OpenRaiser/Intern-Atlas huggingface dataset:
Can pruning improve certified robustness of neural networks?
Venue: arXiv cs.LG 2022
Year: 2022

With the rapid development of deep learning, the sizes of neural networks become larger and larger so that the training and inference often overwhelm the hardware resources. Given the fact that neural networks are often over-parameterized, one effective way to reduce such computational overhead is neural network pruning, by removing redundant parameters from trained neural networks. It has been recently observed that pruning can not only reduce computational overhead but also can improve empirical robustness of deep neural networks (NNs), potentially owing to removing spurious correlations while preserving the predictive accuracies. This paper for the first time demonstrates that pruning can generally improve certified robustness for ReLU-based NNs under the complete verification setting. Using the popular Branch-and-Bound (BaB) framework, we find that pruning can enhance the estimated bound tightness of certified robustness verification, by alleviating linear relaxation and sub-domain split problems. We empirically verify our findings with off-the-shelf pruning methods and further present a new stability-based pruning method tailored for reducing neuron instability, that outperforms existing pruning methods in enhancing certified robustness. Our experiments show that by appropriately pruning an NN, its certified accuracy can be boosted up to 8.2% under standard training, and up to 24.5% under adversarial training on the CIFAR10 dataset. We additionally observe the existence of certified lottery tickets that can match both standard and certified robust accuracies of the original dense models across different datasets. Our findings offer a new angle to study the intriguing interaction between sparsity and robustness, i.e. interpreting the interaction of sparsity and certified robustness via neuron stability. Codes are available at: https://github.com/VITA-Group/CertifiedPruning.
Modern Machine-Learning Predictive Models for Diagnosing Infectious Diseases
Venue: arXiv cs.LG 2022
Year: 2022

Controlling infectious diseases is a major health priority because they can spread and infect humans, thus evolving into epidemics or pandemics. Therefore, early detection of infectious diseases is a significant need, and many researchers have developed models to diagnose them in the early stages. This paper reviewed research articles for recent machine-learning (ML) algorithms applied to infectious disease diagnosis. We searched the Web of Science, ScienceDirect, PubMed, Springer, and IEEE databases from 2015 to 2022, identified the pros and cons of the reviewed ML models, and discussed the possible recommendations to advance the studies in this field. We found that most of the articles used small datasets, and few of them used real-time data. Our results demonstrated that a suitable ML technique depends on the nature of the dataset and the desired goal.
Knowledge4COVID-19: A Semantic-based Approach for Constructing a COVID-19 related Knowledge Graph from Various Sources and Analysing Treatments' Toxicities
Venue: arXiv cs.DB 2022
Year: 2022

In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug-drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the declarative definition of mapping rules using the RDF Mapping Language. Since valuable information about drug treatments, drug-drug interactions, and side effects is present in textual descriptions in scientific databases (e.g., DrugBank) or in scientific literature (e.g., the CORD-19, the Covid-19 Open Research Dataset), the Knowledge4COVID-19 framework implements Natural Language Processing. The Knowledge4COVID-19 framework extracts relevant entities and predicates that enable the fine-grained description of COVID-19 treatments and the potential adverse events that may occur when these treatments are combined with treatments of common comorbidities, e.g., hypertension, diabetes, or asthma. Moreover, on top of the KG, several techniques for the discovery and prediction of interactions and potential adverse effects of drugs have been developed with the aim of suggesting more accurate treatments for treating the virus. We provide services to traverse the KG and visualize the effects that a group of drugs may have on a treatment outcome. Knowledge4COVID-19 was part of the Pan-European hackathon#EUvsVirus in April 2020 and is publicly available as a resource through a GitHub repository (https://github.com/SDM-TIB/Knowledge4COVID-19) and a DOI (https://zenodo.org/record/4701817#.YH336-8zbol).
Estimating Confidence of Predictions of Individual Classifiers and Their Ensembles for the Genre Classification Task
Venue: arXiv cs.CL 2022
Year: 2022

