arXiv subjects

Yixuan Wang

Publications and source records attributed to Yixuan Wang.

At least 163 records · Page 9Linked to original sources

arXiv2022

Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

q-bio.QM↗

arXiv2022

Weak solutions to the equations of stationary compressible flows in active liquid crystals

The equations of stationary compressible flows of active liquid crystals are considered in a bounded three-dimensional domain. The system consists of the stationary Navier-Stokes equations coupled with the equation of Q-tensors and the equation of the active particles. The existence of weak solutions to the stationary problem is established through a two-level approximation scheme, compactness estimates and weak convergence arguments. Novel techniques are developed to overcome the difficulties due to the lower regularity of stationary solutions, a Moser-type iteration is used to deal with the strong coupling of active particles and fluids, and some weighted estimates on the energy functions are achieved so that the weak solutions can be constructed for all values of the adiabatic exponent $γ>1$.

math.AP↗

arXiv2022

Constellation: An Edge-Based Semantic Runtime System for Internet of Things Applications

With the global Internet of Things IoT market size predicted to grow to over 1 trillion dollars in the next 5 years, many large corporations are scrambling to solidify their product line as the defacto device suite for consumers. This has led to each corporation developing their devices in a siloed environment with unique protocols and runtime frameworks that explicitly exclude the ability to work with the competitions devices. This development silo has created problems with programming complexity for application developers as well as concurrency and scalability limitations for applications that involve a network of IoT devices. The Constellation project is a distributed IoT runtime system that attempts to address these challenges by creating an operating system layer that decouples applications from devices. This layer provides mechanisms designed to allow applications to interface with an underlying substrate of IoT devices while abstracting away the complexities of application concurrency, device interoperability, and system scalability. This paper provides an overview of the Constellation system as well as details four new project expansions to improve system scalability.

cs.DC↗

arXiv2022

Physics-Aware Safety-Assured Design of Hierarchical Neural Network based Planner

Neural networks have shown great promises in planning, control, and general decision making for learning-enabled cyber-physical systems (LE-CPSs), especially in improving performance under complex scenarios. However, it is very challenging to formally analyze the behavior of neural network based planners for ensuring system safety, which significantly impedes their applications in safety-critical domains such as autonomous driving. In this work, we propose a hierarchical neural network based planner that analyzes the underlying physical scenarios of the system and learns a system-level behavior planning scheme with multiple scenario-specific motion-planning strategies. We then develop an efficient verification method that incorporates overapproximation of the system state reachable set and novel partition and union techniques for formally ensuring system safety under our physics-aware planner. With theoretical analysis, we show that considering the different physical scenarios and building a hierarchical planner based on such analysis may improve system safety and verifiability. We also empirically demonstrate the effectiveness of our approach and its advantage over other baselines in practical case studies of unprotected left turn and highway merging, two common challenging safety-critical tasks in autonomous driving.

cs.RO↗

arXiv2021

Data Trading with a Monopoly Social Network: Outcomes are Mostly Privacy Welfare Damaging

This paper argues that data of strategic individuals with heterogeneous privacy valuations in a distributed online social network (e.g., Facebook) will be under-priced, if traded in a monopoly buyer setting, and will lead to diminishing utilitarian welfare. This result, for a certain family of online community data trading problems, is in stark contrast to a popular information economics intuition that increased amounts of end-user data signals in a data market improves its efficiency. Our proposed theory paves the way for a future (counter-intuitive) analysis of data trading oligopoly markets for online social networks (OSNs).

cs.SI↗

arXiv2021

CLMB: deep contrastive learning for robust metagenomic binning

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic binning, clustering the assembled contigs into draft genomes. Despite the existing computational tools, most of them neglect one important property of the metagenomic data, that is, the noise. To further improve the metagenomic binning step and reconstruct better metagenomes, we propose a deep Contrastive Learning framework for Metagenome Binning (CLMB), which can efficiently eliminate the disturbance of noise and produce more stable and robust results. Essentially, instead of denoising the data explicitly, we add simulated noise to the training data and force the deep learning model to produce similar and stable representations for both the noise-free data and the distorted data. Consequently, the trained model will be robust to noise and handle it implicitly during usage. CLMB outperforms the previous state-of-the-art binning methods significantly, recovering the most near-complete genomes on almost all the benchmarking datasets (up to 17\% more reconstructed genomes compared to the second-best method). It also improves the performance of bin refinement, reconstructing 8-22 more high-quality genomes and 15-32 more middle-quality genomes than the second-best result. Impressively, in addition to being compatible with the binning refiner, single CLMB even recovers on average 15 more HQ genomes than the refiner of VAMB and Maxbin on the benchmarking datasets. CLMB is open-source and available at https://github.com/zpf0117b/CLMB/.

