OpenRaiser/Intern-Atlas huggingface dataset:
A Hierarchical Block Distance Model for Ultra Low-Dimensional Graph Representations
Venue: arXiv cs.SI 2023
Year: 2023

Graph Representation Learning (GRL) has become central for characterizing structures of complex networks and performing tasks such as link prediction, node classification, network reconstruction, and community detection. Whereas numerous generative GRL models have been proposed, many approaches have prohibitive computational requirements hampering large-scale network analysis, fewer are able to explicitly account for structure emerging at multiple scales, and only a few explicitly respect important network properties such as homophily and transitivity. This paper proposes a novel scalable graph representation learning method named the Hierarchical Block Distance Model (HBDM). The HBDM imposes a multiscale block structure akin to stochastic block modeling (SBM) and accounts for homophily and transitivity by accurately approximating the latent distance model (LDM) throughout the inferred hierarchy. The HBDM naturally accommodates unipartite, directed, and bipartite networks whereas the hierarchy is designed to ensure linearithmic time and space complexity enabling the analysis of very large-scale networks. We evaluate the performance of the HBDM on massive networks consisting of millions of nodes. Importantly, we find that the proposed HBDM framework significantly outperforms recent scalable approaches in all considered downstream tasks. Surprisingly, we observe superior performance even imposing ultra-low two-dimensional embeddings facilitating accurate direct and hierarchical-aware network visualization and interpretation.
LDPC codes: comparing cluster graphs to factor graphs
Venue: arXiv cs.IT 2023
Year: 2023

We present a comparison study between a cluster and factor graph representation of LDPC codes. In probabilistic graphical models, cluster graphs retain useful dependence between random variables during inference, which are advantageous in terms of computational cost, convergence speed, and accuracy of marginal probabilities. This study investigates these benefits in the context of LDPC codes and shows that a cluster graph representation outperforms the traditional factor graph representation.
Visual-Inertial Odometry with Online Calibration of Velocity-Control Based Kinematic Motion Models
Venue: arXiv cs.CV 2023
Year: 2023

Visual-inertial odometry (VIO) is an important technology for autonomous robots with power and payload constraints. In this paper, we propose a novel approach for VIO with stereo cameras which integrates and calibrates the velocity-control based kinematic motion model of wheeled mobile robots online. Including such a motion model can help to improve the accuracy of VIO. Compared to several previous approaches proposed to integrate wheel odometer measurements for this purpose, our method does not require wheel encoders and can be applied when the robot motion can be modeled with velocity-control based kinematic motion model. We use radial basis function (RBF) kernels to compensate for the time delay and deviations between control commands and actual robot motion. The motion model is calibrated online by the VIO system and can be used as a forward model for motion control and planning. We evaluate our approach with data obtained in variously sized indoor environments, demonstrate improvements over a pure VIO method, and evaluate the prediction accuracy of the online calibrated model.
Methods for Efficient Unfolding of Colored Petri Nets
Venue: arXiv cs.LO 2023
Year: 2023

Colored Petri nets offer a compact and user friendly representation of the traditional P/T nets and colored nets with finite color ranges can be unfolded into the underlying P/T nets, however, at the expense of an exponential explosion in size. We present two novel techniques based on static analysis in order to reduce the size of unfolded colored nets. The first method identifies colors that behave equivalently and groups them into equivalence classes, potentially reducing the number of used colors. The second method overapproximates the sets of colors that can appear in places and excludes colors that can never be present in a given place. Both methods are complementary and the combined approach allows us to significantly reduce the size of multiple colored Petri nets from the Model Checking Contest benchmark. We compare the performance of our unfolder with state-of-the-art techniques implemented in the tools MCC, Spike and ITS-Tools, and while our approach is competitive w.r.t. unfolding time, it also outperforms the existing approaches both in the size of unfolded nets as well as in the number of answered model checking queries from the 2021 Model Checking Contest.
Learning and controlling the source-filter representation of speech with a variational autoencoder
Venue: arXiv cs.SD 2023
Year: 2023

Understanding and controlling latent representations in deep generative models is a challenging yet important problem for analyzing, transforming and generating various types of data. In speech processing, inspiring from the anatomical mechanisms of phonation, the source-filter model considers that speech signals are produced from a few independent and physically meaningful continuous latent factors, among which the fundamental frequency $f_0$ and the formants are of primary importance. In this work, we start from a variational autoencoder (VAE) trained in an unsupervised manner on a large dataset of unlabeled natural speech signals, and we show that the source-filter model of speech production naturally arises as orthogonal subspaces of the VAE latent space. Using only a few seconds of labeled speech signals generated with an artificial speech synthesizer, we propose a method to identify the latent subspaces encoding $f_0$ and the first three formant frequencies, we show that these subspaces are orthogonal, and based on this orthogonality, we develop a method to accurately and independently control the source-filter speech factors within the latent subspaces. Without requiring additional information such as text or human-labeled data, this results in a deep generative model of speech spectrograms that is conditioned on $f_0$ and the formant frequencies, and which is applied to the transformation speech signals. Finally, we also propose a robust $f_0$ estimation method that exploits the projection of a speech signal onto the learned latent subspace associated with $f_0$.
The Importance of Credo in Multiagent Learning
Venue: arXiv cs.AI 2023
Year: 2023

