OpenRaiser/Intern-Atlas huggingface dataset:
A Deep Learning Framework for Diffeomorphic Mapping Problems via Quasi-conformal Geometry applied to Imaging
Venue: arXiv cs.CV 2022
Year: 2022

Many imaging problems can be formulated as mapping problems. A general mapping problem aims to obtain an optimal mapping that minimizes an energy functional subject to the given constraints. Existing methods to solve the mapping problems are often inefficient and can sometimes get trapped in local minima. An extra challenge arises when the optimal mapping is required to be diffeomorphic. In this work, we address the problem by proposing a deep-learning framework based on the Quasiconformal (QC) Teichmuller theories. The main strategy is to learn the Beltrami coefficient (BC) that represents a mapping as the latent feature vector in the deep neural network. The BC measures the local geometric distortion under the mapping, with which the interpretability of the deep neural network can be enhanced. Under this framework, the diffeomorphic property of the mapping can be controlled via a simple activation function within the network. The optimal mapping can also be easily regularized by integrating the BC into the loss function. A crucial advantage of the proposed framework is that once the network is successfully trained, the optimized mapping corresponding to each input data information can be obtained in real time. To examine the efficacy of the proposed framework, we apply the method to the diffeomorphic image registration problem. Experimental results outperform other state-of-the-art registration algorithms in both efficiency and accuracy, which demonstrate the effectiveness of our proposed framework to solve the mapping problem.
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C)
Venue: arXiv cs.CL 2022
Year: 2022

While we pay attention to the latest advances in clinical natural language processing (NLP), we can notice some resistance in the clinical and translational research community to adopt NLP models due to limited transparency, interpretability, and usability. In this study, we proposed an open natural language processing development framework. We evaluated it through the implementation of NLP algorithms for the National COVID Cohort Collaborative (N3C). Based on the interests in information extraction from COVID-19 related clinical notes, our work includes 1) an open data annotation process using COVID-19 signs and symptoms as the use case, 2) a community-driven ruleset composing platform, and 3) a synthetic text data generation workflow to generate texts for information extraction tasks without involving human subjects. The corpora were derived from texts from three different institutions (Mayo Clinic, University of Kentucky, University of Minnesota). The gold standard annotations were tested with a single institution's (Mayo) ruleset. This resulted in performances of 0.876, 0.706, and 0.694 in F-scores for Mayo, Minnesota, and Kentucky test datasets, respectively. The study as a consortium effort of the N3C NLP subgroup demonstrates the feasibility of creating a federated NLP algorithm development and benchmarking platform to enhance multi-institution clinical NLP study and adoption. Although we use COVID-19 as a use case in this effort, our framework is general enough to be applied to other domains of interest in clinical NLP.
A Data-Centric Optimization Framework for Machine Learning
Venue: arXiv cs.LG 2022
Year: 2022

Rapid progress in deep learning is leading to a diverse set of quickly changing models, with a dramatically growing demand for compute. However, as frameworks specialize performance optimization to patterns in popular networks, they implicitly constrain novel and diverse models that drive progress in research. We empower deep learning researchers by defining a flexible and user-customizable pipeline for optimizing training of arbitrary deep neural networks, based on data movement minimization. The pipeline begins with standard networks in PyTorch or ONNX and transforms computation through progressive lowering. We define four levels of general-purpose transformations, from local intra-operator optimizations to global data movement reduction. These operate on a data-centric graph intermediate representation that expresses computation and data movement at all levels of abstraction, including expanding basic operators such as convolutions to their underlying computations. Central to the design is the interactive and introspectable nature of the pipeline. Every part is extensible through a Python API, and can be tuned interactively using a GUI. We demonstrate competitive performance or speedups on ten different networks, with interactive optimizations discovering new opportunities in EfficientNet.
Sensing Cox Processes via Posterior Sampling and Positive Bases
Venue: arXiv cs.LG 2022
Year: 2022

We study adaptive sensing of Cox point processes, a widely used model from spatial statistics. We introduce three tasks: maximization of captured events, search for the maximum of the intensity function and learning level sets of the intensity function. We model the intensity function as a sample from a truncated Gaussian process, represented in a specially constructed positive basis. In this basis, the positivity constraint on the intensity function has a simple form. We show how an minimal description positive basis can be adapted to the covariance kernel, non-stationarity and make connections to common positive bases from prior works. Our adaptive sensing algorithms use Langevin dynamics and are based on posterior sampling (\textsc{Cox-Thompson}) and top-two posterior sampling (\textsc{Top2}) principles. With latter, the difference between samples serves as a surrogate to the uncertainty. We demonstrate the approach using examples from environmental monitoring and crime rate modeling, and compare it to the classical Bayesian experimental design approach.
Fusion of complementary 2D and 3D mesostructural datasets using generative adversarial networks
Venue: arXiv cs.CV 2022
Year: 2022