cs.LG↗

arXiv2021

Weak Adaptation Learning -- Addressing Cross-domain Data Insufficiency with Weak Annotator

Data quantity and quality are crucial factors for data-driven learning methods. In some target problem domains, there are not many data samples available, which could significantly hinder the learning process. While data from similar domains may be leveraged to help through domain adaptation, obtaining high-quality labeled data for those source domains themselves could be difficult or costly. To address such challenges on data insufficiency for classification problem in a target domain, we propose a weak adaptation learning (WAL) approach that leverages unlabeled data from a similar source domain, a low-cost weak annotator that produces labels based on task-specific heuristics, labeling rules, or other methods (albeit with inaccuracy), and a small amount of labeled data in the target domain. Our approach first conducts a theoretical analysis on the error bound of the trained classifier with respect to the data quantity and the performance of the weak annotator, and then introduces a multi-stage weak adaptation learning method to learn an accurate classifier by lowering the error bound. Our experiments demonstrate the effectiveness of our approach in learning an accurate classifier with limited labeled data in the target domain and unlabeled data in the source domain.

cs.LG↗

arXiv2021

Schrödinger PCA: On the Duality between Principal Component Analysis and Schrödinger Equation

Principal component analysis (PCA) has achieved great success in unsupervised learning by identifying covariance correlations among features. If the data collection fails to capture the covariance information, PCA will not be able to discover meaningful modes. In particular, PCA will fail the spatial Gaussian Process (GP) model in the undersampling regime, i.e. the averaged distance of neighboring anchor points (spatial features) is greater than the correlation length of GP. Counterintuitively, by drawing the connection between PCA and Schrödinger equation, we can not only attack the undersampling challenge but also compute in an efficient and decoupled way with the proposed algorithm called Schrödinger PCA. Our algorithm only requires variances of features and estimated correlation length as input, constructs the corresponding Schrödinger equation, and solves it to obtain the energy eigenstates, which coincide with principal components. We will also establish the connection of our algorithm to the model reduction techniques in the partial differential equation (PDE) community, where the steady-state Schrödinger operator is identified as a second-order approximation to the covariance function. Numerical experiments are implemented to testify the validity and efficiency of the proposed algorithm, showing its potential for unsupervised learning tasks on general graphs and manifolds.

physics.comp-ph↗

arXiv2021

Learning-based Framework for Sensor Fault-Tolerant Building HVAC Control with Model-assisted Learning

As people spend up to 87% of their time indoors, intelligent Heating, Ventilation, and Air Conditioning (HVAC) systems in buildings are essential for maintaining occupant comfort and reducing energy consumption. These HVAC systems in smart buildings rely on real-time sensor readings, which in practice often suffer from various faults and could also be vulnerable to malicious attacks. Such faulty sensor inputs may lead to the violation of indoor environment requirements (e.g., temperature, humidity, etc.) and the increase of energy consumption. While many model-based approaches have been proposed in the literature for building HVAC control, it is costly to develop accurate physical models for ensuring their performance and even more challenging to address the impact of sensor faults. In this work, we present a novel learning-based framework for sensor fault-tolerant HVAC control, which includes three deep learning based components for 1) generating temperature proposals with the consideration of possible sensor faults, 2) selecting one of the proposals based on the assessment of their accuracy, and 3) applying reinforcement learning with the selected temperature proposal. Moreover, to address the challenge of training data insufficiency in building-related tasks, we propose a model-assisted learning method leveraging an abstract model of building physical dynamics. Through extensive experiments, we demonstrate that the proposed fault-tolerant HVAC control framework can significantly reduce building temperature violations under a variety of sensor fault patterns while maintaining energy efficiency.

eess.SY↗

arXiv2021

Learning to Prevent Leakage: Privacy-Preserving Inference in the Mobile Cloud

Powered by machine learning services in the cloud, numerous learning-driven mobile applications are gaining popularity in the market. As deep learning tasks are mostly computation-intensive, it has become a trend to process raw data on devices and send the deep neural network (DNN) features to the cloud, where the features are further processed to return final results. However, there is always unexpected leakage with the release of features, with which an adversary could infer a significant amount of information about the original data. We propose a privacy-preserving reinforcement learning framework on top of the mobile cloud infrastructure from the perspective of DNN structures. The framework aims to learn a policy to modify the base DNNs to prevent information leakage while maintaining high inference accuracy. The policy can also be readily transferred to large-size DNNs to speed up learning. Extensive evaluations on a variety of DNNs have shown that our framework can successfully find privacy-preserving DNN structures to defend different privacy attacks.

