arXiv subjects

Rose Yu

Publications and source records attributed to Rose Yu.

At least 91 records · Page 5Linked to original sources

arXiv2023

Symmetry Teleportation for Accelerated Optimization

Existing gradient-based optimization methods update parameters locally, in a direction that minimizes the loss function. We study a different approach, symmetry teleportation, that allows parameters to travel a large distance on the loss level set, in order to improve the convergence speed in subsequent steps. Teleportation exploits symmetries in the loss landscape of optimization problems. We derive loss-invariant group actions for test functions in optimization and multi-layer neural networks, and prove a necessary condition for teleportation to improve convergence rate. We also show that our algorithm is closely related to second order methods. Experimentally, we show that teleportation improves the convergence speed of gradient descent and AdaGrad for several optimization problems including test functions, multi-layer regressions, and MNIST classification.

cs.LG↗

arXiv2022

AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to generalize to novel (i.e., never-before-seen) structures. We first unveil the mechanisms responsible for this shortcoming, demonstrating how models rely on shortcuts that leverage the topology of the protein-ligand bipartite network, rather than learning the node features. Then, we introduce AI-Bind, a pipeline that combines network-based sampling strategies with unsupervised pre-training, allowing us to limit the annotation imbalance and improve binding predictions for novel proteins and ligands. We illustrate the value of AI-Bind by predicting drugs and natural compounds with binding affinity to SARS-CoV-2 viral proteins and the associated human proteins. We also validate these predictions via docking simulations and comparison with recent experimental evidence, and step up the process of interpreting machine learning prediction of protein-ligand binding by identifying potential active binding sites on the amino acid sequence. Overall, AI-Bind offers a powerful high-throughput approach to identify drug-target combinations, with the potential of becoming a powerful tool in drug discovery.

q-bio.QM↗

arXiv2022

Meta-Learning Dynamics Forecasting Using Task Inference

Current deep learning models for dynamics forecasting struggle with generalization. They can only forecast in a specific domain and fail when applied to systems with different parameters, external forces, or boundary conditions. We propose a model-based meta-learning method called DyAd which can generalize across heterogeneous domains by partitioning them into different tasks. DyAd has two parts: an encoder which infers the time-invariant hidden features of the task with weak supervision, and a forecaster which learns the shared dynamics of the entire domain. The encoder adapts and controls the forecaster during inference using adaptive instance normalization and adaptive padding. Theoretically, we prove that the generalization error of such procedure is related to the task relatedness in the source domain, as well as the domain differences between source and target. Experimentally, we demonstrate that our model outperforms state-of-the-art approaches on both turbulent flow and real-world ocean data forecasting tasks.

cs.LG↗

arXiv2022

Predicting the Future of AI with AI: High-quality link prediction in an exponentially growing knowledge network

A tool that could suggest new personalized research directions and ideas by taking insights from the scientific literature could significantly accelerate the progress of science. A field that might benefit from such an approach is artificial intelligence (AI) research, where the number of scientific publications has been growing exponentially over the last years, making it challenging for human researchers to keep track of the progress. Here, we use AI techniques to predict the future research directions of AI itself. We develop a new graph-based benchmark based on real-world data -- the Science4Cast benchmark, which aims to predict the future state of an evolving semantic network of AI. For that, we use more than 100,000 research papers and build up a knowledge network with more than 64,000 concept nodes. We then present ten diverse methods to tackle this task, ranging from pure statistical to pure learning methods. Surprisingly, the most powerful methods use a carefully curated set of network features, rather than an end-to-end AI approach. It indicates a great potential that can be unleashed for purely ML approaches without human knowledge. Ultimately, better predictions of new future research directions will be a crucial component of more advanced research suggestion tools.

cs.AI↗

arXiv2022

Data Augmentation vs. Equivariant Networks: A Theory of Generalization on Dynamics Forecasting