Modelling the impact of a material's mesostructure on device level performance typically requires access to 3D image data containing all the relevant information to define the geometry of the simulation domain. This image data must include sufficient contrast between phases to distinguish each material, be of high enough resolution to capture the key details, but also have a large enough field-of-view to be representative of the material in general. It is rarely possible to obtain data with all of these properties from a single imaging technique. In this paper, we present a method for combining information from pairs of distinct but complementary imaging techniques in order to accurately reconstruct the desired multi-phase, high resolution, representative, 3D images. Specifically, we use deep convolutional generative adversarial networks to implement super-resolution, style transfer and dimensionality expansion. To demonstrate the widespread applicability of this tool, two pairs of datasets are used to validate the quality of the volumes generated by fusing the information from paired imaging techniques. Three key mesostructural metrics are calculated in each case to show the accuracy of this method. Having confidence in the accuracy of our method, we then demonstrate its power by applying to a real data pair from a lithium ion battery electrode, where the required 3D high resolution image data is not available anywhere in the literature. We believe this approach is superior to previously reported statistical material reconstruction methods both in terms of its fidelity and ease of use. Furthermore, much of the data required to train this algorithm already exists in the literature, waiting to be combined. As such, our open-access code could precipitate a step change by generating the hard to obtain high quality image volumes necessary to simulate behaviour at the mesoscale.
Soft Lattice Modules that Behave Independently and Collectively
Venue: arXiv cs.RO 2022
Year: 2022

Natural systems integrate the work of many sub-units (cells) toward a large-scale unified goal (morphological and behavioral), which can counteract the effects of unexpected experiences, damage, or simply changes in tasks demands. In this paper, we exploit the opportunities presented by soft, modular, and tensegrity robots to introduce soft lattice modules that parallel the sub-units seen in biological systems. The soft lattice modules are comprised of 3D printed plastic "skeletons", linear contracting shape memory alloy spring actuators, and permanent magnets that enable adhesion between modules. The soft lattice modules are capable of independent locomotion, and can also join with other modules to achieve collective, self-assembled, larger scale tasks such as collective locomotion and moving an object across the surface of the lattice assembly. This work represents a preliminary step toward soft modular systems capable of independent and collective behaviors, and provide a platform for future studies on distributed control.
A Versatile and Efficient Reinforcement Learning Framework for Autonomous Driving
Venue: arXiv cs.RO 2022
Year: 2022

Heated debates continue over the best autonomous driving framework. The classic modular pipeline is widely adopted in the industry owing to its great interpretability and stability, whereas the fully end-to-end paradigm has demonstrated considerable simplicity and learnability along with the rise of deep learning. As a way of marrying the advantages of both approaches, learning a semantically meaningful representation and then use in the downstream driving policy learning tasks provides a viable and attractive solution. However, several key challenges remain to be addressed, including identifying the most effective representation, alleviating the sim-to-real generalization issue as well as balancing model training cost. In this study, we propose a versatile and efficient reinforcement learning framework and build a fully functional autonomous vehicle for real-world validation. Our framework shows great generalizability to various complicated real-world scenarios and superior training efficiency against the competing baselines.
Learning Stable Vector Fields on Lie Groups
Venue: arXiv cs.RO 2022
Year: 2022

Learning robot motions from demonstration requires models able to specify vector fields for the full robot pose when the task is defined in operational space. Recent advances in reactive motion generation have shown that learning adaptive, reactive, smooth, and stable vector fields is possible. However, these approaches define vector fields on a flat Euclidean manifold, while representing vector fields for orientations requires modeling the dynamics in non-Euclidean manifolds, such as Lie Groups. In this paper, we present a novel vector field model that can guarantee most of the properties of previous approaches i.e., stability, smoothness, and reactivity beyond the Euclidean space. In the experimental evaluation, we show the performance of our proposed vector field model to learn stable vector fields for full robot poses as SE(2) and SE(3) in both simulated and real robotics tasks.
Safe rules for the identification of zeros in the solutions of the SLOPE problem
Venue: arXiv cs.LG 2022
Year: 2022

In this paper we propose a methodology to accelerate the resolution of the so-called "Sorted L-One Penalized Estimation" (SLOPE) problem. Our method leverages the concept of "safe screening", well-studied in the literature for \textit{group-separable} sparsity-inducing norms, and aims at identifying the zeros in the solution of SLOPE. More specifically, we derive a set of \(\tfrac{n(n+1)}{2}\) inequalities for each element of the \(n\)-dimensional primal vector and prove that the latter can be safely screened if some subsets of these inequalities are verified. We propose moreover an efficient algorithm to jointly apply the proposed procedure to all the primal variables. Our procedure has a complexity \(\mathcal{O}(n\log n + LT)\) where \(T\leq n\) is a problem-dependent constant and \(L\) is the number of zeros identified by the tests. Numerical experiments confirm that, for a prescribed computational budget, the proposed methodology leads to significant improvements of the solving precision.
Uniquely Decodable Multi-Amplitude Sequence for Grant-Free Multiple-Access Adder Channels
Venue: arXiv cs.IT 2022
Year: 2022