Genre identification is a subclass of non-topical text classification. The main difference between this task and topical classification is that genres, unlike topics, usually do not correspond to simple keywords, and thus they need to be defined in terms of their functions in communication. Neural models based on pre-trained transformers, such as BERT or XLM-RoBERTa, demonstrate SOTA results in many NLP tasks, including non-topical classification. However, in many cases, their downstream application to very large corpora, such as those extracted from social media, can lead to unreliable results because of dataset shifts, when some raw texts do not match the profile of the training set. To mitigate this problem, we experiment with individual models as well as with their ensembles. To evaluate the robustness of all models we use a prediction confidence metric, which estimates the reliability of a prediction in the absence of a gold standard label. We can evaluate robustness via the confidence gap between the correctly classified texts and the misclassified ones on a labeled test corpus, higher gaps make it easier to improve our confidence that our classifier made the right decision. Our results show that for all of the classifiers tested in this study, there is a confidence gap, but for the ensembles, the gap is bigger, meaning that ensembles are more robust than their individual models.
Collaboration Effect by Co-Authorship on Academic Citation and Social Attention of Research
Venue: arXiv cs.DL 2022
Year: 2022

Academic citation and social attention measure different dimensions of the impact of research results. Both measures do not correlate with each other, and they are influenced by many factors. Among these factors are the field of research, the type of access, and co-authorship. In this study, the increase in the impact due to co-authorship in scientific articles disaggregated by field of research and access type, was quantified. For this, the citations and social attention accumulated until the year 2021 by a total of 244,880 research articles published in the year 2018, were analyzed. The data source was Dimensions.ai, and the units of study were research articles in Economics, History and Archaeology, and Mathematics. As the main results, a small proportion of the articles received a large part of the citations and most of the social attention. Both citations and social attention in-creased, in general, with the number of co-authors. Thus, the greater the number of co-authors, the greater the probability of being cited in academic articles and mentioned on social media. The advantage in citation and social attention due to collaboration is independent of the access type for the publication. Furthermore, although collaboration with an additional co-author is in general positive in terms of citation and social attention, these positive effects reduce as the number of co-authors increases.
OpenCitations, an open e-infrastructure to foster maximum reuse of citation data
Venue: arXiv cs.DL 2022
Year: 2022

OpenCitations is an independent not-for-profit infrastructure organization for open scholarship dedicated to the publication of open bibliographic and citation data by the use of Semantic Web (Linked Data) technologies. OpenCitations collaborates with projects that are part of the Open Science ecosystem and complies with the UNESCO founding principles of Open Science, the I4OC recommendations, and the FAIR data principles that data should be Findable, Accessible, Interoperable and Reusable. Since its data satisfies all the Reuse guidelines provided by FAIR in terms of richness, provenance, usage licenses and domain-relevant community standards, OpenCitations provides an example of a successful open e-infrastructure in which the reusability of data is integral to its mission.
What Can Robots Teach Us About The COVID-19 Pandemic? Interactive Demonstrations of Epidemiological Models Using a Swarm of Brushbots
Venue: arXiv cs.RO 2022
Year: 2022

This paper describes the methodology and outcomes of a series of educational events conducted in 2021 which leveraged robot swarms to educate high-school and university students about epidemiological models and how they can inform societal and governmental policies. With a specific focus on the COVID-19 pandemic, the events consisted of 4 online and 3 in-person workshops where students had the chance to interact with a swarm of 20 custom-built brushbots -- small-scale vibration-driven robots optimized for portability and robustness. Through the analysis of data collected during a post-event survey, this paper shows how the events positively impacted the students' views on the scientific method to guide real-world decision making, as well as their interest in robotics.
Normalization, Square Roots, and the Exponential and Logarithmic Maps in Geometric Algebras of Less than 6D
Venue: arXiv cs.CG 2022
Year: 2022

