arXiv subjects

Rose Yu

Publications and source records attributed to Rose Yu.

At least 73 records · Page 4Linked to original sources

arXiv2024

Improving Convergence and Generalization Using Parameter Symmetries

In many neural networks, different values of the parameters may result in the same loss value. Parameter space symmetries are loss-invariant transformations that change the model parameters. Teleportation applies such transformations to accelerate optimization. However, the exact mechanism behind this algorithm's success is not well understood. In this paper, we show that teleportation not only speeds up optimization in the short-term, but gives overall faster time to convergence. Additionally, teleporting to minima with different curvatures improves generalization, which suggests a connection between the curvature of the minimum and generalization ability. Finally, we show that integrating teleportation into a wide range of optimization algorithms and optimization-based meta-learning improves convergence. Our results showcase the versatility of teleportation and demonstrate the potential of incorporating symmetry in optimization.

cs.LG↗

arXiv2024

Long-term Forecasting with TiDE: Time-series Dense Encoder

Recent work has shown that simple linear models can outperform several Transformer based approaches in long term time-series forecasting. Motivated by this, we propose a Multi-layer Perceptron (MLP) based encoder-decoder model, Time-series Dense Encoder (TiDE), for long-term time-series forecasting that enjoys the simplicity and speed of linear models while also being able to handle covariates and non-linear dependencies. Theoretically, we prove that the simplest linear analogue of our model can achieve near optimal error rate for linear dynamical systems (LDS) under some assumptions. Empirically, we show that our method can match or outperform prior approaches on popular long-term time-series forecasting benchmarks while being 5-10x faster than the best Transformer based model.

stat.ML↗

arXiv2024

On the Theoretical Expressive Power and the Design Space of Higher-Order Graph Transformers

Graph transformers have recently received significant attention in graph learning, partly due to their ability to capture more global interaction via self-attention. Nevertheless, while higher-order graph neural networks have been reasonably well studied, the exploration of extending graph transformers to higher-order variants is just starting. Both theoretical understanding and empirical results are limited. In this paper, we provide a systematic study of the theoretical expressive power of order-$k$ graph transformers and sparse variants. We first show that, an order-$k$ graph transformer without additional structural information is less expressive than the $k$-Weisfeiler Lehman ($k$-WL) test despite its high computational cost. We then explore strategies to both sparsify and enhance the higher-order graph transformers, aiming to improve both their efficiency and expressiveness. Indeed, sparsification based on neighborhood information can enhance the expressive power, as it provides additional information about input graph structures. In particular, we show that a natural neighborhood-based sparse order-$k$ transformer model is not only computationally efficient, but also expressive -- as expressive as $k$-WL test. We further study several other sparse graph attention models that are computationally efficient and provide their expressiveness analysis. Finally, we provide experimental results to show the effectiveness of the different sparsification strategies.

cs.LG↗

arXiv2024

Copula Conformal Prediction for Multi-step Time Series Forecasting

Accurate uncertainty measurement is a key step to building robust and reliable machine learning systems. Conformal prediction is a distribution-free uncertainty quantification algorithm popular for its ease of implementation, statistical coverage guarantees, and versatility for underlying forecasters. However, existing conformal prediction algorithms for time series are limited to single-step prediction without considering the temporal dependency. In this paper, we propose a Copula Conformal Prediction algorithm for multivariate, multi-step Time Series forecasting, CopulaCPTS. We prove that CopulaCPTS has finite sample validity guarantee. On several synthetic and real-world multivariate time series datasets, we show that CopulaCPTS produces more calibrated and sharp confidence intervals for multi-step prediction tasks than existing techniques.

cs.LG↗

arXiv2024

Learning Granger Causality from Instance-wise Self-attentive Hawkes Processes

We address the problem of learning Granger causality from asynchronous, interdependent, multi-type event sequences. In particular, we are interested in discovering instance-level causal structures in an unsupervised manner. Instance-level causality identifies causal relationships among individual events, providing more fine-grained information for decision-making. Existing work in the literature either requires strong assumptions, such as linearity in the intensity function, or heuristically defined model parameters that do not necessarily meet the requirements of Granger causality. We propose Instance-wise Self-Attentive Hawkes Processes (ISAHP), a novel deep learning framework that can directly infer the Granger causality at the event instance level. ISAHP is the first neural point process model that meets the requirements of Granger causality. It leverages the self-attention mechanism of the transformer to align with the principles of Granger causality. We empirically demonstrate that ISAHP is capable of discovering complex instance-level causal structures that cannot be handled by classical models. We also show that ISAHP achieves state-of-the-art performance in proxy tasks involving type-level causal discovery and instance-level event type prediction.

