OpenRaiser/Intern-Atlas huggingface dataset:
Ab-initio Contrast Estimation and Denoising of Cryo-EM Images
Venue: arXiv cs.CV 2022
Year: 2022

Background and Objective: The contrast of cryo-EM images varies from one to another, primarily due to the uneven thickness of the ice layer. This contrast variation can affect the quality of 2-D class averaging, 3-D ab-initio modeling, and 3-D heterogeneity analysis. Contrast estimation is currently performed during 3-D iterative refinement. As a result, the estimates are not available at the earlier computational stages of class averaging and ab-initio modeling. This paper aims to solve the contrast estimation problem directly from the picked particle images in the ab-initio stage, without estimating the 3-D volume, image rotations, or class averages. Methods: The key observation underlying our analysis is that the 2-D covariance matrix of the raw images is related to the covariance of the underlying clean images, the noise variance, and the contrast variability between images. We show that the contrast variability can be derived from the 2-D covariance matrix and we apply the existing Covariance Wiener Filtering (CWF) framework to estimate it. We also demonstrate a modification of CWF to estimate the contrast of individual images. Results: Our method improves the contrast estimation by a large margin, compared to the previous CWF method. Its estimation accuracy is often comparable to that of an oracle that knows the ground truth covariance of the clean images. The more accurate contrast estimation also improves the quality of image restoration as demonstrated in both synthetic and experimental datasets. Conclusions: This paper proposes an effective method for contrast estimation directly from noisy images without using any 3-D volume information. It enables contrast correction in the earlier stage of single particle analysis, and may improve the accuracy of downstream processing.
Attracting and Retaining OSS Contributors with a Maintainer Dashboard
Venue: arXiv cs.SE 2022
Year: 2022

Tools and artifacts produced by open source software (OSS) have been woven into the foundation of the technology industry. To keep this foundation intact, the open source community needs to actively invest in sustainable approaches to bring in new contributors and nurture existing ones. We take a first step at this by collaboratively designing a maintainer dashboard that provides recommendations on how to attract and retain open source contributors. For example, by highlighting project goals (e.g., a social good cause) to attract diverse contributors and mechanisms to acknowledge (e.g., a "rising contributor" badge) existing contributors. Next, we conduct a project-specific evaluation with maintainers to better understand use cases in which this tool will be most helpful at supporting their plans for growth. From analyzing feedback, we find recommendations to be useful at signaling projects as welcoming and providing gentle nudges for maintainers to proactively recognize emerging contributors. However, there are complexities to consider when designing recommendations such as the project current development state (e.g., deadlines, milestones, refactoring) and governance model. Finally, we distill our findings to share what the future of recommendations in open source looks like and how to make these recommendations most meaningful over time.
Safe Reinforcement Learning by Imagining the Near Future
Venue: arXiv cs.LG 2022
Year: 2022

Safe reinforcement learning is a promising path toward applying reinforcement learning algorithms to real-world problems, where suboptimal behaviors may lead to actual negative consequences. In this work, we focus on the setting where unsafe states can be avoided by planning ahead a short time into the future. In this setting, a model-based agent with a sufficiently accurate model can avoid unsafe states. We devise a model-based algorithm that heavily penalizes unsafe trajectories, and derive guarantees that our algorithm can avoid unsafe states under certain assumptions. Experiments demonstrate that our algorithm can achieve competitive rewards with fewer safety violations in several continuous control tasks.
Not All Patches are What You Need: Expediting Vision Transformers via Token Reorganizations
Venue: arXiv cs.CV 2022
Year: 2022