Geometric algebras of dimension $n < 6$ are becoming increasingly popular for the modeling of 3D and 3+1D geometry. With this increased popularity comes the need for efficient algorithms for common operations such as normalization, square roots, and exponential and logarithmic maps. The current work presents a signature agnostic analysis of these common operations in all geometric algebras of dimension $n < 6$, and gives efficient numerical implementations in the most popular algebras $\mathbb{R}_{4}$, $\mathbb{R}_{3,1}$, $\mathbb{R}_{3,0,1}$ and $\mathbb{R}_{4,1}$, in the hopes of lowering the threshold for adoption of geometric algebra solutions by code maintainers.
YOU SHALL NOT COMPUTE on my Data: Access Policies for Privacy-Preserving Data Marketplaces and an Implementation for a Distributed Market using MPC
Venue: arXiv cs.CR 2022
Year: 2022

Personal data is an attractive source of insights for a diverse field of research and business. While our data is highly valuable, it is often privacy-sensitive. Thus, regulations like the GDPR restrict what data can be legally published, and what a buyer may do with this sensitive data. While personal data must be protected, we can still sell some insights gathered from our data that do not hurt our privacy. A data marketplace is a platform that helps users to sell their data while assisting buyers in discovering relevant datasets. The major challenge such a marketplace faces is balancing between offering valuable insights into data while preserving privacy requirements. Private data marketplaces try to solve this challenge by offering privacy-preserving computations on personal data. Such computations allow for calculating statistics or training machine learning models on personal data without accessing the data in plain. However, the user selling the data cannot restrict who can buy or what type of computation the data is allowed. We close the latter gap by proposing a flexible access control architecture for private data marketplaces, which can be applied to existing data markets. Our architecture enables data sellers to define detailed policies restricting who can buy their data. Furthermore, a seller can control what computation a specific buyer can purchase on the data, and make constraints on its parameters to mitigate privacy breaches. The data market's computation system then enforces the policies before initiating a computation. To demonstrate the feasibility of our approach, we provide an implementation for the KRAKEN marketplace, a distributed data market using MPC. We show that our approach is practical since it introduces a negligible performance overhead and is secure against several adversaries.
Deep Multi-Task Networks For Occluded Pedestrian Pose Estimation
Venue: arXiv cs.CV 2022
Year: 2022

Most of the existing works on pedestrian pose estimation do not consider estimating the pose of an occluded pedestrian, as the annotations of the occluded parts are not available in relevant automotive datasets. For example, CityPersons, a well-known dataset for pedestrian detection in automotive scenes does not provide pose annotations, whereas MS-COCO, a non-automotive dataset, contains human pose estimation. In this work, we propose a multi-task framework to extract pedestrian features through detection and instance segmentation tasks performed separately on these two distributions. Thereafter, an encoder learns pose specific features using an unsupervised instance-level domain adaptation method for the pedestrian instances from both distributions. The proposed framework has improved state-of-the-art performances of pose estimation, pedestrian detection, and instance segmentation.
Hierarchical Clustering in Graph Streams: Single-Pass Algorithms and Space Lower Bounds
Venue: arXiv cs.DS 2022
Year: 2022