We propose a model for multi-objective optimization, a credo, for agents in a system that are configured into multiple groups (i.e., teams). Our model of credo regulates how agents optimize their behavior for the groups they belong to. We evaluate credo in the context of challenging social dilemmas with reinforcement learning agents. Our results indicate that the interests of teammates, or the entire system, are not required to be fully aligned for achieving globally beneficial outcomes. We identify two scenarios without full common interest that achieve high equality and significantly higher mean population rewards compared to when the interests of all agents are aligned.
Conditional Injective Flows for Bayesian Imaging
Venue: arXiv cs.LG 2023
Year: 2023

Most deep learning models for computational imaging regress a single reconstructed image. In practice, however, ill-posedness, nonlinearity, model mismatch, and noise often conspire to make such point estimates misleading or insufficient. The Bayesian approach models images and (noisy) measurements as jointly distributed random vectors and aims to approximate the posterior distribution of unknowns. Recent variational inference methods based on conditional normalizing flows are a promising alternative to traditional MCMC methods, but they come with drawbacks: excessive memory and compute demands for moderate to high resolution images and underwhelming performance on hard nonlinear problems. In this work, we propose C-Trumpets -- conditional injective flows specifically designed for imaging problems, which greatly diminish these challenges. Injectivity reduces memory footprint and training time while low-dimensional latent space together with architectural innovations like fixed-volume-change layers and skip-connection revnet layers, C-Trumpets outperform regular conditional flow models on a variety of imaging and image restoration tasks, including limited-view CT and nonlinear inverse scattering, with a lower compute and memory budget. C-Trumpets enable fast approximation of point estimates like MMSE or MAP as well as physically-meaningful uncertainty quantification.
Efficient Bayesian Policy Reuse with a Scalable Observation Model in Deep Reinforcement Learning
Venue: arXiv cs.LG 2023
Year: 2023

Bayesian policy reuse (BPR) is a general policy transfer framework for selecting a source policy from an offline library by inferring the task belief based on some observation signals and a trained observation model. In this paper, we propose an improved BPR method to achieve more efficient policy transfer in deep reinforcement learning (DRL). First, most BPR algorithms use the episodic return as the observation signal that contains limited information and cannot be obtained until the end of an episode. Instead, we employ the state transition sample, which is informative and instantaneous, as the observation signal for faster and more accurate task inference. Second, BPR algorithms usually require numerous samples to estimate the probability distribution of the tabular-based observation model, which may be expensive and even infeasible to learn and maintain, especially when using the state transition sample as the signal. Hence, we propose a scalable observation model based on fitting state transition functions of source tasks from only a small number of samples, which can generalize to any signals observed in the target task. Moreover, we extend the offline-mode BPR to the continual learning setting by expanding the scalable observation model in a plug-and-play fashion, which can avoid negative transfer when faced with new unknown tasks. Experimental results show that our method can consistently facilitate faster and more efficient policy transfer.
VSA: Learning Varied-Size Window Attention in Vision Transformers
Venue: arXiv cs.CV 2023
Year: 2023

Attention within windows has been widely explored in vision transformers to balance the performance, computation complexity, and memory footprint. However, current models adopt a hand-crafted fixed-size window design, which restricts their capacity of modeling long-term dependencies and adapting to objects of different sizes. To address this drawback, we propose \textbf{V}aried-\textbf{S}ize Window \textbf{A}ttention (VSA) to learn adaptive window configurations from data. Specifically, based on the tokens within each default window, VSA employs a window regression module to predict the size and location of the target window, i.e., the attention area where the key and value tokens are sampled. By adopting VSA independently for each attention head, it can model long-term dependencies, capture rich context from diverse windows, and promote information exchange among overlapped windows. VSA is an easy-to-implement module that can replace the window attention in state-of-the-art representative models with minor modifications and negligible extra computational cost while improving their performance by a large margin, e.g., 1.1\% for Swin-T on ImageNet classification. In addition, the performance gain increases when using larger images for training and test. Experimental results on more downstream tasks, including object detection, instance segmentation, and semantic segmentation, further demonstrate the superiority of VSA over the vanilla window attention in dealing with objects of different sizes. The code will be released https://github.com/ViTAE-Transformer/ViTAE-VSA.
A Comprehensive Survey on Trustworthy Graph Neural Networks: Privacy, Robustness, Fairness, and Explainability
Venue: arXiv cs.LG 2023
Year: 2023