Vision Transformers (ViTs) take all the image patches as tokens and construct multi-head self-attention (MHSA) among them. Complete leverage of these image tokens brings redundant computations since not all the tokens are attentive in MHSA. Examples include that tokens containing semantically meaningless or distractive image backgrounds do not positively contribute to the ViT predictions. In this work, we propose to reorganize image tokens during the feed-forward process of ViT models, which is integrated into ViT during training. For each forward inference, we identify the attentive image tokens between MHSA and FFN (i.e., feed-forward network) modules, which is guided by the corresponding class token attention. Then, we reorganize image tokens by preserving attentive image tokens and fusing inattentive ones to expedite subsequent MHSA and FFN computations. To this end, our method EViT improves ViTs from two perspectives. First, under the same amount of input image tokens, our method reduces MHSA and FFN computation for efficient inference. For instance, the inference speed of DeiT-S is increased by 50% while its recognition accuracy is decreased by only 0.3% for ImageNet classification. Second, by maintaining the same computational cost, our method empowers ViTs to take more image tokens as input for recognition accuracy improvement, where the image tokens are from higher resolution images. An example is that we improve the recognition accuracy of DeiT-S by 1% for ImageNet classification at the same computational cost of a vanilla DeiT-S. Meanwhile, our method does not introduce more parameters to ViTs. Experiments on the standard benchmarks show the effectiveness of our method. The code is available at https://github.com/youweiliang/evit
An efficient distributed scheduling algorithm for relay-assisted mmWave backhaul networks
Venue: arXiv cs.NI 2022
Year: 2022

In this paper, a novel distributed scheduling algorithm is proposed, which aims to efficiently schedule both the uplink and downlink backhaul traffic in the relay-assisted mmWave backhaul network with a tree topology. The handshaking of control messages, calculation of local schedules, and the determination of final valid schedule are all discussed. Simulation results show that the performance of the distributed algorithm can reach very close to the maximum traffic demand of the backhaul network, and it can also adapt to the dynamic traffic with sharp traffic demand change of small-cell BSs quickly and accurately.
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications
Venue: arXiv cs.LG 2022
Year: 2022

Pretrained Language Models (PLMs) such as BERT have revolutionized the landscape of Natural Language Processing (NLP). Inspired by their proliferation, tremendous efforts have been devoted to Pretrained Graph Models (PGMs). Owing to the powerful model architectures of PGMs, abundant knowledge from massive labeled and unlabeled graph data can be captured. The knowledge implicitly encoded in model parameters can benefit various downstream tasks and help to alleviate several fundamental issues of learning on graphs. In this paper, we provide the first comprehensive survey for PGMs. We firstly present the limitations of graph representation learning and thus introduce the motivation for graph pre-training. Then, we systematically categorize existing PGMs based on a taxonomy from four different perspectives. Next, we present the applications of PGMs in social recommendation and drug discovery. Finally, we outline several promising research directions that can serve as a guideline for future research.
Aryl: An Elastic Cluster Scheduler for Deep Learning
Venue: arXiv cs.DC 2022
Year: 2022

Companies build separate training and inference GPU clusters for deep learning, and use separate schedulers to manage them. This leads to problems for both training and inference: inference clusters have low GPU utilization when the traffic load is low; training jobs often experience long queueing time due to lack of resources. We introduce Aryl, a new cluster scheduler to address these problems. Aryl introduces capacity loaning to loan idle inference GPU servers for training jobs. It further exploits elastic scaling that scales a training job's GPU allocation to better utilize loaned resources. Capacity loaning and elastic scaling create new challenges to cluster management. When the loaned servers need to be returned, we need to minimize the number of job preemptions; when more GPUs become available, we need to allocate them to elastic jobs and minimize the job completion time (JCT). Aryl addresses these combinatorial problems using principled heuristics. It introduces the notion of server preemption cost which it greedily reduces during server reclaiming. It further relies on the JCT reduction value defined for each additional worker for an elastic job to solve the scheduling problem as a multiple-choice knapsack problem. Prototype implementation on a 64-GPU testbed and large-scale simulation with 15-day traces of over 50,000 production jobs show that Aryl brings 1.53x and 1.50x reductions in average queuing time and JCT, and improves cluster usage by up to 26.9% over the cluster scheduler without capacity loaning or elastic scaling.
Error Floor Analysis of Irregular Repetition ALOHA
Venue: arXiv cs.IT 2022
Year: 2022