Grant-free multiple-access (GFMA) is a valuable research topic, since it can support multiuser transmission with low latency. This paper constructs novel uniquely-decodable multi-amplitude sequence (UDAS) sets for GFMA systems, which can provide high spectrum efficiency (SE) with low-complexity active user detection (AUD) algorithm. First of all, we propose an UDAS-based multi-dimensional bit interleaving coded modulation (MD-BICM) transmitter; then introduce the definition of UDAS and construct two kinds of UDAS sets based on cyclic and quasi-cyclic matrix modes. Besides, we present a statistic of UDAS feature based AUD algorithm (SoF-AUD), and a joint multiuser detection and improved message passing algorithm for the proposed system. Finally, the active user error rate (AUER) and Shannon limits of the proposed system are deduced in details. Simulation results show that our proposed system can simultaneously support four users without additional redundancy, and the AUER can reach an extremely low value $10^{-5}$ when $E_b/N_0$ is $0$ dB and the length of transmit block is larger than a given value, i.e., 784, verifying the validity and flexibility of the proposed UDAS sets.
Conditionally Gaussian PAC-Bayes
Venue: arXiv cs.LG 2022
Year: 2022

Recent studies have empirically investigated different methods to train stochastic neural networks on a classification task by optimising a PAC-Bayesian bound via stochastic gradient descent. Most of these procedures need to replace the misclassification error with a surrogate loss, leading to a mismatch between the optimisation objective and the actual generalisation bound. The present paper proposes a novel training algorithm that optimises the PAC-Bayesian bound, without relying on any surrogate loss. Empirical results show that this approach outperforms currently available PAC-Bayesian training methods.
Look behind the Censorship: Reposting-User Characterization and Muted-Topic Restoration
Venue: arXiv cs.SI 2022
Year: 2022

The emergence of social media has largely eased the way people receive information and participate in public discussions. However, in countries with strict regulations on discussions in the public space, social media is no exception. To limit the degree of dissent or inhibit the spread of "harmful" information, a common approach is to impose information operations such as censorship/suspension on social media. In this paper, we focus on a study of censorship on Weibo, the counterpart of Twitter in China. Specifically, we 1) create a web-scraping pipeline and collect a large dataset solely focus on the reposts from Weibo; 2) discover the characteristics of users whose reposts contain censored information, in terms of gender, device, and account type; and 3) conduct a thematic analysis by extracting and analyzing topic information. Note that although the original posts are no longer visible, we can use comments users wrote when reposting the original post to infer the topic of the original content. We find that such efforts can recover the discussions around social events that triggered massive discussions but were later muted. Further, we show the variations of inferred topics across different user groups and time frames.
A Simple Baseline for Low-Budget Active Learning
Venue: arXiv cs.CV 2022
Year: 2022

Active learning focuses on choosing a subset of unlabeled data to be labeled. However, most such methods assume that a large subset of the data can be annotated. We are interested in low-budget active learning where only a small subset (e.g., 0.2% of ImageNet) can be annotated. Instead of proposing a new query strategy to iteratively sample batches of unlabeled data given an initial pool, we learn rich features by an off-the-shelf self-supervised learning method only once, and then study the effectiveness of different sampling strategies given a low labeling budget on a variety of datasets including ImageNet. We show that although the state-of-the-art active learning methods work well given a large labeling budget, a simple K-means clustering algorithm can outperform them on low budgets. We believe this method can be used as a simple baseline for low-budget active learning on image classification. Code is available at: https://github.com/UCDvision/low-budget-al
Causal Effect Identification with Context-specific Independence Relations of Control Variables
Venue: arXiv cs.LG 2022
Year: 2022

We study the problem of causal effect identification from observational distribution given the causal graph and some context-specific independence (CSI) relations. It was recently shown that this problem is NP-hard, and while a sound algorithm to learn the causal effects is proposed in Tikka et al. (2019), no complete algorithm for the task exists. In this work, we propose a sound and complete algorithm for the setting when the CSI relations are limited to observed nodes with no parents in the causal graph. One limitation of the state of the art in terms of its applicability is that the CSI relations among all variables, even unobserved ones, must be given (as opposed to learned). Instead, We introduce a set of graphical constraints under which the CSI relations can be learned from mere observational distribution. This expands the set of identifiable causal effects beyond the state of the art.
Off-policy Reinforcement Learning with Optimistic Exploration and Distribution Correction
Venue: arXiv cs.LG 2022
Year: 2022

