NeurIPS 2024 Papers

Large Language Models (LLMs) are consistently improving at increasingly realistic software engineering (SE) tasks. In real-world software stacks, significant SE effort is spent developing foundational system software like the Linux kernel. Unlike application-level software, a systems codebase like Linux is multilingual (low-level C/Assembly/Bash/Rust); gigantic (>20 million lines); critical (impacting billions of devices worldwide), and highly concurrent (involving complex multi-threading). To evaluate if machine learning (ML) models are useful while developing such large-scale systems-level software, we introduce kGym (a platform) and kBench (a dataset). The kGym platform provides a SE environment for large-scale experiments on the Linux kernel, including compiling and running kernels in parallel across several virtual machines, detecting operations and crashes, inspecting logs, and querying and patching the code base. We use kGym to facilitate evaluation on kBench, a crash resolution benchmark drawn from real-world Linux kernel bugs. An example bug in kBench contains crashing stack traces, a bug-reproducer file, a developer-written fix, and other associated data. To understand current performance, we conduct baseline experiments by prompting LLMs to resolve Linux kernel crashes. Our initial evaluations reveal that the best performing LLM achieves 0.72\% and 5.38\% in the unassisted and assisted (i.e., buggy files disclosed to the model) settings, respectively. These results highlight the need for further research to enhance model performance in SE tasks. Improving performance on kBench requires models to master new learning skills, including understanding the cause of crashes and repairing faults, writing memory-safe and hardware-aware code, and understanding concurrency. As a result, this work opens up multiple avenues of research at the intersection of machine learning and systems software.

This work studies the problem of out-of-distribution fluid dynamics modeling. Previous works usually design effective neural operators to learn from mesh-based data structures. However, in real-world applications, they would suffer from distribution shifts from the variance of system parameters and temporal evolution of the dynamical system. In this paper, we propose a novel approach named \underline{P}rompt Evol\underline{u}tion with G\underline{r}aph OD\underline{E} (\method{}) for out-of-distribution fluid dynamics modeling. The core of our \method{} is to learn time-evolving prompts using a graph ODE to adapt spatio-temporal forecasting models to different scenarios. In particular, our \method{} first learns from historical observations and system parameters in the frequency domain to explore multi-view context information, which could effectively initialize prompt embeddings. More importantly, we incorporate the interpolation of observation sequences into a graph ODE, which can capture the temporal evolution of prompt embeddings for model adaptation. These time-evolving prompt embeddings are then incorporated into basic forecasting models to overcome temporal distribution shifts. We also minimize the mutual information between prompt embeddings and observation embeddings to enhance the robustness of our model to different distributions. Extensive experiments on various benchmark datasets validate the superiority of the proposed \method{} in comparison to various baselines.

We introduce a general framework for solving partial differential equations (PDEs) using generative diffusion models. In particular, we focus on the scenarios where we do not have the full knowledge of the scene necessary to apply classical solvers. Most existing forward or inverse PDE approaches perform poorly when the observations on the data or the underlying coefficients are incomplete, which is a common assumption for real-world measurements. In this work, we propose DiffusionPDE that can simultaneously fill in the missing information and solve a PDE by modeling the joint distribution of the solution and coefficient spaces. We show that the learned generative priors lead to a versatile framework for accurately solving a wide range of PDEs under partial observation, significantly outperforming the state-of-the-art methods for both forward and inverse directions.

Garment animation is ubiquitous in various applications, such as virtual reality, gaming, and film producing. Recently, learning-based approaches obtain compelling performance in animating diverse garments under versatile scenarios. Nevertheless, to mimic the deformations of the observed garments, data-driven methods require large scale of garment data, which are both resource-wise expensive and time-consuming. In addition, forcing models to match the dynamics of observed garment animation may hinder the potentials to generalize to unseen cases. In this paper, instead of using garment-wise supervised-learning we adopt a disentangled scheme to learn how to animate observed garments: 1). learning constitutive behaviors from the observed cloth; 2). dynamically animate various garments constrained by the learned constitutive laws. Specifically, we propose Energy Unit network (EUNet) to model the constitutive relations in the format of energy. Without the priors from analytical physics models and differentiable simulation engines, EUNet is able to directly capture the constitutive behaviors from the observed piece of cloth and uniformly describes the change of energy caused by deformations, such as stretching and bending. We further apply the pre-trained EUNet to animate various garments based on energy optimizations. The disentangled scheme alleviates the need of garment data and enables us to utilize the dynamics of a piece of cloth for animating garments. Experiments show that while EUNet effectively delivers the energy gradients due to the deformations, models constrained by EUNet achieve more stable and physically plausible performance comparing with those trained in garment-wise supervised manner.