cs.LG↗

arXiv2024

MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling

Current generative models for drug discovery primarily use molecular docking to evaluate the quality of generated compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. We propose a multi-fidelity approach, Multi-Fidelity Bind (MFBind), to achieve the optimal trade-off between accuracy and computational cost. MFBind integrates docking and binding free energy simulators to train a multi-fidelity deep surrogate model with active learning. Our deep surrogate model utilizes a pretraining technique and linear prediction heads to efficiently fit small amounts of high-fidelity data. We perform extensive experiments and show that MFBind (1) outperforms other state-of-the-art single and multi-fidelity baselines in surrogate modeling, and (2) boosts the performance of generative models with markedly higher quality compounds.

q-bio.BM↗

arXiv2023

Target-Free Compound Activity Prediction via Few-Shot Learning

Predicting the activities of compounds against protein-based or phenotypic assays using only a few known compounds and their activities is a common task in target-free drug discovery. Existing few-shot learning approaches are limited to predicting binary labels (active/inactive). However, in real-world drug discovery, degrees of compound activity are highly relevant. We study Few-Shot Compound Activity Prediction (FS-CAP) and design a novel neural architecture to meta-learn continuous compound activities across large bioactivity datasets. Our model aggregates encodings generated from the known compounds and their activities to capture assay information. We also introduce a separate encoder for the unknown compound. We show that FS-CAP surpasses traditional similarity-based techniques as well as other state of the art few-shot learning methods on a variety of target-free drug discovery settings and datasets.

cs.LG↗

arXiv2023

Automatic Integration for Spatiotemporal Neural Point Processes

Learning continuous-time point processes is essential to many discrete event forecasting tasks. However, integration poses a major challenge, particularly for spatiotemporal point processes (STPPs), as it involves calculating the likelihood through triple integrals over space and time. Existing methods for integrating STPP either assume a parametric form of the intensity function, which lacks flexibility; or approximating the intensity with Monte Carlo sampling, which introduces numerical errors. Recent work by Omi et al. [2019] proposes a dual network approach for efficient integration of flexible intensity function. However, their method only focuses on the 1D temporal point process. In this paper, we introduce a novel paradigm: AutoSTPP (Automatic Integration for Spatiotemporal Neural Point Processes) that extends the dual network approach to 3D STPP. While previous work provides a foundation, its direct extension overly restricts the intensity function and leads to computational challenges. In response, we introduce a decomposable parametrization for the integral network using ProdNet. This approach, leveraging the product of simplified univariate graphs, effectively sidesteps the computational complexities inherent in multivariate computational graphs. We prove the consistency of AutoSTPP and validate it on synthetic data and benchmark real-world datasets. AutoSTPP shows a significant advantage in recovering complex intensity functions from irregular spatiotemporal events, particularly when the intensity is sharply localized. Our code is open-source at https://github.com/Rose-STL-Lab/AutoSTPP.

cs.LG↗

arXiv2023

DYffusion: A Dynamics-informed Diffusion Model for Spatiotemporal Forecasting

While diffusion models can successfully generate data and make predictions, they are predominantly designed for static images. We propose an approach for efficiently training diffusion models for probabilistic spatiotemporal forecasting, where generating stable and accurate rollout forecasts remains challenging, Our method, DYffusion, leverages the temporal dynamics in the data, directly coupling it with the diffusion steps in the model. We train a stochastic, time-conditioned interpolator and a forecaster network that mimic the forward and reverse processes of standard diffusion models, respectively. DYffusion naturally facilitates multi-step and long-range forecasting, allowing for highly flexible, continuous-time sampling trajectories and the ability to trade-off performance with accelerated sampling at inference time. In addition, the dynamics-informed diffusion process in DYffusion imposes a strong inductive bias and significantly improves computational efficiency compared to traditional Gaussian noise-based diffusion models. Our approach performs competitively on probabilistic forecasting of complex dynamics in sea surface temperatures, Navier-Stokes flows, and spring mesh systems.