Exploiting symmetry in dynamical systems is a powerful way to improve the generalization of deep learning. The model learns to be invariant to transformation and hence is more robust to distribution shift. Data augmentation and equivariant networks are two major approaches to injecting symmetry into learning. However, their exact role in improving generalization is not well understood. In this work, we derive the generalization bounds for data augmentation and equivariant networks, characterizing their effect on learning in a unified framework. Unlike most prior theories for the i.i.d. setting, we focus on non-stationary dynamics forecasting with complex temporal dependencies.

cs.LG↗

arXiv2022

LIMO: Latent Inceptionism for Targeted Molecule Generation

Generation of drug-like molecules with high binding affinity to target proteins remains a difficult and resource-intensive task in drug discovery. Existing approaches primarily employ reinforcement learning, Markov sampling, or deep generative models guided by Gaussian processes, which can be prohibitively slow when generating molecules with high binding affinity calculated by computationally-expensive physics-based methods. We present Latent Inceptionism on Molecules (LIMO), which significantly accelerates molecule generation with an inceptionism-like technique. LIMO employs a variational autoencoder-generated latent space and property prediction by two neural networks in sequence to enable faster gradient-based reverse-optimization of molecular properties. Comprehensive experiments show that LIMO performs competitively on benchmark tasks and markedly outperforms state-of-the-art techniques on the novel task of generating drug-like compounds with high binding affinity, reaching nanomolar range against two protein targets. We corroborate these docking-based results with more accurate molecular dynamics-based calculations of absolute binding free energy and show that one of our generated drug-like compounds has a predicted $K_D$ (a measure of binding affinity) of $6 \cdot 10^{-14}$ M against the human estrogen receptor, well beyond the affinities of typical early-stage drug candidates and most FDA-approved drugs to their respective targets. Code is available at https://github.com/Rose-STL-Lab/LIMO.

cs.LG↗

arXiv2022

Approximately Equivariant Networks for Imperfectly Symmetric Dynamics

Incorporating symmetry as an inductive bias into neural network architecture has led to improvements in generalization, data efficiency, and physical consistency in dynamics modeling. Methods such as CNNs or equivariant neural networks use weight tying to enforce symmetries such as shift invariance or rotational equivariance. However, despite the fact that physical laws obey many symmetries, real-world dynamical data rarely conforms to strict mathematical symmetry either due to noisy or incomplete data or to symmetry breaking features in the underlying dynamical system. We explore approximately equivariant networks which are biased towards preserving symmetry but are not strictly constrained to do so. By relaxing equivariance constraints, we find that our models can outperform both baselines with no symmetry bias and baselines with overly strict symmetry in both simulated turbulence domains and real-world multi-stream jet flow.

cs.LG↗

arXiv2022

Multi-fidelity Hierarchical Neural Processes

Science and engineering fields use computer simulation extensively. These simulations are often run at multiple levels of sophistication to balance accuracy and efficiency. Multi-fidelity surrogate modeling reduces the computational cost by fusing different simulation outputs. Cheap data generated from low-fidelity simulators can be combined with limited high-quality data generated by an expensive high-fidelity simulator. Existing methods based on Gaussian processes rely on strong assumptions of the kernel functions and can hardly scale to high-dimensional settings. We propose Multi-fidelity Hierarchical Neural Processes (MF-HNP), a unified neural latent variable model for multi-fidelity surrogate modeling. MF-HNP inherits the flexibility and scalability of Neural Processes. The latent variables transform the correlations among different fidelity levels from observations to latent space. The predictions across fidelities are conditionally independent given the latent states. It helps alleviate the error propagation issue in existing methods. MF-HNP is flexible enough to handle non-nested high dimensional data at different fidelity levels with varying input and output dimensions. We evaluate MF-HNP on epidemiology and climate modeling tasks, achieving competitive performance in terms of accuracy and uncertainty estimation. In contrast to deep Gaussian Processes with only low-dimensional (< 10) tasks, our method shows great promise for speeding up high-dimensional complex simulations (over 7000 for epidemiology modeling and 45000 for climate modeling).