A fundamental problem in quantum many-body physics is that of finding ground states of local Hamiltonians. A number of recent works gave provably efficient machine learning (ML) algorithms for learning ground states. Specifically, [Huang et al. Science 2022], introduced an approach for learning properties of the ground state of an $n$-qubit gapped local Hamiltonian $H$ from only $n^{\mathcal{O}(1)}$ data points sampled from Hamiltonians in the same phase of matter. This was subsequently improved by [Lewis et al. Nature Communications 2024], to $\mathcal{O}(\log 𝑛)$ samples when the geometry of the $n$-qubit system is known. In this work, we introduce two approaches that achieve a constant sample complexity, independent of system size $n$, for learning ground state properties. Our first algorithm consists of a simple modification of the ML model used by Lewis et al. and applies to a property of interest known beforehand. Our second algorithm, which applies even if a description of the property is not known, is a deep neural network model. While empirical results showing the performance of neural networks have been demonstrated, to our knowledge, this is the first rigorous sample complexity bound on a neural network model for predicting ground state properties. We also perform numerical experiments that confirm the improved scaling of our approach compared to earlier results.

We propose a novel and general method to learn Bregman divergences from raw high-dimensional data that measure similarity between images in pixel space. As a prototypical application, we learn divergences that consider real-world corruptions of images (e.g., blur) as close to the original and noisy perturbations as far, even if in $L^p$-distance the opposite holds. We also show that the learned Bregman divergence excels on datasets of human perceptual similarity judgment, suggesting its utility in a range of applications. We then define adversarial attacks by replacing the projected gradient descent (PGD) with the mirror descent associated with the learned Bregman divergence, and use them to improve the state-of-the-art in robustness through adversarial training for common image corruptions. In particular, for the contrast corruption that was found problematic in prior work we achieve an accuracy that exceeds the $L^p$- and the LPIPS-based adversarially trained neural networks by a margin of 27.16\% on the CIFAR-10-C corruption data set.

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show preliminary results on scaling to protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Recent advances in automated theorem proving leverages language models to explore expanded search spaces by step-by-step proof generation. However, such approaches are usually based on short-sighted heuristics (e.g., log probability or value function scores) that potentially lead to suboptimal or even distracting subgoals, preventing us from finding longer proofs. To address this challenge, we propose POETRY (PrOvE Theorems RecursivelY), which proves theorems in a recursive, level-by-level manner in the Isabelle theorem prover. Unlike previous step-by-step methods, POETRY searches for a verifiable sketch of the proof at each level and focuses on solving the current level's theorem or conjecture. Detailed proofs of intermediate conjectures within the sketch are temporarily replaced by a placeholder tactic called sorry, deferring their proofs to subsequent levels. This approach allows the theorem to be tackled incrementally by outlining the overall theorem at the first level and then solving the intermediate conjectures at deeper levels. Experiments are conducted on the miniF2F and PISA datasets and significant performance gains are observed in our POETRY approach over state-of-the-art methods. POETRY on miniF2F achieves an average proving success rate improvement of 5.1%. Moreover, we observe a substantial increase in the maximum proof length found by POETRY, from 10 to 26.

Sequential recommender systems (SRS) aim to predict users' subsequent choices based on their historical interactions and have found applications in diverse fields such as e-commerce and social media. However, in real-world systems, most users interact with only a handful of items, while the majority of items are seldom consumed. These two issues, known as the long-tail user and long-tail item challenges, often pose difficulties for existing SRS. These challenges can adversely affect user experience and seller benefits, making them crucial to address. Though a few works have addressed the challenges, they still struggle with the seesaw or noisy issues due to the intrinsic scarcity of interactions. The advancements in large language models (LLMs) present a promising solution to these problems from a semantic perspective. As one of the pioneers in this field, we propose the Large Language Models Enhancement framework for Sequential Recommendation (LLM-ESR). This framework utilizes semantic embeddings derived from LLMs to enhance SRS without adding extra inference load. To address the long-tail item challenge, we design a dual-view modeling framework that combines semantics from LLMs and collaborative signals from conventional SRS. For the long-tail user challenge, we propose a retrieval augmented self-distillation method to enhance user preference representation using more informative interactions from similar users. To verify the effectiveness and versatility of our proposed enhancement framework, we conduct extensive experiments on three real-world datasets using three popular SRS models. The results consistently show that our method surpasses existing baselines. The implementation code is available in Supplementary Material.

Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the molecular structure, including the presence or absence of functional groups. Chemists leverage the complementary nature of the different methods to their advantage. However, the lack of a comprehensive multimodal dataset, containing spectra from a variety of spectroscopic techniques, has limited machine-learning approaches mostly to single-modality tasks for predicting molecular structures from spectra. Here we introduce a dataset comprising simulated $^1$H-NMR, $^{13}$C-NMR, HSQC-NMR, Infrared, and Mass spectra (positive and negative ion modes) for 790k molecules extracted from chemical reactions in patent data. This dataset enables the development of foundation models for integrating information from multiple spectroscopic modalities, emulating the approach employed by human experts. Additionally, we provide benchmarks for evaluating single-modality tasks such as structure elucidation, predicting the spectra for a target molecule, and functional group predictions. This dataset has the potential automate structure elucidation, streamlining the molecular discovery pipeline from synthesis to structure determination. The dataset and code for the benchmarks can be found at https://rxn4chemistry.github.io/multimodal-spectroscopic-dataset (Available upon submission of the supporting information).

This paper introduces SICSM, a novel structural inference framework that integrates Selective State Space Models (selective SSMs) with Generative Flow Networks (GFNs) to handle the challenges posed by dynamical systems with irregularly sampled trajectories and partial observations. By utilizing the robust temporal modeling capabilities of selective SSMs, our approach learns input-dependent transition functions that adapt to non-uniform time intervals, thereby enhancing the accuracy of structural inference. By aggregating dynamics across diverse temporal dependencies and channeling them into the GFN, the SICSM adeptly approximates the posterior distribution of the system's structure. This process not only enables precise inference of complex interactions within partially observed systems but also ensures the seamless integration of prior knowledge, enhancing the model’s accuracy and robustness. Extensive evaluations on sixteen diverse datasets demonstrate that SICSM outperforms existing methods, particularly in scenarios characterized by irregular sampling and incomplete observations, which highlight its potential as a reliable tool for scientific discovery and system diagnostics in disciplines that demand precise modeling of complex interactions.

To reduce annotation costs, it is common in crowdsourcing to collect only a few noisy labels from different crowd workers for each instance. However, the limited noisy labels restrict the performance of label integration algorithms in inferring the unknown true label for the instance. Recent works have shown that leveraging neighbor instances can help alleviate this problem. Yet, these works all assume that each instance has the same neighborhood size, which defies common sense. To address this gap, we propose a novel label integration algorithm called K-free nearest neighbor (KFNN). In KFNN, the neighborhood size of each instance is automatically determined based on its attributes and noisy labels. Specifically, KFNN initially estimates a Mahalanobis distance distribution from the attribute space to model the relationship between each instance and all classes. This distance distribution is then utilized to enhance the multiple noisy label distribution of each instance. Subsequently, a Kalman filter is designed to mitigate the impact of noise incurred by neighbor instances. Finally, KFNN determines the optimal neighborhood size by the max-margin learning. Extensive experimental results demonstrate that KFNN significantly outperforms all the other state-of-the-art algorithms and exhibits greater robustness in various crowdsourcing scenarios.

Exploiting symmetry inherent in data can significantly improve the sample efficiency of a learning procedure and the generalization of learned models. When data clearly reveals underlying symmetry, leveraging this symmetry can naturally inform the design of model architectures or learning strategies. Yet, in numerous real-world scenarios, identifying the specific symmetry within a given data distribution often proves ambiguous. To tackle this, some existing works learn symmetry in a data-driven manner, parameterizing and learning expected symmetry through data. However, these methods often rely on explicit knowledge, such as pre-defined Lie groups, which are typically restricted to linear or affine transformations. In this paper, we propose a novel symmetry learning algorithm based on transformations defined with one-parameter groups, continuously parameterized transformations flowing along the directions of vector fields called infinitesimal generators. Our method is built upon minimal inductive biases, encompassing not only commonly utilized symmetries rooted in Lie groups but also extending to symmetries derived from nonlinear generators. To learn these symmetries, we introduce a notion of a validity score that examine whether the transformed data is still valid for the given task. The validity score is designed to be fully differentiable and easily computable, enabling effective searches for transformations that achieve symmetries innate to the data. We apply our method mainly in two domains: image data and partial differential equations, and demonstrate its advantages. Our codes are available at \url{https://github.com/kogyeonghoon/learning-symmetry-from-scratch.git}.

Physics-informed neural networks (PINNs) have been widely applied to solve partial differential equations (PDEs) by enforcing outputs and gradients of deep models to satisfy target equations. Due to the limitation of numerical computation, PINNs are conventionally optimized on finite selected points. However, since PDEs are usually defined on continuous domains, solely optimizing models on scattered points may be insufficient to obtain an accurate solution for the whole domain. To mitigate this inherent deficiency of the default scatter-point optimization, this paper proposes and theoretically studies a new training paradigm as region optimization. Concretely, we propose to extend the optimization process of PINNs from isolated points to their continuous neighborhood regions, which can theoretically decrease the generalization error, especially for hidden high-order constraints of PDEs. A practical training algorithm, Region Optimized PINN (RoPINN), is seamlessly derived from this new paradigm, which is implemented by a straightforward but effective Monte Carlo sampling method. By calibrating the sampling process into trust regions, RoPINN finely balances optimization and generalization error. Experimentally, RoPINN consistently boosts the performance of diverse PINNs on a wide range of PDEs without extra backpropagation or gradient calculation. Code is available at this repository: https://github.com/thuml/RoPINN.