cs.LG↗

arXiv2021

Verification in the Loop: Correct-by-Construction Control Learning with Reach-avoid Guarantees

In the current control design of safety-critical autonomous systems, formal verification techniques are typically applied after the controller is designed to evaluate whether the required properties (e.g., safety) are satisfied. However, due to the increasing system complexity and the fundamental hardness of designing a controller with formal guarantees, such an open-loop process of design-then-verify often results in many iterations and fails to provide the necessary guarantees. In this paper, we propose a correct-by-construction control learning framework that integrates the verification into the control design process in a closed-loop manner, i.e., design-while-verify. Specifically, we leverage the verification results (computed reachable set of the system state) to construct feedback metrics for control learning, which measure how likely the current design of control parameters can meet the required reach-avoid property for safety and goal-reaching. We formulate an optimization problem based on such metrics for tuning the controller parameters, and develop an approximated gradient descent algorithm with a difference method to solve the optimization problem and learn the controller. The learned controller is formally guaranteed to meet the required reach-avoid property. By treating verifiability as a first-class objective and effectively leveraging the verification results during the control learning process, our approach can significantly improve the chance of finding a control design with formal property guarantees. This is demonstrated via a set of experiments on both linear and non-linear systems that use model-based or neural network based controllers.

eess.SY↗

arXiv2021

Exponential Convergence for Multiscale Linear Elliptic PDEs via Adaptive Edge Basis Functions

In this paper, we introduce a multiscale framework based on adaptive edge basis functions to solve second-order linear elliptic PDEs with rough coefficients. One of the main results is that we prove the proposed multiscale method achieves nearly exponential convergence in the approximation error with respect to the computational degrees of freedom. Our strategy is to perform an energy orthogonal decomposition of the solution space into a coarse scale component comprising $a$-harmonic functions in each element of the mesh, and a fine scale component named the bubble part that can be computed locally and efficiently. The coarse scale component depends entirely on function values on edges. Our approximation on each edge is made in the Lions-Magenes space $H_{00}^{1/2}(e)$, which we will demonstrate to be a natural and powerful choice. We construct edge basis functions using local oversampling and singular value decomposition. When local information of the right-hand side is adaptively incorporated into the edge basis functions, we prove a nearly exponential convergence rate of the approximation error. Numerical experiments validate and extend our theoretical analysis; in particular, we observe no obvious degradation in accuracy for high-contrast media problems.

math.NA↗

arXiv2021

Cocktail: Learn a Better Neural Network Controller from Multiple Experts via Adaptive Mixing and Robust Distillation

Neural networks are being increasingly applied to control and decision-making for learning-enabled cyber-physical systems (LE-CPSs). They have shown promising performance without requiring the development of complex physical models; however, their adoption is significantly hindered by the concerns on their safety, robustness, and efficiency. In this work, we propose COCKTAIL, a novel design framework that automatically learns a neural network-based controller from multiple existing control methods (experts) that could be either model-based or neural network-based. In particular, COCKTAIL first performs reinforcement learning to learn an optimal system-level adaptive mixing strategy that incorporates the underlying experts with dynamically-assigned weights and then conducts a teacher-student distillation with probabilistic adversarial training and regularization to synthesize a student neural network controller with improved control robustness (measured by a safe control rate metric with respect to adversarial attacks or measurement noises), control energy efficiency, and verifiability (measured by the computation time for verification). Experiments on three non-linear systems demonstrate significant advantages of our approach on these properties over various baseline methods.

eess.SY↗

arXiv2020

Strong solution for compressible liquid crystal system with random force

We study the three-dimensional compressible Navier-Stokes equations coupled with the $Q$-tensor equation perturbed by a multiplicative stochastic force, which describes the motion of nematic liquid crystal flows. The local existence and uniqueness of strong pathwise solution up to a positive stopping time is established where ``strong" is in both PDE and probability sense. The proof relies on the Galerkin approximation scheme, stochastic compactness, identification of the limit, uniqueness and a cutting-off argument. In the stochastic setting, we develop an extra layer approximation to overcome the difficulty arising from the stochastic integral while constructing the approximate solution. Due to the complex structure of the coupled system, the estimates of the high-order items are also the challenging part in the article.

