arXiv subjects

Liwei Wang

Publications and source records attributed to Liwei Wang.

At least 127 records · Page 7Linked to original sources

arXiv2023

One Transformer Can Understand Both 2D & 3D Molecular Data

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D space. For molecular representation learning, most previous works designed neural networks only for a particular data format, making the learned models likely to fail for other data formats. We believe a general-purpose neural network model for chemistry should be able to handle molecular tasks across data modalities. To achieve this goal, in this work, we develop a novel Transformer-based Molecular model called Transformer-M, which can take molecular data of 2D or 3D formats as input and generate meaningful semantic representations. Using the standard Transformer as the backbone architecture, Transformer-M develops two separated channels to encode 2D and 3D structural information and incorporate them with the atom features in the network modules. When the input data is in a particular format, the corresponding channel will be activated, and the other will be disabled. By training on 2D and 3D molecular data with properly designed supervised signals, Transformer-M automatically learns to leverage knowledge from different data modalities and correctly capture the representations. We conducted extensive experiments for Transformer-M. All empirical results show that Transformer-M can simultaneously achieve strong performance on 2D and 3D tasks, suggesting its broad applicability. The code and models will be made publicly available at https://github.com/lsj2408/Transformer-M.

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arXiv2023

DSVT: Dynamic Sparse Voxel Transformer with Rotated Sets

Designing an efficient yet deployment-friendly 3D backbone to handle sparse point clouds is a fundamental problem in 3D perception. Compared with the customized sparse convolution, the attention mechanism in Transformers is more appropriate for flexibly modeling long-range relationships and is easier to be deployed in real-world applications. However, due to the sparse characteristics of point clouds, it is non-trivial to apply a standard transformer on sparse points. In this paper, we present Dynamic Sparse Voxel Transformer (DSVT), a single-stride window-based voxel Transformer backbone for outdoor 3D perception. In order to efficiently process sparse points in parallel, we propose Dynamic Sparse Window Attention, which partitions a series of local regions in each window according to its sparsity and then computes the features of all regions in a fully parallel manner. To allow the cross-set connection, we design a rotated set partitioning strategy that alternates between two partitioning configurations in consecutive self-attention layers. To support effective downsampling and better encode geometric information, we also propose an attention-style 3D pooling module on sparse points, which is powerful and deployment-friendly without utilizing any customized CUDA operations. Our model achieves state-of-the-art performance with a broad range of 3D perception tasks. More importantly, DSVT can be easily deployed by TensorRT with real-time inference speed (27Hz). Code will be available at \url{https://github.com/Haiyang-W/DSVT}.

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arXiv2023

Proactive Rumor Control: When Impression Counts (Full Version)

The spread of rumors in online networks threatens public safety and results in economic losses. To overcome this problem, a lot of work studies the problem of rumor control which aims at limiting the spread of rumors. However, all previous work ignores the relationship between the influence block effect and counts of impressions on the user. In this paper, we study the problem of minimizing the spread of rumors when impression counts. Given a graph $G(V,E)$, a rumor set $R \in V$ and a budget $k$, it aims to find a protector set $P \in V \backslash R$ to minimize the spread of the rumor set $R$ under the budget $k$. Due to the impression counts, two following challenges of our problem need to be overcome: (1) our problem is NP-hard; (2) the influence block is non-submodular, which means a straightforward greedy approach is not applicable. Hence, we devise a branch-and-bound framework for this problem with a ($1-1/e-ε$) approximation ratio. To further improve the efficiency, we speed up our framework with a progressive upper bound estimation method, which achieves a ($1-1/e-ε- ρ$) approximation ratio. We conduct experiments on real-world datasets to verify the efficiency, effectiveness, and scalability of our methods.