With the rapid expansion of the Internet of Things, the efficient sharing of the wireless medium by a large amount of simple transmitters is becoming essential. Scheduling-based solutions are inefficient for this setting, where small data units are broadcast sporadically by terminals that most of the time are idle. Modern random access has embraced the challenge and provides suitable slot-synchronous and asynchronous multiple access solutions based on replicating the packets and exploiting successive interference cancellation (SIC) at the receiver. In this work, we focus on asynchronous modern random access. Specifically, we derive an analytical approximation of the performance of irregular repetition ALOHA (IRA) in the so-called error floor region. Numerical results show the tightness of the derived approximation under various scenarios.
Energy Efficiency in Rate-Splitting Multiple Access with Mixed Criticality
Venue: arXiv cs.IT 2022
Year: 2022

Future sixth generation (6G) wireless communication networks face the need to similarly meet unprecedented quality of service (QoS) demands while also providing a larger energy efficiency (EE) to minimize their carbon footprint. Moreover, due to the diverseness of network participants, mixed criticality QoS levels are assigned to the users of such networks. In this work, with a focus on a cloud-radio access network (C-RAN), the fulfillment of desired QoS and minimized transmit power use is optimized jointly within a rate-splitting paradigm. Thereby, the optimization problem is non-convex. Hence, a low-complexity algorithm is proposed based on fractional programming. Numerical results validate that there is a trade-off between the QoS fulfillment and power minimization. Moreover, the energy efficiency of the proposed rate-splitting algorithm is larger than in comparative schemes, especially with mixed criticality.
TimeREISE: Time-series Randomized Evolving Input Sample Explanation
Venue: arXiv cs.LG 2022
Year: 2022

Deep neural networks are one of the most successful classifiers across different domains. However, due to their limitations concerning interpretability their use is limited in safety critical context. The research field of explainable artificial intelligence addresses this problem. However, most of the interpretability methods are aligned to the image modality by design. The paper introduces TimeREISE a model agnostic attribution method specifically aligned to success in the context of time series classification. The method shows superior performance compared to existing approaches concerning different well-established measurements. TimeREISE is applicable to any time series classification network, its runtime does not scale in a linear manner concerning the input shape and it does not rely on prior data knowledge.
Unified smoke and fire detection in an evolutionary framework with self-supervised progressive data augment
Venue: arXiv cs.CV 2022
Year: 2022

Few researches have studied simultaneous detection of smoke and flame accompanying fires due to their different physical natures that lead to uncertain fluid patterns. In this study, we collect a large image data set to re-label them as a multi-label image classification problem so as to identify smoke and flame simultaneously. In order to solve the generalization ability of the detection model on account of the movable fluid objects with uncertain shapes like fire and smoke, and their not compactible natures as well as the complex backgrounds with high variations, we propose a data augment method by random image stitch to deploy resizing, deforming, position variation, and background altering so as to enlarge the view of the learner. Moreover, we propose a self-learning data augment method by using the class activation map to extract the highly trustable region as new data source of positive examples to further enhance the data augment. By the mutual reinforcement between the data augment and the detection model that are performed iteratively, both modules make progress in an evolutionary manner. Experiments show that the proposed method can effectively improve the generalization performance of the model for concurrent smoke and fire detection.
HDC-MiniROCKET: Explicit Time Encoding in Time Series Classification with Hyperdimensional Computing
Venue: arXiv cs.LG 2022
Year: 2022