The Hierarchical Clustering (HC) problem consists of building a hierarchy of clusters to represent a given dataset. Motivated by the modern large-scale applications, we study the problem in the \streaming model, in which the memory is heavily limited and only a single or very few passes over the input are allowed. Specifically, we investigate whether a good hierarchical clustering can be obtained, or at least whether we can approximately estimate the value of the optimal hierarchy. To measure the quality of a hierarchy, we use the HC minimization objective introduced by Dasgupta. Assuming that the input is an $n$-vertex weighted graph whose edges arrive in a stream, we derive the following results on space-vs-accuracy tradeoffs: * With $O(n\cdot \text{polylog}\,{n})$ space, we develop a single-pass algorithm, whose approximation ratio matches the currently best offline algorithm. * When the space is more limited, namely, $n^{1-o(1)}$, we prove that no algorithm can even estimate the value of optimum HC tree to within an $o(\frac{\log{n}}{\log\log{n}})$ factor, even when allowed $\text{polylog}{\,{n}}$ passes over the input. * In the most stringent setting of $\text{polylog}\,{n}$ space, we rule out algorithms that can even distinguish between "highly"-vs-"poorly" clusterable graphs, namely, graphs that have an $n^{1/2-o(1)}$ factor gap between their HC objective value. * Finally, we prove that any single-pass streaming algorithm that computes an optimal HC tree requires to store almost the entire input even if allowed exponential time. Our algorithmic results establish a general structural result that proves that cut sparsifiers of input graph can preserve cost of "balanced" HC trees to within a constant factor. Our lower bound results include a new streaming lower bound for a novel problem "One-vs-Many-Expanders", which can be of independent interest.
Calibrating Agent-based Models to Microdata with Graph Neural Networks
Venue: arXiv cs.MA 2022
Year: 2022

Calibrating agent-based models (ABMs) to data is among the most fundamental requirements to ensure the model fulfils its desired purpose. In recent years, simulation-based inference methods have emerged as powerful tools for performing this task when the model likelihood function is intractable, as is often the case for ABMs. In some real-world use cases of ABMs, both the observed data and the ABM output consist of the agents' states and their interactions over time. In such cases, there is a tension between the desire to make full use of the rich information content of such granular data on the one hand, and the need to reduce the dimensionality of the data to prevent difficulties associated with high-dimensional learning tasks on the other. A possible resolution is to construct lower-dimensional time-series through the use of summary statistics describing the macrostate of the system at each time point. However, a poor choice of summary statistics can result in an unacceptable loss of information from the original dataset, dramatically reducing the quality of the resulting calibration. In this work, we instead propose to learn parameter posteriors associated with granular microdata directly using temporal graph neural networks. We will demonstrate that such an approach offers highly compelling inductive biases for Bayesian inference using the raw ABM microstates as output.
SP-ViT: Learning 2D Spatial Priors for Vision Transformers
Venue: arXiv cs.CV 2022
Year: 2022

Recently, transformers have shown great potential in image classification and established state-of-the-art results on the ImageNet benchmark. However, compared to CNNs, transformers converge slowly and are prone to overfitting in low-data regimes due to the lack of spatial inductive biases. Such spatial inductive biases can be especially beneficial since the 2D structure of an input image is not well preserved in transformers. In this work, we present Spatial Prior-enhanced Self-Attention (SP-SA), a novel variant of vanilla Self-Attention (SA) tailored for vision transformers. Spatial Priors (SPs) are our proposed family of inductive biases that highlight certain groups of spatial relations. Unlike convolutional inductive biases, which are forced to focus exclusively on hard-coded local regions, our proposed SPs are learned by the model itself and take a variety of spatial relations into account. Specifically, the attention score is calculated with emphasis on certain kinds of spatial relations at each head, and such learned spatial foci can be complementary to each other. Based on SP-SA we propose the SP-ViT family, which consistently outperforms other ViT models with similar GFlops or parameters. Our largest model SP-ViT-L achieves a record-breaking 86.3% Top-1 accuracy with a reduction in the number of parameters by almost 50% compared to previous state-of-the-art model (150M for SP-ViT-L vs 271M for CaiT-M-36) among all ImageNet-1K models trained on 224x224 and fine-tuned on 384x384 resolution w/o extra data.
Reconstructing Ultrametric Trees from Noisy Experiments
Venue: arXiv cs.DS 2022
Year: 2022