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arXiv2023

A Cross-institutional Evaluation on Breast Cancer Phenotyping NLP Algorithms on Electronic Health Records

Objective: The generalizability of clinical large language models is usually ignored during the model development process. This study evaluated the generalizability of BERT-based clinical NLP models across different clinical settings through a breast cancer phenotype extraction task. Materials and Methods: Two clinical corpora of breast cancer patients were collected from the electronic health records from the University of Minnesota and the Mayo Clinic, and annotated following the same guideline. We developed three types of NLP models (i.e., conditional random field, bi-directional long short-term memory and CancerBERT) to extract cancer phenotypes from clinical texts. The models were evaluated for their generalizability on different test sets with different learning strategies (model transfer vs. locally trained). The entity coverage score was assessed with their association with the model performances. Results: We manually annotated 200 and 161 clinical documents at UMN and MC, respectively. The corpora of the two institutes were found to have higher similarity between the target entities than the overall corpora. The CancerBERT models obtained the best performances among the independent test sets from two clinical institutes and the permutation test set. The CancerBERT model developed in one institute and further fine-tuned in another institute achieved reasonable performance compared to the model developed on local data (micro-F1: 0.925 vs 0.932). Conclusions: The results indicate the CancerBERT model has the best learning ability and generalizability among the three types of clinical NLP models. The generalizability of the models was found to be correlated with the similarity of the target entities between the corpora.

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arXiv2023

Denoising Masked AutoEncoders Help Robust Classification

In this paper, we propose a new self-supervised method, which is called Denoising Masked AutoEncoders (DMAE), for learning certified robust classifiers of images. In DMAE, we corrupt each image by adding Gaussian noises to each pixel value and randomly masking several patches. A Transformer-based encoder-decoder model is then trained to reconstruct the original image from the corrupted one. In this learning paradigm, the encoder will learn to capture relevant semantics for the downstream tasks, which is also robust to Gaussian additive noises. We show that the pre-trained encoder can naturally be used as the base classifier in Gaussian smoothed models, where we can analytically compute the certified radius for any data point. Although the proposed method is simple, it yields significant performance improvement in downstream classification tasks. We show that the DMAE ViT-Base model, which just uses 1/10 parameters of the model developed in recent work arXiv:2206.10550, achieves competitive or better certified accuracy in various settings. The DMAE ViT-Large model significantly surpasses all previous results, establishing a new state-of-the-art on ImageNet dataset. We further demonstrate that the pre-trained model has good transferability to the CIFAR-10 dataset, suggesting its wide adaptability. Models and code are available at https://github.com/quanlin-wu/dmae.

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arXiv2023

Provable Sim-to-real Transfer in Continuous Domain with Partial Observations

Sim-to-real transfer trains RL agents in the simulated environments and then deploys them in the real world. Sim-to-real transfer has been widely used in practice because it is often cheaper, safer and much faster to collect samples in simulation than in the real world. Despite the empirical success of the sim-to-real transfer, its theoretical foundation is much less understood. In this paper, we study the sim-to-real transfer in continuous domain with partial observations, where the simulated environments and real-world environments are modeled by linear quadratic Gaussian (LQG) systems. We show that a popular robust adversarial training algorithm is capable of learning a policy from the simulated environment that is competitive to the optimal policy in the real-world environment. To achieve our results, we design a new algorithm for infinite-horizon average-cost LQGs and establish a regret bound that depends on the intrinsic complexity of the model class. Our algorithm crucially relies on a novel history clipping scheme, which might be of independent interest.

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arXiv2023

Nearly Minimax Optimal Offline Reinforcement Learning with Linear Function Approximation: Single-Agent MDP and Markov Game

Offline reinforcement learning (RL) aims at learning an optimal strategy using a pre-collected dataset without further interactions with the environment. While various algorithms have been proposed for offline RL in the previous literature, the minimax optimality has only been (nearly) established for tabular Markov decision processes (MDPs). In this paper, we focus on offline RL with linear function approximation and propose a new pessimism-based algorithm for offline linear MDP. At the core of our algorithm is the uncertainty decomposition via a reference function, which is new in the literature of offline RL under linear function approximation. Theoretical analysis demonstrates that our algorithm can match the performance lower bound up to logarithmic factors. We also extend our techniques to the two-player zero-sum Markov games (MGs), and establish a new performance lower bound for MGs, which tightens the existing result, and verifies the nearly minimax optimality of the proposed algorithm. To the best of our knowledge, these are the first computationally efficient and nearly minimax optimal algorithms for offline single-agent MDPs and MGs with linear function approximation.

