NeurIPS 2024 Papers

The operations and maintenance of satellite networks heavily depend on traffic measurements. Due to the large-scale and highly dynamic nature of satellite networks, global measurement encounters significant challenges in terms of complexity and overhead. Estimating global network traffic data from partial traffic measurements is a promising solution. However, the majority of current estimation methods concentrate on low-rank linear decomposition, which is unable to accurately estimate. The reason lies in its inability to capture the intricate nonlinear spatio-temporal relationship found in large-scale, highly dynamic traffic data. This paper proposes Satformer, an accurate and robust method for estimating traffic data in satellite networks. In Satformer, we innovatively incorporate an adaptive sparse spatio-temporal attention mechanism. In the mechanism, more attention is paid to specific local regions of the input tensor to improve the model's sensitivity on details and patterns. This method enhances its capability to capture nonlinear spatio-temporal relationships. Experiments on small, medium, and large-scale satellite networks datasets demonstrate that Satformer outperforms mathematical and neural baseline methods notably. It provides substantial improvements in reducing errors and maintaining robustness, especially for larger networks. The approach shows promise for deployment in actual systems.

Link prediction is a critical problem in graph learning with broad applications such as recommender systems and knowledge graph completion. Numerous research efforts have been directed at solving this problem, including approaches based on similarity metrics and Graph Neural Networks (GNN). However, most existing solutions are still rooted in conventional supervised learning, which makes it challenging to adapt over time to changing customer interests and to address the inherent dilemma of exploitation versus exploration in link prediction. To tackle these challenges, this paper reformulates link prediction as a sequential decision-making process, where each link prediction interaction occurs sequentially. We propose a novel fusion algorithm, PRB (PageRank Bandits), which is the first to combine contextual bandits with PageRank for collaborative exploitation and exploration. We also introduce a new reward formulation and provide a theoretical performance guarantee for PRB. Finally, we extensively evaluate PRB in both online and offline settings, comparing it with bandit-based and graph-based methods. The empirical success of PRB demonstrates the value of the proposed fusion approach. Our code is released at https://github.com/jiaruzouu/PRB.

Training neural networks on NP-complete problems typically demands very large amounts of training data and often needs to be coupled with computationally expensive symbolic verifiers to ensure output correctness. In this paper, we present NeuRes, a neuro-symbolic approach to address both challenges for propositional satisfiability, being the quintessential NP-complete problem. By combining certificate-driven training and expert iteration, our model learns better representations than models trained for classification only, with a much higher data efficiency -- requiring orders of magnitude less training data. NeuRes employs propositional resolution as a proof system to generate proofs of unsatisfiability and to accelerate the process of finding satisfying truth assignments, exploring both possibilities in parallel. To realize this, we propose an attention-based architecture that autoregressively selects pairs of clauses from a dynamic formula embedding to derive new clauses. Furthermore, we employ expert iteration whereby model-generated proofs progressively replace longer teacher proofs as the new ground truth. This enables our model to reduce a dataset of proofs generated by an advanced solver by $\sim$$32$% after training on it with no extra guidance. This shows that NeuRes is not limited by the optimality of the teacher algorithm owing to its self-improving workflow. We show that our model achieves far better performance than NeuroSAT in terms of both correctly classified and proven instances.

Neural operators effectively solve PDE problems from data without knowing the explicit equations, which learn the map from the input sequences of observed samples to the predicted values. Most existing works build the model in the original geometric space, leading to high computational costs when the number of sample points is large. We present the Latent Neural Operator (LNO) solving PDEs in the latent space. In particular, we first propose Physics-Cross-Attention (PhCA) transforming representation from the geometric space to the latent space, then learn the operator in the latent space, and finally recover the real-world geometric space via the inverse PhCA map. Our model retains flexibility that can decode values in any position not limited to locations defined in the training set, and therefore can naturally perform interpolation and extrapolation tasks particularly useful for inverse problems. Moreover, the proposed LNO improves both prediction accuracy and computational efficiency. Experiments show that LNO reduces the GPU memory by 50%, speeds up training 1.8 times, and reaches state-of-the-art accuracy on four out of six benchmarks for forward problems and a benchmark for inverse problem. Code is available at https://github.com/L-I-M-I-T/LatentNeuralOperator.

