noise, and can generalize to previously unseen datasets. We extensively evaluate the quality of our registrations on diverse data. We demonstrate the robustness and generalizability of our model with in-the-wild face scans across different modalities, sensor types, and resolutions. Finally, we show that, by learning to register scans, SMF produces a hybrid linear and non-linear morphable model. Manipulation of the latent space of SMF allows for shape generation, and morphing applications such as expression transfer in-the-wild. We train SMF on a dataset of human faces comprising 9 large-scale databases on commodity hardware.
Polyblur: Removing mild blur by polynomial reblurring
Venue: arXiv cs.CV 2021
Year: 2021

We present a highly efficient blind restoration method to remove mild blur in natural images. Contrary to the mainstream, we focus on removing slight blur that is often present, damaging image quality and commonly generated by small out-of-focus, lens blur, or slight camera motion. The proposed algorithm first estimates image blur and then compensates for it by combining multiple applications of the estimated blur in a principled way. To estimate blur we introduce a simple yet robust algorithm based on empirical observations about the distribution of the gradient in sharp natural images. Our experiments show that, in the context of mild blur, the proposed method outperforms traditional and modern blind deblurring methods and runs in a fraction of the time. Our method can be used to blindly correct blur before applying off-the-shelf deep super-resolution methods leading to superior results than other highly complex and computationally demanding techniques. The proposed method estimates and removes mild blur from a 12MP image on a modern mobile phone in a fraction of a second.