math.AP↗

arXiv2020

Preference-Based Privacy Trading

The question we raise through this paper is: Is it economically feasible to trade consumer personal information with their formal consent (permission) and in return provide them incentives (monetary or otherwise)?. In view of (a) the behavioral assumption that humans are `compromising' beings and have privacy preferences, (b) privacy as a good not having strict boundaries, and (c) the practical inevitability of inappropriate data leakage by data holders downstream in the data-release supply-chain, we propose a design of regulated efficient/bounded inefficient economic mechanisms for oligopoly data trading markets using a novel preference function bidding approach on a simplified sellers-broker market. Our methodology preserves the heterogeneous privacy preservation constraints (at a grouped consumer, i.e., app, level) upto certain compromise levels, and at the same time satisfies information demand (via the broker) of agencies (e.g., advertising organizations) that collect client data for the purpose of targeted behavioral advertising.

cs.CY↗

arXiv2020

Tracking Partially-Occluded Deformable Objects while Enforcing Geometric Constraints

In order to manipulate a deformable object, such as rope or cloth, in unstructured environments, robots need a way to estimate its current shape. However, tracking the shape of a deformable object can be challenging because of the object's high flexibility, (self-)occlusion, and interaction with obstacles. Building a high-fidelity physics simulation to aid in tracking is difficult for novel environments. Instead we focus on tracking the object based on RGBD images and geometric motion estimates and obstacles. Our key contributions over previous work in this vein are: 1) A better way to handle severe occlusion by using a motion model to regularize the tracking estimate; and 2) The formulation of \textit{convex} geometric constraints, which allow us to prevent self-intersection and penetration into known obstacles via a post-processing step. These contributions allow us to outperform previous methods by a large margin in terms of accuracy in scenarios with severe occlusion and obstacles.

cs.RO↗

arXiv2020

One for Many: Transfer Learning for Building HVAC Control

The design of building heating, ventilation, and air conditioning (HVAC) system is critically important, as it accounts for around half of building energy consumption and directly affects occupant comfort, productivity, and health. Traditional HVAC control methods are typically based on creating explicit physical models for building thermal dynamics, which often require significant effort to develop and are difficult to achieve sufficient accuracy and efficiency for runtime building control and scalability for field implementations. Recently, deep reinforcement learning (DRL) has emerged as a promising data-driven method that provides good control performance without analyzing physical models at runtime. However, a major challenge to DRL (and many other data-driven learning methods) is the long training time it takes to reach the desired performance. In this work, we present a novel transfer learning based approach to overcome this challenge. Our approach can effectively transfer a DRL-based HVAC controller trained for the source building to a controller for the target building with minimal effort and improved performance, by decomposing the design of neural network controller into a transferable front-end network that captures building-agnostic behavior and a back-end network that can be efficiently trained for each specific building. We conducted experiments on a variety of transfer scenarios between buildings with different sizes, numbers of thermal zones, materials and layouts, air conditioner types, and ambient weather conditions. The experimental results demonstrated the effectiveness of our approach in significantly reducing the training time, energy cost, and temperature violations.

eess.SY↗

arXiv2020

Energy-Efficient Control Adaptation with Safety Guarantees for Learning-Enabled Cyber-Physical Systems

Neural networks have been increasingly applied for control in learning-enabled cyber-physical systems (LE-CPSs) and demonstrated great promises in improving system performance and efficiency, as well as reducing the need for complex physical models. However, the lack of safety guarantees for such neural network based controllers has significantly impeded their adoption in safety-critical CPSs. In this work, we propose a controller adaptation approach that automatically switches among multiple controllers, including neural network controllers, to guarantee system safety and improve energy efficiency. Our approach includes two key components based on formal methods and machine learning. First, we approximate each controller with a Bernstein-polynomial based hybrid system model under bounded disturbance, and compute a safe invariant set for each controller based on its corresponding hybrid system. Intuitively, the invariant set of a controller defines the state space where the system can always remain safe under its control. The union of the controllers' invariants sets then define a safe adaptation space that is larger than (or equal to) that of each controller. Second, we develop a deep reinforcement learning method to learn a controller switching strategy for reducing the control/actuation energy cost, while with the help of a safety guard rule, ensuring that the system stays within the safe space. Experiments on a linear adaptive cruise control system and a non-linear Van der Pol's oscillator demonstrate the effectiveness of our approach on energy saving and safety enhancement.

eess.SY↗