Improving the sample efficiency of reinforcement learning algorithms requires effective exploration. Following the principle of $\textit{optimism in the face of uncertainty}$ (OFU), we train a separate exploration policy to maximize the approximate upper confidence bound of the critics in an off-policy actor-critic framework. However, this introduces extra differences between the replay buffer and the target policy regarding their stationary state-action distributions. To mitigate the off-policy-ness, we adapt the recently introduced DICE framework to learn a distribution correction ratio for off-policy RL training. In particular, we correct the training distribution for both policies and critics. Empirically, we evaluate our proposed method in several challenging continuous control tasks and show superior performance compared to state-of-the-art methods. We also conduct extensive ablation studies to demonstrate the effectiveness and rationality of the proposed method.
Gaussian Process Sampling and Optimization with Approximate Upper and Lower Bounds
Venue: arXiv cs.LG 2022
Year: 2022

Many functions have approximately-known upper and/or lower bounds, potentially aiding the modeling of such functions. In this paper, we introduce Gaussian process models for functions where such bounds are (approximately) known. More specifically, we propose the first use of such bounds to improve Gaussian process (GP) posterior sampling and Bayesian optimization (BO). That is, we transform a GP model satisfying the given bounds, and then sample and weight functions from its posterior. To further exploit these bounds in BO settings, we present bounded entropy search (BES) to select the point gaining the most information about the underlying function, estimated by the GP samples, while satisfying the output constraints. We characterize the sample variance bounds and show that the decision made by BES is explainable. Our proposed approach is conceptually straightforward and can be used as a plug in extension to existing methods for GP posterior sampling and Bayesian optimization.
Characterizing The Limits of Linear Modeling of Non-Linear Swarm Behaviors
Venue: arXiv cs.RO 2022
Year: 2022

We study the limits of linear modeling of swarm behavior by characterizing the inflection point beyond which linear models of swarm collective behavior break down. The problem we consider is a central place object gathering task. We design a linear model which strives to capture the underlying dynamics of object gathering in robot swarms from first principles, rather than extensively relying on post-hoc model fitting. We evaluate our model with swarms of up to 8,000 robots in simulation, demonstrating that it accurately captures underlying swarm behavioral dynamics when the swarm can be approximated using the mean-field model, and when it cannot, and finite-size effects are present. We further apply our model to swarms exhibiting non-linear behaviors, and show that it still provides accurate predictions in some scenarios, thereby establishing better practical limits on linear modeling of swarm behaviors.
Using Motion History Images with 3D Convolutional Networks in Isolated Sign Language Recognition
Venue: arXiv cs.CV 2022
Year: 2022

Sign language recognition using computational models is a challenging problem that requires simultaneous spatio-temporal modeling of the multiple sources, i.e. faces, hands, body, etc. In this paper, we propose an isolated sign language recognition model based on a model trained using Motion History Images (MHI) that are generated from RGB video frames. RGB-MHI images represent spatio-temporal summary of each sign video effectively in a single RGB image. We propose two different approaches using this RGB-MHI model. In the first approach, we use the RGB-MHI model as a motion-based spatial attention module integrated into a 3D-CNN architecture. In the second approach, we use RGB-MHI model features directly with the features of a 3D-CNN model using a late fusion technique. We perform extensive experiments on two recently released large-scale isolated sign language datasets, namely AUTSL and BosphorusSign22k. Our experiments show that our models, which use only RGB data, can compete with the state-of-the-art models in the literature that use multi-modal data.
Paperfetcher: A tool to automate handsearch for systematic reviews
Venue: arXiv cs.IR 2022
Year: 2022

Handsearch is an important technique that contributes to thorough literature search in systematic reviews. Traditional handsearch requires reviewers to systematically browse through each issue of a curated list of field-specific journals and conference proceedings to find articles relevant to their review. This manual process is not only time-consuming, laborious, costly, and error-prone, but it also lacks replicability and cross-checking mechanisms. In an attempt to solve these problems, this paper presents a free and open-source Python package and an accompanying web-app, Paperfetcher, to automate handsearch for systematic reviews. With Paperfetcher's assistance, researchers can retrieve articles from designated journals within a specified time frame with just a few clicks. In addition to handsearch, this tool also incorporates snowballing in both directions. Paperfetcher allows researchers to download retrieved studies as a list of DOIs or as an RIS database to facilitate seamless import into citation management and systematic review screening software. To our knowledge, Paperfetcher is the first tool that automates handsearch with high usability and a multi-disciplinary focus.