Shibo Li

Shibo Li, Xin Yu, Wei Xing et al.

Fourier Neural Operator (FNO) is a popular operator learning framework. It not only achieves the state-of-the-art performance in many tasks, but also is efficient in training and prediction. However, collecting training data for the FNO can be a costly bottleneck in practice, because it often demands expensive physical simulations. To overcome this problem, we propose Multi-Resolution Active learning of FNO (MRA-FNO), which can dynamically select the input functions and resolutions to lower the data cost as much as possible while optimizing the learning efficiency. Specifically, we propose a probabilistic multi-resolution FNO and use ensemble Monte-Carlo to develop an effective posterior inference algorithm. To conduct active learning, we maximize a utility-cost ratio as the acquisition function to acquire new examples and resolutions at each step. We use moment matching and the matrix determinant lemma to enable tractable, efficient utility computation. Furthermore, we develop a cost annealing framework to avoid over-penalizing high-resolution queries at the early stage. The over-penalization is severe when the cost difference is significant between the resolutions, which renders active learning often stuck at low-resolution queries and inferior performance. Our method overcomes this problem and applies to general multi-fidelity active learning and optimization problems. We have shown the advantage of our method in several benchmark operator learning tasks. The code is available at https://github.com/shib0li/MRA-FNO.

Zheng Wang, Shikai Fang, Shibo Li et al.

Tensor decomposition is an important tool for multiway data analysis. In practice, the data is often sparse yet associated with rich temporal information. Existing methods, however, often under-use the time information and ignore the structural knowledge within the sparsely observed tensor entries. To overcome these limitations and to better capture the underlying temporal structure, we propose Dynamic EMbedIngs fOr dynamic Tensor dEcomposition (DEMOTE). We develop a neural diffusion-reaction process to estimate dynamic embeddings for the entities in each tensor mode. Specifically, based on the observed tensor entries, we build a multi-partite graph to encode the correlation between the entities. We construct a graph diffusion process to co-evolve the embedding trajectories of the correlated entities and use a neural network to construct a reaction process for each individual entity. In this way, our model can capture both the commonalities and personalities during the evolution of the embeddings for different entities. We then use a neural network to model the entry value as a nonlinear function of the embedding trajectories. For model estimation, we combine ODE solvers to develop a stochastic mini-batch learning algorithm. We propose a stratified sampling method to balance the cost of processing each mini-batch so as to improve the overall efficiency. We show the advantage of our approach in both simulation study and real-world applications. The code is available at https://github.com/wzhut/Dynamic-Tensor-Decomposition-via-Neural-Diffusion-Reaction-Processes.

Zheng Wang, Yiming Xu, Conor Tillinghast et al.

High-order interaction events are common in real-world applications. Learning embeddings that encode the complex relationships of the participants from these events is of great importance in knowledge mining and predictive tasks. Despite the success of existing approaches, e.g. Poisson tensor factorization, they ignore the sparse structure underlying the data, namely the occurred interactions are far less than the possible interactions among all the participants. In this paper, we propose Nonparametric Embeddings of Sparse High-order interaction events (NESH). We hybridize a sparse hypergraph (tensor) process and a matrix Gaussian process to capture both the asymptotic structural sparsity within the interactions and nonlinear temporal relationships between the participants. We prove strong asymptotic bounds (including both a lower and an upper bound) of the sparsity ratio, which reveals the asymptotic properties of the sampled structure. We use batch-normalization, stick-breaking construction, and sparse variational GP approximations to develop an efficient, scalable model inference algorithm. We demonstrate the advantage of our approach in several real-world applications.

Jun Li, Shibo Li, Ying Hu et al.

Automatic radiology report generation is essential to computer-aided diagnosis. Through the success of image captioning, medical report generation has been achievable. However, the lack of annotated disease labels is still the bottleneck of this area. In addition, the image-text data bias problem and complex sentences make it more difficult to generate accurate reports. To address these gaps, we pre-sent a self-guided framework (SGF), a suite of unsupervised and supervised deep learning methods to mimic the process of human learning and writing. In detail, our framework obtains the domain knowledge from medical reports with-out extra disease labels and guides itself to extract fined-grain visual features as-sociated with the text. Moreover, SGF successfully improves the accuracy and length of medical report generation by incorporating a similarity comparison mechanism that imitates the process of human self-improvement through compar-ative practice. Extensive experiments demonstrate the utility of our SGF in the majority of cases, showing its superior performance over state-of-the-art meth-ods. Our results highlight the capacity of the proposed framework to distinguish fined-grained visual details between words and verify its advantage in generating medical reports.

Zheng Wang, Shibo Li, Shikai Fang et al.

Multi-fidelity surrogate learning is important for physical simulation related applications in that it avoids running numerical solvers from scratch, which is known to be costly, and it uses multi-fidelity examples for training and greatly reduces the cost of data collection. Despite the variety of existing methods, they all build a model to map the input parameters outright to the solution output. Inspired by the recent breakthrough in generative models, we take an alternative view and consider the solution output as generated from random noises. We develop a diffusion-generative multi-fidelity (DGMF) learning method based on stochastic differential equations (SDE), where the generation is a continuous denoising process. We propose a conditional score model to control the solution generation by the input parameters and the fidelity. By conditioning on additional inputs (temporal or spacial variables), our model can efficiently learn and predict multi-dimensional solution arrays. Our method naturally unifies discrete and continuous fidelity modeling. The advantage of our method in several typical applications shows a promising new direction for multi-fidelity learning.