cs.LG↗

arXiv2022

Faster Optimization on Sparse Graphs via Neural Reparametrization

In mathematical optimization, second-order Newton's methods generally converge faster than first-order methods, but they require the inverse of the Hessian, hence are computationally expensive. However, we discover that on sparse graphs, graph neural networks (GNN) can implement an efficient Quasi-Newton method that can speed up optimization by a factor of 10-100x. Our method, neural reparametrization, modifies the optimization parameters as the output of a GNN to reshape the optimization landscape. Using a precomputed Hessian as the propagation rule, the GNN can effectively utilize the second-order information, reaching a similar effect as adaptive gradient methods. As our method solves optimization through architecture design, it can be used in conjunction with any optimizers such as Adam and RMSProp. We show the application of our method on scientifically relevant problems including heat diffusion, synchronization and persistent homology.

cs.LG↗

arXiv2022

SELFIES and the future of molecular string representations

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The machine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, SMILES, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, SMILES has several shortcomings -- most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100\% robustness: SELFIES (SELF-referencIng Embedded Strings). SELFIES has since simplified and enabled numerous new applications in chemistry. In this manuscript, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete Future Projects for robust molecular representations. These involve the extension toward new chemical domains, exciting questions at the interface of AI and robust languages and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.

physics.chem-ph↗

arXiv2022

Taming the Long Tail of Deep Probabilistic Forecasting

Deep probabilistic forecasting is gaining attention in numerous applications ranging from weather prognosis, through electricity consumption estimation, to autonomous vehicle trajectory prediction. However, existing approaches focus on improvements on the most common scenarios without addressing the performance on rare and difficult cases. In this work, we identify a long tail behavior in the performance of state-of-the-art deep learning methods on probabilistic forecasting. We present two moment-based tailedness measurement concepts to improve performance on the difficult tail examples: Pareto Loss and Kurtosis Loss. Kurtosis loss is a symmetric measurement as the fourth moment about the mean of the loss distribution. Pareto loss is asymmetric measuring right tailedness, modeling the loss using a generalized Pareto distribution (GPD). We demonstrate the performance of our approach on several real-world datasets including time series and spatiotemporal trajectories, achieving significant improvements on the tail examples.

cs.LG↗

arXiv2021

Automatic Symmetry Discovery with Lie Algebra Convolutional Network

Existing equivariant neural networks require prior knowledge of the symmetry group and discretization for continuous groups. We propose to work with Lie algebras (infinitesimal generators) instead of Lie groups. Our model, the Lie algebra convolutional network (L-conv) can automatically discover symmetries and does not require discretization of the group. We show that L-conv can serve as a building block to construct any group equivariant feedforward architecture. Both CNNs and Graph Convolutional Networks can be expressed as L-conv with appropriate groups. We discover direct connections between L-conv and physics: (1) group invariant loss generalizes field theory (2) Euler-Lagrange equation measures the robustness, and (3) equivariance leads to conservation laws and Noether current.These connections open up new avenues for designing more general equivariant networks and applying them to important problems in physical sciences

cs.LG↗

arXiv2021

Quantifying Uncertainty in Deep Spatiotemporal Forecasting

Deep learning is gaining increasing popularity for spatiotemporal forecasting. However, prior works have mostly focused on point estimates without quantifying the uncertainty of the predictions. In high stakes domains, being able to generate probabilistic forecasts with confidence intervals is critical to risk assessment and decision making. Hence, a systematic study of uncertainty quantification (UQ) methods for spatiotemporal forecasting is missing in the community. In this paper, we describe two types of spatiotemporal forecasting problems: regular grid-based and graph-based. Then we analyze UQ methods from both the Bayesian and the frequentist point of view, casting in a unified framework via statistical decision theory. Through extensive experiments on real-world road network traffic, epidemics, and air quality forecasting tasks, we reveal the statistical and computational trade-offs for different UQ methods: Bayesian methods are typically more robust in mean prediction, while confidence levels obtained from frequentist methods provide more extensive coverage over data variations. Computationally, quantile regression type methods are cheaper for a single confidence interval but require re-training for different intervals. Sampling based methods generate samples that can form multiple confidence intervals, albeit at a higher computational cost.