Graph Neural Networks (GNNs) have made rapid developments in the recent years. Due to their great ability in modeling graph-structured data, GNNs are vastly used in various applications, including high-stakes scenarios such as financial analysis, traffic predictions, and drug discovery. Despite their great potential in benefiting humans in the real world, recent study shows that GNNs can leak private information, are vulnerable to adversarial attacks, can inherit and magnify societal bias from training data and lack interpretability, which have risk of causing unintentional harm to the users and society. For example, existing works demonstrate that attackers can fool the GNNs to give the outcome they desire with unnoticeable perturbation on training graph. GNNs trained on social networks may embed the discrimination in their decision process, strengthening the undesirable societal bias. Consequently, trustworthy GNNs in various aspects are emerging to prevent the harm from GNN models and increase the users' trust in GNNs. In this paper, we give a comprehensive survey of GNNs in the computational aspects of privacy, robustness, fairness, and explainability. For each aspect, we give the taxonomy of the related methods and formulate the general frameworks for the multiple categories of trustworthy GNNs. We also discuss the future research directions of each aspect and connections between these aspects to help achieve trustworthiness.
Pre-training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding
Venue: arXiv cs.CE 2023
Year: 2023

The latest biological findings observe that the traditional motionless 'lock-and-key' theory is not generally applicable because the receptor and ligand are constantly moving. Nonetheless, remarkable changes in associated atomic sites and binding pose can provide vital information in understanding the process of drug binding. Based on this mechanism, molecular dynamics (MD) simulations were invented as a useful tool for investigating the dynamic properties of a molecular system. However, the computational expenditure limits the growth and application of protein trajectory-related studies, thus hindering the possibility of supervised learning. To tackle this obstacle, we present a novel spatial-temporal pre-training method based on the modified Equivariant Graph Matching Networks (EGMN), dubbed ProtMD, which has two specially designed self-supervised learning tasks: an atom-level prompt-based denoising generative task and a conformation-level snapshot ordering task to seize the flexibility information inside MD trajectories with very fine temporal resolutions. The ProtMD can grant the encoder network the capacity to capture the time-dependent geometric mobility of conformations along MD trajectories. Two downstream tasks are chosen, i.e., the binding affinity prediction and the ligand efficacy prediction, to verify the effectiveness of ProtMD through linear detection and task-specific fine-tuning. We observe a huge improvement from current state-of-the-art methods, with a decrease of 4.3% in RMSE for the binding affinity problem and an average increase of 13.8% in AUROC and AUPRC for the ligand efficacy problem. The results demonstrate valuable insight into a strong correlation between the magnitude of conformation's motion in the 3D space (i.e., flexibility) and the strength with which the ligand binds with its receptor.
ROI: A method for identifying organizations receiving personal data
Venue: arXiv cs.CR 2023
Year: 2023

Many studies have exposed the massive collection of personal data in the digital ecosystem through, for instance, websites, mobile apps, or smart devices. This fact goes unnoticed by most users, who are also unaware that the collectors are sharing their personal data with many different organizations around the globe. This paper assesses techniques available in the state of the art to identify the organizations receiving this personal data. Based on our findings, we propose ROI (Receiver Organization Identifier), a fully automated method that combines different techniques to achieve a 95.71% precision score in identifying an organization receiving personal data. We demonstrate our method in the wild by evaluating 10,000 Android apps and exposing the organizations that receive users' personal data.
BliMe: Verifiably Secure Outsourced Computation with Hardware-Enforced Taint Tracking
Venue: arXiv cs.CR 2023
Year: 2023

Outsourced computing is widely used today. However, current approaches for protecting client data in outsourced computing fall short: use of cryptographic techniques like fully-homomorphic encryption incurs substantial costs, whereas use of hardware-assisted trusted execution environments has been shown to be vulnerable to run-time and side-channel attacks. We present Blinded Memory (BliMe), an architecture to realize efficient and secure outsourced computation. BliMe consists of a novel and minimal set of instruction set architecture (ISA) extensions implementing a taint-tracking policy to ensure the confidentiality of client data even in the presence of server vulnerabilities. To secure outsourced computation, the BliMe extensions can be used together with an attestable, fixed-function hardware security module (HSM) and an encryption engine that provides atomic decrypt-and-taint and encrypt-and-untaint operations. Clients rely on remote attestation and key agreement with the HSM to ensure that their data can be transferred securely to and from the encryption engine and will always be protected by BliMe's taint-tracking policy while at the server. We provide an RTL implementation BliMe-BOOM based on the BOOM RISC-V core. BliMe-BOOM requires no reduction in clock frequency relative to unmodified BOOM, and has minimal power ($<\!1.5\%$) and FPGA resource ($\leq\!9.0\%$) overheads. Various implementations of BliMe incur only moderate performance overhead ($8--25\%$). We also provide a machine-checked security proof of a simplified model ISA with BliMe extensions.
An Attention-Based Model for Predicting Contextual Informativeness and Curriculum Learning Applications
Venue: arXiv cs.CL 2023
Year: 2023