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arXiv2023

Learning Physics-Informed Neural Networks without Stacked Back-propagation

Physics-Informed Neural Network (PINN) has become a commonly used machine learning approach to solve partial differential equations (PDE). But, facing high-dimensional secondorder PDE problems, PINN will suffer from severe scalability issues since its loss includes second-order derivatives, the computational cost of which will grow along with the dimension during stacked back-propagation. In this work, we develop a novel approach that can significantly accelerate the training of Physics-Informed Neural Networks. In particular, we parameterize the PDE solution by the Gaussian smoothed model and show that, derived from Stein's Identity, the second-order derivatives can be efficiently calculated without back-propagation. We further discuss the model capacity and provide variance reduction methods to address key limitations in the derivative estimation. Experimental results show that our proposed method can achieve competitive error compared to standard PINN training but is significantly faster. Our code is released at https://github.com/LithiumDA/PINN-without-Stacked-BP.

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arXiv2023

Designing BERT for Convolutional Networks: Sparse and Hierarchical Masked Modeling

We identify and overcome two key obstacles in extending the success of BERT-style pre-training, or the masked image modeling, to convolutional networks (convnets): (i) convolution operation cannot handle irregular, random-masked input images; (ii) the single-scale nature of BERT pre-training is inconsistent with convnet's hierarchical structure. For (i), we treat unmasked pixels as sparse voxels of 3D point clouds and use sparse convolution to encode. This is the first use of sparse convolution for 2D masked modeling. For (ii), we develop a hierarchical decoder to reconstruct images from multi-scale encoded features. Our method called Sparse masKed modeling (SparK) is general: it can be used directly on any convolutional model without backbone modifications. We validate it on both classical (ResNet) and modern (ConvNeXt) models: on three downstream tasks, it surpasses both state-of-the-art contrastive learning and transformer-based masked modeling by similarly large margins (around +1.0%). Improvements on object detection and instance segmentation are more substantial (up to +3.5%), verifying the strong transferability of features learned. We also find its favorable scaling behavior by observing more gains on larger models. All this evidence reveals a promising future of generative pre-training on convnets. Codes and models are released at https://github.com/keyu-tian/SparK.

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arXiv2022

Pessimistic Minimax Value Iteration: Provably Efficient Equilibrium Learning from Offline Datasets

We study episodic two-player zero-sum Markov games (MGs) in the offline setting, where the goal is to find an approximate Nash equilibrium (NE) policy pair based on a dataset collected a priori. When the dataset does not have uniform coverage over all policy pairs, finding an approximate NE involves challenges in three aspects: (i) distributional shift between the behavior policy and the optimal policy, (ii) function approximation to handle large state space, and (iii) minimax optimization for equilibrium solving. We propose a pessimism-based algorithm, dubbed as pessimistic minimax value iteration (PMVI), which overcomes the distributional shift by constructing pessimistic estimates of the value functions for both players and outputs a policy pair by solving NEs based on the two value functions. Furthermore, we establish a data-dependent upper bound on the suboptimality which recovers a sublinear rate without the assumption on uniform coverage of the dataset. We also prove an information-theoretical lower bound, which suggests that the data-dependent term in the upper bound is intrinsic. Our theoretical results also highlight a notion of "relative uncertainty", which characterizes the necessary and sufficient condition for achieving sample efficiency in offline MGs. To the best of our knowledge, we provide the first nearly minimax optimal result for offline MGs with function approximation.

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arXiv2022

Is $L^2$ Physics-Informed Loss Always Suitable for Training Physics-Informed Neural Network?