cs.AI↗

arXiv2021

Bridging Physics-based and Data-driven modeling for Learning Dynamical Systems

How can we learn a dynamical system to make forecasts, when some variables are unobserved? For instance, in COVID-19, we want to forecast the number of infected and death cases but we do not know the count of susceptible and exposed people. While mechanics compartment models are widely used in epidemic modeling, data-driven models are emerging for disease forecasting. We first formalize the learning of physics-based models as AutoODE, which leverages automatic differentiation to estimate the model parameters. Through a benchmark study on COVID-19 forecasting, we notice that physics-based mechanistic models significantly outperform deep learning. Our method obtains a 57.4% reduction in mean absolute errors for 7-day ahead COVID-19 forecasting compared with the best deep learning competitor. Such performance differences highlight the generalization problem in dynamical system learning due to distribution shift. We identify two scenarios where distribution shift can occur: changes in data domain and changes in parameter domain (system dynamics). Through systematic experiments on several dynamical systems, we found that deep learning models fail to forecast well under both scenarios. While much research on distribution shift has focused on changes in the data domain, our work calls attention to rethink generalization for learning dynamical systems.

cs.LG↗

arXiv2021

Traffic Forecasting using Vehicle-to-Vehicle Communication

We take the first step in using vehicle-to-vehicle (V2V) communication to provide real-time on-board traffic predictions. In order to best utilize real-world V2V communication data, we integrate first principle models with deep learning. Specifically, we train recurrent neural networks to improve the predictions given by first principle models. Our approach is able to predict the velocity of individual vehicles up to a minute into the future with improved accuracy over first principle-based baselines. We conduct a comprehensive study to evaluate different methods of integrating first principle models with deep learning techniques. The source code for our models is available at https://github.com/Rose-STL-Lab/V2V-traffic-forecast .

cs.LG↗

arXiv2021

DeepGLEAM: A hybrid mechanistic and deep learning model for COVID-19 forecasting

We introduce DeepGLEAM, a hybrid model for COVID-19 forecasting. DeepGLEAM combines a mechanistic stochastic simulation model GLEAM with deep learning. It uses deep learning to learn the correction terms from GLEAM, which leads to improved performance. We further integrate various uncertainty quantification methods to generate confidence intervals. We demonstrate DeepGLEAM on real-world COVID-19 mortality forecasting tasks.

cs.LG↗

arXiv2021

Trajectory Prediction using Equivariant Continuous Convolution

Trajectory prediction is a critical part of many AI applications, for example, the safe operation of autonomous vehicles. However, current methods are prone to making inconsistent and physically unrealistic predictions. We leverage insights from fluid dynamics to overcome this limitation by considering internal symmetry in real-world trajectories. We propose a novel model, Equivariant Continous COnvolution (ECCO) for improved trajectory prediction. ECCO uses rotationally-equivariant continuous convolutions to embed the symmetries of the system. On both vehicle and pedestrian trajectory datasets, ECCO attains competitive accuracy with significantly fewer parameters. It is also more sample efficient, generalizing automatically from few data points in any orientation. Lastly, ECCO improves generalization with equivariance, resulting in more physically consistent predictions. Our method provides a fresh perspective towards increasing trust and transparency in deep learning models.

cs.LG↗

arXiv2021

Incorporating Symmetry into Deep Dynamics Models for Improved Generalization

Recent work has shown deep learning can accelerate the prediction of physical dynamics relative to numerical solvers. However, limited physical accuracy and an inability to generalize under distributional shift limit its applicability to the real world. We propose to improve accuracy and generalization by incorporating symmetries into convolutional neural networks. Specifically, we employ a variety of methods each tailored to enforce a different symmetry. Our models are both theoretically and experimentally robust to distributional shift by symmetry group transformations and enjoy favorable sample complexity. We demonstrate the advantage of our approach on a variety of physical dynamics including Rayleigh Bénard convection and real-world ocean currents and temperatures. Compared with image or text applications, our work is a significant step towards applying equivariant neural networks to high-dimensional systems with complex dynamics. We open-source our simulation, data, and code at \url{https://github.com/Rose-STL-Lab/Equivariant-Net}.

cs.LG↗