Classification of time series data is an important task for many application domains. One of the best existing methods for this task, in terms of accuracy and computation time, is MiniROCKET. In this work, we extend this approach to provide better global temporal encodings using hyperdimensional computing (HDC) mechanisms. HDC (also known as Vector Symbolic Architectures, VSA) is a general method to explicitly represent and process information in high-dimensional vectors. It has previously been used successfully in combination with deep neural networks and other signal processing algorithms. We argue that the internal high-dimensional representation of MiniROCKET is well suited to be complemented by the algebra of HDC. This leads to a more general formulation, HDC-MiniROCKET, where the original algorithm is only a special case. We will discuss and demonstrate that HDC-MiniROCKET can systematically overcome catastrophic failures of MiniROCKET on simple synthetic datasets. These results are confirmed by experiments on the 128 datasets from the UCR time series classification benchmark. The extension with HDC can achieve considerably better results on datasets with high temporal dependence without increasing the computational effort for inference.
NeVerMore: Exploiting RDMA Mistakes in NVMe-oF Storage Applications
Venue: arXiv cs.CR 2022
Year: 2022

This paper presents a security analysis of the InfiniBand architecture, a prevalent RDMA standard, and NVMe-over-Fabrics (NVMe-oF), a prominent protocol for industrial disaggregated storage that exploits RDMA protocols to achieve low-latency and high-bandwidth access to remote solid-state devices. Our work, NeVerMore, discovers new vulnerabilities in RDMA protocols that unveils several attack vectors on RDMA-enabled applications and the NVMe-oF protocol, showing that the current security mechanisms of the NVMe-oF protocol do not address the security vulnerabilities posed by the use of RDMA. In particular, we show how an unprivileged user can inject packets into any RDMA connection created on a local network controller, bypassing security mechanisms of the operating system and its kernel, and how the injection can be used to acquire unauthorized block access to NVMe-oF devices. Overall, we implement four attacks on RDMA protocols and seven attacks on the NVMe-oF protocol and verify them on the two most popular implementations of NVMe-oF: SPDK and the Linux kernel. To mitigate the discovered attacks we propose multiple mechanisms that can be implemented by RDMA and NVMe-oF providers.
Sparse Polynomial Interpolation and Division in Soft-linear Time
Venue: arXiv cs.SC 2022
Year: 2022

Given a way to evaluate an unknown polynomial with integer coefficients, we present new algorithms to recover its nonzero coefficients and corresponding exponents. As an application, we adapt this interpolation algorithm to the problem of computing the exact quotient of two given polynomials. These methods are efficient in terms of the bit-length of the sparse representation, that is, the number of nonzero terms, the size of coefficients, the number of variables, and the logarithm of the degree. At the core of our results is a new Monte Carlo randomized algorithm to recover a polynomial $f(x)$ with integer coefficients given a way to evaluate $f(θ) \bmod m$ for any chosen integers $θ$ and $m$. This algorithm has nearly-optimal bit complexity, meaning that the total bit-length of the probes, as well as the computational running time, is softly linear (ignoring logarithmic factors) in the bit-length of the resulting sparse polynomial. To our knowledge, this is the first sparse interpolation algorithm with soft-linear bit complexity in the total output size. For polynomials with integer coefficients, the best previously known results have at least a cubic dependency on the bit-length of the exponents.
XFBoost: Improving Text Generation with Controllable Decoders
Venue: arXiv cs.CL 2022
Year: 2022

Multimodal conditionality in transformer-based natural language models has demonstrated state-of-the-art performance in the task of product description generation. Recent approaches condition a language model on one or more images and other textual metadata to achieve near-human performance for describing products from e-commerce stores. However, generated descriptions may exhibit degrees of inaccuracy or even contradictory claims relative to the inputs of a given product. In this paper, we propose a controllable language generation framework called Extract-Finetune-Boost (XFBoost), which addresses the problem of inaccurate low-quality inference. By using visual semantic attributes as constraints at the decoding stage of the generation process and finetuning the language model with policy gradient techniques, the XFBoost framework is found to produce significantly more descriptive text with higher image relevancy, outperforming baselines and lowering the frequency of factually inaccurate descriptions. We further demonstrate the application of XFBoost to online learning wherein human-in-the-loop critics improve language models with active feedback.
GrADyS-SIM -- A OMNET++/INET simulation framework for Internet of Flying things
Venue: arXiv cs.NI 2022
Year: 2022