The Physics-Informed Neural Network (PINN) approach is a new and promising way to solve partial differential equations using deep learning. The $L^2$ Physics-Informed Loss is the de-facto standard in training Physics-Informed Neural Networks. In this paper, we challenge this common practice by investigating the relationship between the loss function and the approximation quality of the learned solution. In particular, we leverage the concept of stability in the literature of partial differential equation to study the asymptotic behavior of the learned solution as the loss approaches zero. With this concept, we study an important class of high-dimensional non-linear PDEs in optimal control, the Hamilton-Jacobi-Bellman(HJB) Equation, and prove that for general $L^p$ Physics-Informed Loss, a wide class of HJB equation is stable only if $p$ is sufficiently large. Therefore, the commonly used $L^2$ loss is not suitable for training PINN on those equations, while $L^{\infty}$ loss is a better choice. Based on the theoretical insight, we develop a novel PINN training algorithm to minimize the $L^{\infty}$ loss for HJB equations which is in a similar spirit to adversarial training. The effectiveness of the proposed algorithm is empirically demonstrated through experiments. Our code is released at https://github.com/LithiumDA/L_inf-PINN.

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arXiv2022

Discrimination, calibration, and point estimate accuracy of GRU-D-Weibull architecture for real-time individualized endpoint prediction

Real-time individual endpoint prediction has always been a challenging task but of great clinic utility for both patients and healthcare providers. With 6,879 chronic kidney disease stage 4 (CKD4) patients as a use case, we explored the feasibility and performance of gated recurrent units with decay that models Weibull probability density function (GRU-D-Weibull) as a semi-parametric longitudinal model for real-time individual endpoint prediction. GRU-D-Weibull has a maximum C-index of 0.77 at 4.3 years of follow-up, compared to 0.68 achieved by competing models. The L1-loss of GRU-D-Weibull is ~66% of XGB(AFT), ~60% of MTLR, and ~30% of AFT model at CKD4 index date. The average absolute L1-loss of GRU-D-Weibull is around one year, with a minimum of 40% Parkes serious error after index date. GRU-D-Weibull is not calibrated and significantly underestimates true survival probability. Feature importance tests indicate blood pressure becomes increasingly important during follow-up, while eGFR and blood albumin are less important. Most continuous features have non-linear/parabola impact on predicted survival time, and the results are generally consistent with existing knowledge. GRU-D-Weibull as a semi-parametric temporal model shows advantages in built-in parameterization of missing, native support for asynchronously arrived measurement, capability of output both probability and point estimates at arbitrary time point for arbitrary prediction horizon, improved discrimination and point estimate accuracy after incorporating newly arrived data. Further research on its performance with more comprehensive input features, in-process or post-process calibration are warranted to benefit CKD4 or alike terminally-ill patients.

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arXiv2022

Nearly Optimal Policy Optimization with Stable at Any Time Guarantee

Policy optimization methods are one of the most widely used classes of Reinforcement Learning (RL) algorithms. However, theoretical understanding of these methods remains insufficient. Even in the episodic (time-inhomogeneous) tabular setting, the state-of-the-art theoretical result of policy-based method in \citet{shani2020optimistic} is only $\tilde{O}(\sqrt{S^2AH^4K})$ where $S$ is the number of states, $A$ is the number of actions, $H$ is the horizon, and $K$ is the number of episodes, and there is a $\sqrt{SH}$ gap compared with the information theoretic lower bound $\tildeΩ(\sqrt{SAH^3K})$. To bridge such a gap, we propose a novel algorithm Reference-based Policy Optimization with Stable at Any Time guarantee (\algnameacro), which features the property "Stable at Any Time". We prove that our algorithm achieves $\tilde{O}(\sqrt{SAH^3K} + \sqrt{AH^4K})$ regret. When $S > H$, our algorithm is minimax optimal when ignoring logarithmic factors. To our best knowledge, RPO-SAT is the first computationally efficient, nearly minimax optimal policy-based algorithm for tabular RL.

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arXiv2022

A Unified Mutual Supervision Framework for Referring Expression Segmentation and Generation

Reference Expression Segmentation (RES) and Reference Expression Generation (REG) are mutually inverse tasks that can be naturally jointly trained. Though recent work has explored such joint training, the mechanism of how RES and REG can benefit each other is still unclear. In this paper, we propose a unified mutual supervision framework that enables two tasks to improve each other. Our mutual supervision contains two directions. On the one hand, Disambiguation Supervision leverages the expression unambiguity measurement provided by RES to enhance the language generation of REG. On the other hand, Generation Supervision uses expressions automatically generated by REG to scale up the training of RES. Such unified mutual supervision effectively improves two tasks by solving their bottleneck problems. Extensive experiments show that our approach significantly outperforms all existing methods on REG and RES tasks under the same setting, and detailed ablation studies demonstrate the effectiveness of all components in our framework.