We develop a novel measurement framework based on Gaussian process coregionalization model to address a long-lasting debate in psychometrics: whether psychological features like personality share a common structure across the population or vary uniquely for individuals. We propose idiographic personality Gaussian process (IPGP), an intermediate model that accommodates both shared trait structure across individuals and "idiographic" deviations. IPGP leverages the Gaussian process coregionalization model to conceptualize responses of grouped survey batteries but adjusted to non-Gaussian ordinal data, and exploits stochastic variational inference for latent factor estimation. Using both synthetic data and a novel survey, we show that IPGP improves both prediction of actual responses and estimation of intrapersonal response patterns compared to existing benchmarks. In the survey study, IPGP also identifies unique clusters of personality taxonomies, displaying great potential in advancing individualized approaches to psychological diagnosis.

We investigate learning the eigenfunctions of evolution operators for time-reversal invariant stochastic processes, a prime example being the Langevin equation used in molecular dynamics. Many physical or chemical processes described by this equation involve transitions between metastable states separated by high potential barriers that can hardly be crossed during a simulation. To overcome this bottleneck, data are collected via biased simulations that explore the state space more rapidly. We propose a framework for learning from biased simulations rooted in the infinitesimal generator of the process {and the associated resolvent operator}. We contrast our approach to more common ones based on the transfer operator, showing that it can provably learn the spectral properties of the unbiased system from biased data. In experiments, we highlight the advantages of our method over transfer operator approaches and recent developments based on generator learning, demonstrating its effectiveness in estimating eigenfunctions and eigenvalues. Importantly, we show that even with datasets containing only a few relevant transitions due to sub-optimal biasing, our approach recovers relevant information about the transition mechanism.

Machine learning models provide alternatives for efficiently recognizing complex patterns from data, but the main concern in applying them to modeling physical systems stems from their physics-agnostic design, leading to learning methods that lack interpretability, robustness, and data efficiency. This paper mitigates this concern by incorporating the Helmholtz-Hodge decomposition into a Gaussian process model, leading to a versatile framework that simultaneously learns the curl-free and divergence-free components of a dynamical system. Learning a predictive model in this form facilitates the exploitation of symmetry priors. In addition to improving predictive power, these priors make the model indentifiable, thus the identified features can be linked to comprehensible scientific properties of the system. We show that compared to baseline models, our model achieves better predictive performance on several benchmark dynamical systems while allowing physically meaningful decomposition of the systems from noisy and sparse data.

Learning safe policies has presented a longstanding challenge for the reinforcement learning (RL) community. Various formulations of safe RL have been proposed; However, fundamentally, tabula rasa RL must learn safety constraints through experience, which is problematic for real-world applications. Imitation learning is often preferred in real-world settings because the experts' safety preferences are embedded in the data the agent imitates. However, imitation learning is limited in its extensibility to new tasks, which can only be learned by providing the agent with expert trajectories. For safety-critical applications with sub-optimal or inexact expert data, it would be preferable to learn only the safety aspects of the policy through imitation, while still allowing for task learning with RL. The field of inverse constrained RL, which seeks to infer constraints from expert data, is a promising step in this direction. However, prior work in this area has relied on complex tri-level optimizations in order to infer safe behavior (constraints). This challenging optimization landscape leads to sub-optimal performance on several benchmark tasks. In this work, we present a simplified version of constraint inference that performs as well or better than prior work across a collection of continuous-control benchmarks. Moreover, besides improving performance, this simplified framework is easier to implement, tune, and more readily lends itself to various extensions, such as offline constraint inference.

Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's $h$-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's $h$-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks.