This technical report describes GrADyS-SIM, a framework for simulating cooperating swarms of UAVs in joint mission in hypothetical landscape and communicating through RF radios. The framework was created to aid and verify the communication, coordination and context-awareness protocols being developed in the GrADyS project. GrADyS-SIM uses the OMNeT++ simulation library and its INET model suite and and allows for addition of modified or customized versions of some simulated components, network configurations and vehicle coordination, so that new coordination protocols can be developed and tested through the framework. The framework simulates UAV movement dictated by file containing some MAVLink instructions and affected on the fly by different network situations. The UAV swarm coordination protocol emerges from individual interactions between UAVs and has the objective of optimizing the collection of sensor data over an area. It also allows for the simulation of some types of failures to test the protocol adaptability. Every node in the simulation is highly configurable making testing different network opographies, coordination protocols, node hardware configurations and more a quick task.
The Adversarial Security Mitigations of mmWave Beamforming Prediction Models using Defensive Distillation and Adversarial Retraining
Venue: arXiv cs.CR 2022
Year: 2022

The design of a security scheme for beamforming prediction is critical for next-generation wireless networks (5G, 6G, and beyond). However, there is no consensus about protecting the beamforming prediction using deep learning algorithms in these networks. This paper presents the security vulnerabilities in deep learning for beamforming prediction using deep neural networks (DNNs) in 6G wireless networks, which treats the beamforming prediction as a multi-output regression problem. It is indicated that the initial DNN model is vulnerable against adversarial attacks, such as Fast Gradient Sign Method (FGSM), Basic Iterative Method (BIM), Projected Gradient Descent (PGD), and Momentum Iterative Method (MIM), because the initial DNN model is sensitive to the perturbations of the adversarial samples of the training data. This study also offers two mitigation methods, such as adversarial training and defensive distillation, for adversarial attacks against artificial intelligence (AI)-based models used in the millimeter-wave (mmWave) beamforming prediction. Furthermore, the proposed scheme can be used in situations where the data are corrupted due to the adversarial examples in the training data. Experimental results show that the proposed methods effectively defend the DNN models against adversarial attacks in next-generation wireless networks.
"Way back then": A Data-driven View of 25+ years of Web Evolution
Venue: arXiv cs.CY 2022
Year: 2022

Since the inception of the first web page three decades back, the Web has evolved considerably, from static HTML pages in the beginning to the dynamic web pages of today, from mainly the text-based pages of the 1990s to today's multimedia rich pages, etc. Although much of this is known anecdotally, to our knowledge, there is no quantitative documentation of the extent and timing of these changes. This paper attempts to address this gap in the literature by looking at the top 100 Alexa websites for over 25 years from the Internet Archive or the "Wayback Machine", archive.org. We study the changes in popularity, from Geocities and Yahoo! in the mid-to-late 1990s to the likes of Google, Facebook, and Tiktok of today. We also look at different categories of websites and their popularity over the years and find evidence for the decline in popularity of news and education-related websites, which have been replaced by streaming media and social networking sites. We explore the emergence and relative prevalence of different MIME-types (text vs. image vs. video vs. javascript and json) and study whether the use of text on the Internet is declining.
The learning phases in NN: From Fitting the Majority to Fitting a Few
Venue: arXiv cs.LG 2022
Year: 2022

The learning dynamics of deep neural networks are subject to controversy. Using the information bottleneck (IB) theory separate fitting and compression phases have been put forward but have since been heavily debated. We approach learning dynamics by analyzing a layer's reconstruction ability of the input and prediction performance based on the evolution of parameters during training. We show that a prototyping phase decreasing reconstruction loss initially, followed by reducing classification loss of a few samples, which increases reconstruction loss, exists under mild assumptions on the data. Aside from providing a mathematical analysis of single layer classification networks, we also assess the behavior using common datasets and architectures from computer vision such as ResNet and VGG.