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arXiv2022

Eliciting Knowledge from Large Pre-Trained Models for Unsupervised Knowledge-Grounded Conversation

Recent advances in large-scale pre-training provide large models with the potential to learn knowledge from the raw text. It is thus natural to ask whether it is possible to leverage these large models as knowledge bases for downstream tasks. In this work, we answer the aforementioned question in unsupervised knowledge-grounded conversation. We explore various methods that best elicit knowledge from large models. Our human study indicates that, though hallucinations exist, large models post the unique advantage of being able to output common sense and summarize facts that cannot be directly retrieved from the search engine. To better exploit such generated knowledge in dialogue generation, we treat the generated knowledge as a noisy knowledge source and propose the posterior-based reweighing as well as the noisy training strategy. Empirical results on two benchmarks show advantages over the state-of-the-art methods.

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arXiv2022

FlowEval: A Consensus-Based Dialogue Evaluation Framework Using Segment Act Flows

Despite recent progress in open-domain dialogue evaluation, how to develop automatic metrics remains an open problem. We explore the potential of dialogue evaluation featuring dialog act information, which was hardly explicitly modeled in previous methods. However, defined at the utterance level in general, dialog act is of coarse granularity, as an utterance can contain multiple segments possessing different functions. Hence, we propose segment act, an extension of dialog act from utterance level to segment level, and crowdsource a large-scale dataset for it. To utilize segment act flows, sequences of segment acts, for evaluation, we develop the first consensus-based dialogue evaluation framework, FlowEval. This framework provides a reference-free approach for dialog evaluation by finding pseudo-references. Extensive experiments against strong baselines on three benchmark datasets demonstrate the effectiveness and other desirable characteristics of our FlowEval, pointing out a potential path for better dialogue evaluation.

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arXiv2022

A 5G Enabled Adaptive Computing Workflow for Greener Power Grid

5G wireless technology can deliver higher data speeds, ultra low latency, more reliability, massive network capacity, increased availability, and a more uniform user experience to users. It brings additional power to help address the challenges brought by renewable integration and decarbonization. In this paper, a 5G enabled adaptive computing workflow has been presented that consists of various computing resources, such as 5G equipment, edge computing, cluster, Graphics processing unit (GPU) and cloud computing, with two examples showing technical feasibility for edge-grid-cloud interaction for power system real-time monitoring, security assessment, and forecasting. Benefiting from the high speed data transport and massive connection capability of 5G, the workflow shows its potential to seamlessly integrate various applications at distributed and/or centralized locations to build more complex and powerful functions, with better flexibility.

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arXiv2022

Your Transformer May Not be as Powerful as You Expect

Relative Positional Encoding (RPE), which encodes the relative distance between any pair of tokens, is one of the most successful modifications to the original Transformer. As far as we know, theoretical understanding of the RPE-based Transformers is largely unexplored. In this work, we mathematically analyze the power of RPE-based Transformers regarding whether the model is capable of approximating any continuous sequence-to-sequence functions. One may naturally assume the answer is in the affirmative -- RPE-based Transformers are universal function approximators. However, we present a negative result by showing there exist continuous sequence-to-sequence functions that RPE-based Transformers cannot approximate no matter how deep and wide the neural network is. One key reason lies in that most RPEs are placed in the softmax attention that always generates a right stochastic matrix. This restricts the network from capturing positional information in the RPEs and limits its capacity. To overcome the problem and make the model more powerful, we first present sufficient conditions for RPE-based Transformers to achieve universal function approximation. With the theoretical guidance, we develop a novel attention module, called Universal RPE-based (URPE) Attention, which satisfies the conditions. Therefore, the corresponding URPE-based Transformers become universal function approximators. Extensive experiments covering typical architectures and tasks demonstrate that our model is parameter-efficient and can achieve superior performance to strong baselines in a wide range of applications. The code will be made publicly available at https://github.com/lsj2408/URPE.

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