cs.LG↗

arXiv2023

On the Connection Between MPNN and Graph Transformer

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

cs.LG↗

arXiv2023

Generative Adversarial Symmetry Discovery

Despite the success of equivariant neural networks in scientific applications, they require knowing the symmetry group a priori. However, it may be difficult to know which symmetry to use as an inductive bias in practice. Enforcing the wrong symmetry could even hurt the performance. In this paper, we propose a framework, LieGAN, to automatically discover equivariances from a dataset using a paradigm akin to generative adversarial training. Specifically, a generator learns a group of transformations applied to the data, which preserve the original distribution and fool the discriminator. LieGAN represents symmetry as interpretable Lie algebra basis and can discover various symmetries such as the rotation group $\mathrm{SO}(n)$, restricted Lorentz group $\mathrm{SO}(1,3)^+$ in trajectory prediction and top-quark tagging tasks. The learned symmetry can also be readily used in several existing equivariant neural networks to improve accuracy and generalization in prediction.

cs.LG↗

arXiv2023

Deep Bayesian Active Learning for Accelerating Stochastic Simulation

Stochastic simulations such as large-scale, spatiotemporal, age-structured epidemic models are computationally expensive at fine-grained resolution. While deep surrogate models can speed up the simulations, doing so for stochastic simulations and with active learning approaches is an underexplored area. We propose Interactive Neural Process (INP), a deep Bayesian active learning framework for learning deep surrogate models to accelerate stochastic simulations. INP consists of two components, a spatiotemporal surrogate model built upon Neural Process (NP) family and an acquisition function for active learning. For surrogate modeling, we develop Spatiotemporal Neural Process (STNP) to mimic the simulator dynamics. For active learning, we propose a novel acquisition function, Latent Information Gain (LIG), calculated in the latent space of NP based models. We perform a theoretical analysis and demonstrate that LIG reduces sample complexity compared with random sampling in high dimensions. We also conduct empirical studies on three complex spatiotemporal simulators for reaction diffusion, heat flow, and infectious disease. The results demonstrate that STNP outperforms the baselines in the offline learning setting and LIG achieves the state-of-the-art for Bayesian active learning.

cs.LG↗

arXiv2023

Disentangled Multi-Fidelity Deep Bayesian Active Learning

To balance quality and cost, various domain areas of science and engineering run simulations at multiple levels of sophistication. Multi-fidelity active learning aims to learn a direct mapping from input parameters to simulation outputs at the highest fidelity by actively acquiring data from multiple fidelity levels. However, existing approaches based on Gaussian processes are hardly scalable to high-dimensional data. Deep learning-based methods often impose a hierarchical structure in hidden representations, which only supports passing information from low-fidelity to high-fidelity. These approaches can lead to the undesirable propagation of errors from low-fidelity representations to high-fidelity ones. We propose a novel framework called Disentangled Multi-fidelity Deep Bayesian Active Learning (D-MFDAL), which learns the surrogate models conditioned on the distribution of functions at multiple fidelities. On benchmark tasks of learning deep surrogates of partial differential equations including heat equation, Poisson's equation and fluid simulations, our approach significantly outperforms state-of-the-art in prediction accuracy and sample efficiency.

cs.LG↗

arXiv2023

Probabilistic Symmetry for Multi-Agent Dynamics

Learning multi-agent dynamics is a core AI problem with broad applications in robotics and autonomous driving. While most existing works focus on deterministic prediction, producing probabilistic forecasts to quantify uncertainty and assess risks is critical for downstream decision-making tasks such as motion planning and collision avoidance. Multi-agent dynamics often contains internal symmetry. By leveraging symmetry, specifically rotation equivariance, we can improve not only the prediction accuracy but also uncertainty calibration. We introduce Energy Score, a proper scoring rule, to evaluate probabilistic predictions. We propose a novel deep dynamics model, Probabilistic Equivariant Continuous COnvolution (PECCO) for probabilistic prediction of multi-agent trajectories. PECCO extends equivariant continuous convolution to model the joint velocity distribution of multiple agents. It uses dynamics integration to propagate the uncertainty from velocity to position. On both synthetic and real-world datasets, PECCO shows significant improvements in accuracy and calibration compared to non-equivariant baselines.