Shibo Li, Hengliang Cheng, Weihua Li

The widespread application of Electronic Health Records (EHR) data in the medical field has led to early successes in disease risk prediction using deep learning methods. These methods typically require extensive data for training due to their large parameter sets. However, existing works do not exploit the full potential of EHR data. A significant challenge arises from the infrequent occurrence of many medical codes within EHR data, limiting their clinical applicability. Current research often lacks in critical areas: 1) incorporating disease domain knowledge; 2) heterogeneously learning disease representations with rich meanings; 3) capturing the temporal dynamics of disease progression. To overcome these limitations, we introduce a novel heterogeneous graph learning model designed to assimilate disease domain knowledge and elucidate the intricate relationships between drugs and diseases. This model innovatively incorporates temporal data into visit-level embeddings and leverages a time-aware transformer alongside an adaptive attention mechanism to produce patient representations. When evaluated on two healthcare datasets, our approach demonstrated notable enhancements in both prediction accuracy and interpretability over existing methodologies, signifying a substantial advancement towards personalized and proactive healthcare management.

Sipeng Chen, Yan Zhang, Shibo Li

Implicit Neural Representations (INRs) have emerged as a transformative paradigm in signal processing and computer vision, excelling in tasks from image reconstruction to 3D shape modeling. Yet their effectiveness is fundamentally limited by the absence of principled strategies for optimal configuration - spanning activation selection, initialization scales, layer-wise adaptation, and their intricate interdependencies. These choices dictate performance, stability, and generalization, but current practice relies on ad-hoc heuristics, brute-force grid searches, or task-specific tuning, often leading to inconsistent results across modalities. This work introduces OptiINR, the first unified framework that formulates INR configuration as a rigorous optimization problem. Leveraging Bayesian optimization, OptiINR efficiently explores the joint space of discrete activation families - such as sinusoidal (SIREN), wavelet-based (WIRE), and variable-periodic (FINER) - and their associated continuous initialization parameters. This systematic approach replaces fragmented manual tuning with a coherent, data-driven optimization process. By delivering globally optimal configurations, OptiINR establishes a principled foundation for INR design, consistently maximizing performance across diverse signal processing applications.

Shibo Li, Zheng Wang, Akil Narayan et al.

Model Agnostic Meta Learning (MAML) is widely used to find a good initialization for a family of tasks. Despite its success, a critical challenge in MAML is to calculate the gradient w.r.t. the initialization of a long training trajectory for the sampled tasks, because the computation graph can rapidly explode and the computational cost is very expensive. To address this problem, we propose Adjoint MAML (A-MAML). We view gradient descent in the inner optimization as the evolution of an Ordinary Differential Equation (ODE). To efficiently compute the gradient of the validation loss w.r.t. the initialization, we use the adjoint method to construct a companion, backward ODE. To obtain the gradient w.r.t. the initialization, we only need to run the standard ODE solver twice -- one is forward in time that evolves a long trajectory of gradient flow for the sampled task; the other is backward and solves the adjoint ODE. We need not create or expand any intermediate computational graphs, adopt aggressive approximations, or impose proximal regularizers in the training loss. Our approach is cheap, accurate, and adaptable to different trajectory lengths. We demonstrate the advantage of our approach in both synthetic and real-world meta-learning tasks.

Shibo Li, Wei Xing, Mike Kirby et al.

Bayesian optimization (BO) is a popular framework to optimize black-box functions. In many applications, the objective function can be evaluated at multiple fidelities to enable a trade-off between the cost and accuracy. To reduce the optimization cost, many multi-fidelity BO methods have been proposed. Despite their success, these methods either ignore or over-simplify the strong, complex correlations across the fidelities, and hence can be inefficient in estimating the objective function. To address this issue, we propose Deep Neural Network Multi-Fidelity Bayesian Optimization (DNN-MFBO) that can flexibly capture all kinds of complicated relationships between the fidelities to improve the objective function estimation and hence the optimization performance. We use sequential, fidelity-wise Gauss-Hermite quadrature and moment-matching to fulfill a mutual information-based acquisition function, which is computationally tractable and efficient. We show the advantages of our method in both synthetic benchmark datasets and real-world applications in engineering design.

Shibo Li, Wei Xing, Mike Kirby et al.

Gaussian process regression networks (GPRN) are powerful Bayesian models for multi-output regression, but their inference is intractable. To address this issue, existing methods use a fully factorized structure (or a mixture of such structures) over all the outputs and latent functions for posterior approximation, which, however, can miss the strong posterior dependencies among the latent variables and hurt the inference quality. In addition, the updates of the variational parameters are inefficient and can be prohibitively expensive for a large number of outputs. To overcome these limitations, we propose a scalable variational inference algorithm for GPRN, which not only captures the abundant posterior dependencies but also is much more efficient for massive outputs. We tensorize the output space and introduce tensor/matrix-normal variational posteriors to capture the posterior correlations and to reduce the parameters. We jointly optimize all the parameters and exploit the inherent Kronecker product structure in the variational model evidence lower bound to accelerate the computation. We demonstrate the advantages of our method in several real-world applications.