Digital Twins (DTs) are computational models that simulate the states and temporal dynamics of real-world systems, playing a crucial role in prediction, understanding, and decision-making across diverse domains. However, existing approaches to DTs often struggle to generalize to unseen conditions in data-scarce settings, a crucial requirement for such models. To address these limitations, our work begins by establishing the essential desiderata for effective DTs. Hybrid Digital Twins (**HDTwins**) represent a promising approach to address these requirements, modeling systems using a composition of both mechanistic and neural components. This hybrid architecture simultaneously leverages (partial) domain knowledge and neural network expressiveness to enhance generalization, with its modular design facilitating improved evolvability. While existing hybrid models rely on expert-specified architectures with only parameters optimized on data, *automatically* specifying and optimizing HDTwins remains intractable due to the complex search space and the need for flexible integration of domain priors. To overcome this complexity, we propose an evolutionary algorithm (**HDTwinGen**) that employs Large Language Models (LLMs) to autonomously propose, evaluate, and optimize HDTwins. Specifically, LLMs iteratively generate novel model specifications, while offline tools are employed to optimize emitted parameters. Correspondingly, proposed models are evaluated and evolved based on targeted feedback, enabling the discovery of increasingly effective hybrid models. Our empirical results reveal that HDTwinGen produces generalizable, sample-efficient, and evolvable models, significantly advancing DTs' efficacy in real-world applications.

Graph Neural Networks (GNNs) have emerged as the predominant approach for learning over graph-structured data. However, most GNNs operate as black-box models and require post-hoc explanations, which may not suffice in high-stakes scenarios where transparency is crucial. In this paper, we present a GNN that is interpretable by design. Our model, Graph Neural Additive Network (GNAN), is a novel extension of the interpretable class of Generalized Additive Models, and can be visualized and fully understood by humans. GNAN is designed to be fully interpretable, offering both global and local explanations at the feature and graph levels through direct visualization of the model. These visualizations describe exactly how the model uses the relationships between the target variable, the features, and the graph. We demonstrate the intelligibility of GNANs in a series of examples on different tasks and datasets. In addition, we show that the accuracy of GNAN is on par with black-box GNNs, making it suitable for critical applications where transparency is essential, alongside high accuracy.

In this paper, we obtain the Berry–Esseen bound for multivariate normal approximation for the Polyak-Ruppert averaged iterates of the linear stochastic approximation (LSA) algorithm with decreasing step size. Moreover, we prove the non-asymptotic validity of the confidence intervals for parameter estimation with LSA based on multiplier bootstrap. This procedure updates the LSA estimate together with a set of randomly perturbed LSA estimates upon the arrival of subsequent observations. We illustrate our findings in the setting of temporal difference learning with linear function approximation.

Molecule generation ideally in its 3-D form has enjoyed wide applications in material, chemistry, life science, etc. We propose the first quantum parametric circuit for 3-D molecule generation for its potential quantum advantage especially considering the arrival of Noisy Intermediate-Scale Quantum (NISQ) era. We choose the Variational AutoEncoder (VAE) scheme for its simplicity and one-shot generation ability, which we believe is more quantum-friendly compared with the auto-regressive generative models or diffusion models as used in classic approaches. Specifically, we present a quantum encoding scheme designed for 3-D molecules with qubits complexity $\mathcal{O}(C\log n)$ ($n$ is the number of atoms) and adopt a von Mises-Fisher (vMF) distributed latent space to meet the inherent coherence of the quantum system. We further design to encode conditions into quantum circuits for property-specified generation. Experimentally, our model could generate plausible 3-D molecules and achieve competitive quantitative performance with significantly reduced circuit parameters compared with their classic counterparts. The source code will be released upon publication.

Human motion capture from monocular videos has made significant progress in recent years. However, modern approaches often produce temporal artifacts, e.g. in form of jittery motion and struggle to achieve smooth and physically plausible motions. Explicitly integrating physics, in form of internal forces and exterior torques, helps alleviating these artifacts. Current state-of-the-art approaches make use of an automatic PD controller to predict torques and reaction forces in order to re-simulate the input kinematics, i.e. the joint angles of a predefined skeleton. However, due to imperfect physical models, these methods often require simplifying assumptions and extensive preprocessing of the input kinematics to achieve good performance. To this end, we propose a novel method to selectively incorporate the physics models with the kinematics observations in an online setting, inspired by a neural Kalman-filtering approach. We develop a control loop as a meta-PD controller to predict internal joint torques and external reaction forces, followed by a physics-based motion simulation. A recurrent neural network is introduced to realize a Kalman filter that attentively balances the kinematics input and simulated motion, resulting in an optimal-state dynamics prediction. We show that this filtering step is crucial to provide an online supervision that helps balancing the shortcoming of the respective input motions, thus being important for not only capturing accurate global motion trajectories but also producing physically plausible human poses. The proposed approach excels in the physics-based human pose estimation task and demonstrates the physical plausibility of the predictive dynamics, compared to state of the art. The code is available on https://github.com/cuongle1206/OSDCap.