In recent years, machine learning has established itself as a powerful tool for high-resolution weather forecasting. While most current machine learning models focus on deterministic forecasts, accurately capturing the uncertainty in the chaotic weather system calls for probabilistic modeling. We propose a probabilistic weather forecasting model called Graph-EFM, combining a flexible latent-variable formulation with the successful graph-based forecasting framework. The use of a hierarchical graph construction allows for efficient sampling of spatially coherent forecasts. Requiring only a single forward pass per time step, Graph-EFM allows for fast generation of arbitrarily large ensembles. We experiment with the model on both global and limited area forecasting. Ensemble forecasts from Graph-EFM achieve equivalent or lower errors than comparable deterministic models, with the added benefit of accurately capturing forecast uncertainty.

Existing neural operator architectures face challenges when solving multiphysics problems with coupled partial differential equations (PDEs) due to complex geometries, interactions between physical variables, and the limited amounts of high-resolution training data. To address these issues, we propose *Codomain Attention Neural Operator* (CoDA-NO), which tokenizes functions along the codomain or channel space, enabling self-supervised learning or pretraining of multiple PDE systems. Specifically, we extend positional encoding, self-attention, and normalization layers to function spaces. CoDA-NO can learn representations of different PDE systems with a single model. We evaluate CoDA-NO's potential as a backbone for learning multiphysics PDEs over multiple systems by considering few-shot learning settings. On complex downstream tasks with limited data, such as fluid flow simulations, fluid-structure interactions, and Rayleigh-Bénard convection, we found CoDA-NO to outperform existing methods by over 36%.

Recently, Conditional Neural Fields (NeFs) have emerged as a powerful modelling paradigm for PDEs, by learning solutions as flows in the latent space of the Conditional NeF. Although benefiting from favourable properties of NeFs such as grid-agnosticity and space-time-continuous dynamics modelling, this approach limits the ability to impose known constraints of the PDE on the solutions -- such as symmetries or boundary conditions -- in favour of modelling flexibility. Instead, we propose a space-time continuous NeF-based solving framework that - by preserving geometric information in the latent space of the Conditional NeF - preserves known symmetries of the PDE. We show that modelling solutions as flows of pointclouds over the group of interest $G$ improves generalization and data-efficiency. Furthermore, we validate that our framework readily generalizes to unseen spatial and temporal locations, as well as geometric transformations of the initial conditions - where other NeF-based PDE forecasting methods fail -, and improve over baselines in a number of challenging geometries.

Precision matrix estimation is a ubiquitous task featuring numerous applications such as rare disease diagnosis and neural connectivity exploration. However, this task becomes challenging in small sample settings, where the number of samples is significantly less than the number of dimensions, leading to unreliable estimates. Previous approaches either fail to perform well in small sample settings or suffer from inefficient estimation processes, even when incorporating meta-learning techniques. To this end, we propose a novel approach FasMe for Fast and Sample-efficient Meta Precision Matrix Learning, which first extracts meta-knowledge through a multi-task learning diagram. Then, meta-knowledge constraints are applied using a maximum determinant matrix completion algorithm for the novel task. As a result, we reduce the sample size requirements to $O(\log p/K)$ per meta-training task and $O(\log\vert \mathcal{G}\vert)$ for the meta-testing task. Moreover, the hereby proposed model only needs $O(p \log\epsilon^{-1})$ time and $O(p)$ memory for converging to an $\epsilon$-accurate solution. On multiple synthetic and biomedical datasets, FasMe is at least ten times faster than the four baselines while promoting prediction accuracy in small sample settings.

Energy-based models (EBMs) offer a flexible framework for probabilistic modelling across various data domains. However, training EBMs on data in discrete or mixed state spaces poses significant challenges due to the lack of robust and fast sampling methods. In this work, we propose to train discrete EBMs with Energy Discrepancy, a loss function which only requires the evaluation of the energy function at data points and their perturbed counterparts, thus eliminating the need for Markov chain Monte Carlo. We introduce perturbations of the data distribution by simulating a diffusion process on the discrete state space endowed with a graph structure. This allows us to inform the choice of perturbation from the structure of the modelled discrete variable, while the continuous time parameter enables fine-grained control of the perturbation. Empirically, we demonstrate the efficacy of the proposed approaches in a wide range of applications, including the estimation of discrete densities with non-binary vocabulary and binary image modelling. We also introduce the first application of EBMs to tabular data sets with applications in synthetic data generation and calibrated classification.