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the results of `experiments' on triples of leaves (a,b,c), which return the pair with the deepest least common ancestor. If the tree is assumed to be an ultrametric (i.e., all root-leaf paths have the same length), the experiment can be equivalently seen to return the closest pair of leaves. In this model, efficient algorithms are known for tree reconstruction. In reality, since the data on which these `experiments' are run is itself generated by the stochastic process of evolution, these experiments are noisy. In all reasonable models of evolution, if the branches leading to the leaves in a triple separate from each other at common ancestors that are very close to each other in the tree, the result of the experiment should be close to uniformly random. Motivated by this, we consider a model where the noise on any triple is just dependent on the three pairwise distances (referred to as distance based noise). Our results are the following: 1. Suppose the length of every edge in the unknown tree is at least $\tilde{O}(\frac{1}{\sqrt n})$ fraction of the length of a root-leaf path. Then, we give an efficient algorithm to reconstruct the topology of the tree for a broad family of distance-based noise models. Further, we show that if the edges are asymptotically shorter, then topology reconstruction is information-theoretically impossible. 2. Further, for a specific distance-based noise model--which we refer to as the homogeneous noise model--we show that the edge weights can also be approximately reconstructed under the same quantitative lower bound on the edge lengths.
Decentralized WebRCT P2P network using Kademlia
Venue: arXiv cs.NI 2022
Year: 2022

Web Real-Time Communication (WebRTC) is a new standard and industry effort that extends the web browsing model. For the first time, browsers are able to directly exchange real-time media with other browsers in a peer-to-peer fashion. Before WebRTC was introduced, it was cumbersome to build smooth chat and video applications, users often experience unstable connections, blurry videos, and unclear sounds. WebRTC's peer-to-peer communication paradigm establishes the real-time connection between browsers using the SIP(Session Initiation Protocol) Trapezoid. A wide set of protocols are bundled in WebRTC API, such as connection management, encoding/decoding negotiation, media control, selection and control, firewall and NAT element traversal, etc. However, almost all current WebRTC applications are using centralized signaling infrastructure which brings the problems of scalability, stability, and fault-tolerance. In this paper, I am presenting a decentralized architecture by introducing the Kademlia network into WebRTC to reduce the need for a centralized signaling service for WebRTC.
Diffusion Models for Video Prediction and Infilling
Venue: arXiv cs.CV 2022
Year: 2022

Predicting and anticipating future outcomes or reasoning about missing information in a sequence are critical skills for agents to be able to make intelligent decisions. This requires strong, temporally coherent generative capabilities. Diffusion models have shown remarkable success in several generative tasks, but have not been extensively explored in the video domain. We present Random-Mask Video Diffusion (RaMViD), which extends image diffusion models to videos using 3D convolutions, and introduces a new conditioning technique during training. By varying the mask we condition on, the model is able to perform video prediction, infilling, and upsampling. Due to our simple conditioning scheme, we can utilize the same architecture as used for unconditional training, which allows us to train the model in a conditional and unconditional fashion at the same time. We evaluate RaMViD on two benchmark datasets for video prediction, on which we achieve state-of-the-art results, and one for video generation. High-resolution videos are provided at https://sites.google.com/view/video-diffusion-prediction.
Masked Siamese ConvNets
Venue: arXiv cs.CV 2022
Year: 2022

Self-supervised learning has shown superior performances over supervised methods on various vision benchmarks. The siamese network, which encourages embeddings to be invariant to distortions, is one of the most successful self-supervised visual representation learning approaches. Among all the augmentation methods, masking is the most general and straightforward method that has the potential to be applied to all kinds of input and requires the least amount of domain knowledge. However, masked siamese networks require particular inductive bias and practically only work well with Vision Transformers. This work empirically studies the problems behind masked siamese networks with ConvNets. We propose several empirical designs to overcome these problems gradually. Our method performs competitively on low-shot image classification and outperforms previous methods on object detection benchmarks. We discuss several remaining issues and hope this work can provide useful data points for future general-purpose self-supervised learning.