cs.LG↗

arXiv2023

Symmetries, flat minima, and the conserved quantities of gradient flow

Empirical studies of the loss landscape of deep networks have revealed that many local minima are connected through low-loss valleys. Yet, little is known about the theoretical origin of such valleys. We present a general framework for finding continuous symmetries in the parameter space, which carve out low-loss valleys. Our framework uses equivariances of the activation functions and can be applied to different layer architectures. To generalize this framework to nonlinear neural networks, we introduce a novel set of nonlinear, data-dependent symmetries. These symmetries can transform a trained model such that it performs similarly on new samples, which allows ensemble building that improves robustness under certain adversarial attacks. We then show that conserved quantities associated with linear symmetries can be used to define coordinates along low-loss valleys. The conserved quantities help reveal that using common initialization methods, gradient flow only explores a small part of the global minimum. By relating conserved quantities to convergence rate and sharpness of the minimum, we provide insights on how initialization impacts convergence and generalizability.

cs.LG↗

arXiv2023

Understanding why shooters shoot -- An AI-powered engine for basketball performance profiling

Understanding player shooting profiles is an essential part of basketball analysis: knowing where certain opposing players like to shoot from can help coaches neutralize offensive gameplans from their opponents; understanding where their players are most comfortable can lead them to developing more effective offensive strategies. An automatic tool that can provide these performance profiles in a timely manner can become invaluable for coaches to maximize both the effectiveness of their game plan as well as the time dedicated to practice and other related activities. Additionally, basketball is dictated by many variables, such as playstyle and game dynamics, that can change the flow of the game and, by extension, player performance profiles. It is crucial that the performance profiles can reflect the diverse playstyles, as well as the fast-changing dynamics of the game. We present a tool that can visualize player performance profiles in a timely manner while taking into account factors such as play-style and game dynamics. Our approach generates interpretable heatmaps that allow us to identify and analyze how non-spatial factors, such as game dynamics or playstyle, affect player performance profiles.

cs.LG↗

arXiv2023

Physics-Guided Deep Learning for Dynamical Systems: A Survey

Modeling complex physical dynamics is a fundamental task in science and engineering. Traditional physics-based models are sample efficient, and interpretable but often rely on rigid assumptions. Furthermore, direct numerical approximation is usually computationally intensive, requiring significant computational resources and expertise, and many real-world systems do not have fully-known governing laws. While deep learning (DL) provides novel alternatives for efficiently recognizing complex patterns and emulating nonlinear dynamics, its predictions do not necessarily obey the governing laws of physical systems, nor do they generalize well across different systems. Thus, the study of physics-guided DL emerged and has gained great progress. Physics-guided DL aims to take the best from both physics-based modeling and state-of-the-art DL models to better solve scientific problems. In this paper, we provide a structured overview of existing methodologies of integrating prior physical knowledge or physics-based modeling into DL, with a special emphasis on learning dynamical systems. We also discuss the fundamental challenges and emerging opportunities in the area.

cs.LG↗

arXiv2023

Koopman Neural Forecaster for Time Series with Temporal Distribution Shifts

Temporal distributional shifts, with underlying dynamics changing over time, frequently occur in real-world time series and pose a fundamental challenge for deep neural networks (DNNs). In this paper, we propose a novel deep sequence model based on the Koopman theory for time series forecasting: Koopman Neural Forecaster (KNF) which leverages DNNs to learn the linear Koopman space and the coefficients of chosen measurement functions. KNF imposes appropriate inductive biases for improved robustness against distributional shifts, employing both a global operator to learn shared characteristics and a local operator to capture changing dynamics, as well as a specially-designed feedback loop to continuously update the learned operators over time for rapidly varying behaviors. We demonstrate that \ours{} achieves superior performance compared to the alternatives, on multiple time series datasets that are shown to suffer from distribution shifts.

cs.LG↗