Both humans and machines learn the meaning of unknown words through contextual information in a sentence, but not all contexts are equally helpful for learning. We introduce an effective method for capturing the level of contextual informativeness with respect to a given target word. Our study makes three main contributions. First, we develop models for estimating contextual informativeness, focusing on the instructional aspect of sentences. Our attention-based approach using pre-trained embeddings demonstrates state-of-the-art performance on our single-context dataset and an existing multi-sentence context dataset. Second, we show how our model identifies key contextual elements in a sentence that are likely to contribute most to a reader's understanding of the target word. Third, we examine how our contextual informativeness model, originally developed for vocabulary learning applications for students, can be used for developing better training curricula for word embedding models in batch learning and few-shot machine learning settings. We believe our results open new possibilities for applications that support language learning for both human and machine learners.
INSPIRE: Distributed Bayesian Optimization for ImproviNg SPatIal REuse in Dense WLANs
Venue: arXiv cs.NI 2023
Year: 2023

WLANs, which have overtaken wired networks to become the primary means of connecting devices to the Internet, are prone to performance issues due to the scarcity of space in the radio spectrum. As a response, IEEE 802.11ax and subsequent amendments aim at increasing the spatial reuse of a radio channel by allowing the dynamic update of two key parameters in wireless transmission: the transmission power (TX_POWER) and the sensitivity threshold (OBSS_PD). In this paper, we present INSPIRE, a distributed solution performing local Bayesian optimizations based on Gaussian processes to improve the spatial reuse in WLANs. INSPIRE makes no explicit assumptions about the topology of WLANs and favors altruistic behaviors of the access points, leading them to find adequate configurations of their TX_POWER and OBSS_PD parameters for the "greater good" of the WLANs. We demonstrate the superiority of INSPIRE over other state-of-the-art strategies using the ns-3 simulator and two examples inspired by real-life deployments of dense WLANs. Our results show that, in only a few seconds, INSPIRE is able to drastically increase the quality of service of operational WLANs by improving their fairness and throughput.
Message Flow Analysis with Complex Causal Links for Distributed ROS 2 Systems
Venue: arXiv cs.RO 2023
Year: 2023

Distributed robotic systems rely heavily on the publish-subscribe communication paradigm and middleware frameworks that support it, such as the Robot Operating System (ROS), to efficiently implement modular computation graphs. The ROS 2 executor, a high-level task scheduler which handles ROS 2 messages, is a performance bottleneck. We extend ros2_tracing, a framework with instrumentation and tools for real-time tracing of ROS 2, with the analysis and visualization of the flow of messages across distributed ROS 2 systems. Our method detects one-to-many and many-to-many causal links between input and output messages, including indirect causal links through simple user-level annotations. We validate our method on both synthetic and real robotic systems, and demonstrate its low runtime overhead. Moreover, the underlying intermediate execution representation database can be further leveraged to extract additional metrics and high-level results. This can provide valuable timing and scheduling information to further study and improve the ROS 2 executor as well as optimize any ROS 2 system. The source code is available at: https://github.com/christophebedard/ros2-message-flow-analysis.
A Hierarchical N-Gram Framework for Zero-Shot Link Prediction
Venue: arXiv cs.CL 2023
Year: 2023

Due to the incompleteness of knowledge graphs (KGs), zero-shot link prediction (ZSLP) which aims to predict unobserved relations in KGs has attracted recent interest from researchers. A common solution is to use textual features of relations (e.g., surface name or textual descriptions) as auxiliary information to bridge the gap between seen and unseen relations. Current approaches learn an embedding for each word token in the text. These methods lack robustness as they suffer from the out-of-vocabulary (OOV) problem. Meanwhile, models built on character n-grams have the capability of generating expressive representations for OOV words. Thus, in this paper, we propose a Hierarchical N-Gram framework for Zero-Shot Link Prediction (HNZSLP), which considers the dependencies among character n-grams of the relation surface name for ZSLP. Our approach works by first constructing a hierarchical n-gram graph on the surface name to model the organizational structure of n-grams that leads to the surface name. A GramTransformer, based on the Transformer is then presented to model the hierarchical n-gram graph to construct the relation embedding for ZSLP. Experimental results show the proposed HNZSLP achieved state-of-the-art performance on two ZSLP datasets.