Widely adopted in modern Vision Transformer designs, Softmax attention can effectively capture long-range visual information; however, it incurs excessive computational cost when dealing with high-resolution inputs. In contrast, linear attention naturally enjoys linear complexity and has great potential to scale up to higher-resolution images. Nonetheless, the unsatisfactory performance of linear attention greatly limits its practical application in various scenarios. In this paper, we take a step forward to close the gap between the linear and Softmax attention with novel theoretical analyses, which demystify the core factors behind the performance deviations. Specifically, we present two key perspectives to understand and alleviate the limitations of linear attention: the injective property and the local modeling ability. Firstly, we prove that linear attention is not injective, which is prone to assign identical attention weights to different query vectors, thus adding to severe semantic confusion since different queries correspond to the same outputs. Secondly, we confirm that effective local modeling is essential for the success of Softmax attention, in which linear attention falls short. The aforementioned two fundamental differences significantly contribute to the disparities between these two attention paradigms, which is demonstrated by our substantial empirical validation in the paper. In addition, more experiment results indicate that linear attention, as long as endowed with these two properties, can outperform Softmax attention across various tasks while maintaining lower computation complexity. Code is available at https://github.com/LeapLabTHU/InLine.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further research of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we also evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research and application. The code is available at \url{https://github.com/Westlake-OmicsAI/NovoBench}.

This paper considers the problem of learning from multiple sets of inaccurate labels, which can be easily obtained from low-cost annotators, such as rule-based annotators. Previous works typically concentrate on aggregating information from all the annotators, overlooking the significance of data refinement. This paper presents a collaborative refining approach for learning from inaccurate labels. To refine the data, we introduce the annotator agreement as an instrument, which refers to whether multiple annotators agree or disagree on the labels for a given sample. For samples where some annotators disagree, a comparative strategy is proposed to filter noise. Through theoretical analysis, the connections among multiple sets of labels, the respective models trained on them, and the true labels are uncovered to identify relatively reliable labels. For samples where all annotators agree, an aggregating strategy is designed to mitigate potential noise. Guided by theoretical bounds on loss values, a sample selection criterion is introduced and modified to be more robust against potentially problematic values. Through these two methods, all the samples are refined during training, and these refined samples are used to train a lightweight model simultaneously. Extensive experiments are conducted on benchmark and real-world datasets to demonstrate the superiority of our methods.

Tuning scientific and probabilistic machine learning models - for example, partial differential equations, Gaussian processes, or Bayesian neural networks - often relies on evaluating functions of matrices whose size grows with the data set or the number of parameters. While the state-of-the-art for _evaluating_ these quantities is almost always based on Lanczos and Arnoldi iterations, the present work is the first to explain how to _differentiate_ these workhorses of numerical linear algebra efficiently. To get there, we derive previously unknown adjoint systems for Lanczos and Arnoldi iterations, implement them in JAX, and show that the resulting code can compete with Diffrax when it comes to differentiating PDEs, GPyTorch for selecting Gaussian process models and beats standard factorisation methods for calibrating Bayesian neural networks. All this is achieved without any problem-specific code optimisation. Find the code at [link redacted] and install the library with *pip install [redacted]*.

Optimizing discrete black-box functions is key in several domains, e.g. protein engineering and drug design. Due to the lack of gradient information and the need for sample efficiency, Bayesian optimization is an ideal candidate for these tasks. Several methods for high-dimensional continuous and categorical Bayesian optimization have been proposed recently. However, our survey of the field reveals highly heterogeneous experimental set-ups across methods and technical barriers for the replicability and application of published algorithms to real-world tasks. To address these issues, we develop a unified framework to test a vast array of high-dimensional Bayesian optimization methods and a collection of standardized black-box functions representing real-world application domains in chemistry and biology. These two components of the benchmark are each supported by flexible, scalable, and easily extendable software libraries (poli and poli-baselines), allowing practitioners to readily incorporate new optimization objectives or discrete optimizers. Project website: https://machinelearninglifescience.github.io/hdbo_benchmark.