NeurIPS 2024 Papers

We introduce an efficient method for learning linear models from uncertain data, where uncertainty is represented as a set of possible variations in the data, leading to predictive multiplicity. Our approach leverages abstract interpretation and zonotopes, a type of convex polytope, to compactly represent these dataset variations, enabling the symbolic execution of gradient descent on all possible worlds simultaneously. We develop techniques to ensure that this process converges to a fixed point and derive closed-form solutions for this fixed point. Our method provides sound over-approximations of all possible optimal models and viable prediction ranges. We demonstrate the effectiveness of our approach through theoretical and empirical analysis, highlighting its potential to reason about model and prediction uncertainty due to data quality issues in training data.

Electromagnetic field simulation is central to designing, optimizing, and validating photonic devices and circuits. However, costly computation associated with numerical simulation poses a significant bottleneck, hindering scalability and turnaround time in the photonic circuit design process. Neural operators offer a promising alternative, but existing SOTA approaches, Neurolight, struggle with predicting high-fidelity fields for real-world complicated photonic devices, with the best reported 0.38 normalized mean absolute error in Neurolight. The interplays of highly complex light-matter interaction, e.g., scattering and resonance, sensitivity to local structure details, non-uniform learning complexity for full-domain simulation, and rich frequency information, contribute to the failure of existing neural PDE solvers. In this work, we boost the prediction fidelity to an unprecedented level for simulating complex photonic devices with a novel operator design driven by the above challenges. We propose a novel cross-axis factorized PACE operator with a strong long-distance modeling capacity to connect the full-domain complex field pattern with local device structures. Inspired by human learning, we further divide and conquer the simulation task for extremely hard cases into two progressively easy tasks, with a first-stage model learning an initial solution refined by a second model. On various complicated photonic device benchmarks, we demonstrate one sole PACE model is capable of achieving 73% lower error with 50% fewer parameters compared with various recent ML for PDE solvers. The two-stage setup further advances high-fidelity simulation for even more intricate cases. In terms of runtime, PACE demonstrates 154-577x and 11.8-12x simulation speedup over numerical solver using scipy or highly-optimized pardiso solver, respectively. We open-sourced the code and *complicated* optical device dataset at [PACE-Light](https://github.com/zhuhanqing/PACE-Light).

Despite recent popularity of attention-based neural architectures in core AI fields like natural language processing (NLP) and computer vision (CV), their potential in modeling complex physical systems remains under-explored. Learning problems in physical systems are often characterized as discovering operators that map between function spaces based on a few instances of function pairs. This task frequently presents a severely ill-posed PDE inverse problem. In this work, we propose a novel neural operator architecture based on the attention mechanism, which we coin Nonlocal Attention Operator (NAO), and explore its capability towards developing a foundation physical model. In particular, we show that the attention mechanism is equivalent to a double integral operator that enables nonlocal interactions among spatial tokens, with a data-dependent kernel characterizing the inverse mapping from data to the hidden parameter field of the underlying operator. As such, the attention mechanism extracts global prior information from training data generated by multiple systems, and suggests the exploratory space in the form of a nonlinear kernel map. Consequently, NAO can address ill-posedness and rank deficiency in inverse PDE problems by encoding regularization and achieving generalizability. Lastly, we empirically demonstrate the advantages of NAO over baseline neural models in terms of the generalizability to unseen data resolutions and system states. Our work not only suggests a novel neural operator architecture for learning an interpretable foundation model of physical systems, but also offers a new perspective towards understanding the attention mechanism.

Data-driven algorithm design is a paradigm that uses statistical and machine learning techniques to select from a class of algorithms for a computational problem an algorithm that has the best expected performance with respect to some (unknown) distribution on the instances of the problem. We build upon recent work in this line of research by considering the setup where, instead of selecting a single algorithm that has the best performance, we allow the possibility of selecting an algorithm based on the instance to be solved, using neural networks. In particular, given a representative sample of instances, we learn a neural network that maps an instance of the problem to the most appropriate algorithm *for that instance*. We formalize this idea and derive rigorous sample complexity bounds for this learning problem, in the spirit of recent work in data-driven algorithm design. We then apply this approach to the problem of making good decisions in the branch-and-cut framework for mixed-integer optimization (e.g., which cut to add?). In other words, the neural network will take as input a mixed-integer optimization instance and output a decision that will result in a small branch-and-cut tree for that instance. Our computational results provide evidence that our particular way of using neural networks for cut selection can make a significant impact in reducing branch-and-cut tree sizes, compared to previous data-driven approaches.

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for Masked Language Model (MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.

We study a generalization of classical active learning to real-world settings with concrete prediction targets where sampling is restricted to an accessible region of the domain, while prediction targets may lie outside this region. We analyze a family of decision rules that sample adaptively to minimize uncertainty about prediction targets. We are the first to show, under general regularity assumptions, that such decision rules converge uniformly to the smallest possible uncertainty obtainable from the accessible data. We demonstrate their strong sample efficiency in two key applications: active fine-tuning of large neural networks and safe Bayesian optimization, where they achieve state-of-the-art performance.

Graphs data is crucial for many applications, and much of it exists in the relations described in textual format. As a result, being able to accurately recall and encode a graph described in earlier text is a basic yet pivotal ability that LLMs need to demonstrate if they are to perform reasoning tasks that involve graph-structured information. Human performance at graph recall by has been studied by cognitive scientists for decades, and has been found to often exhibit certain structural patterns of bias that align with human handling of social relationships. To date, however, we know little about how LLMs behave in analogous graph recall tasks: do their recalled graphs also exhibit certain biased patterns, and if so, how do they compare with humans and affect other graph reasoning tasks? In this work, we perform the first systematical study of graph recall by LLMs, investigating the accuracy and biased microstructures (local structural patterns) in their recall. We find that LLMs not only underperform often in graph recall, but also tend to favor more triangles and alternating 2-paths. Moreover, we find that more advanced LLMs have a striking dependence on the domain that a real-world graph comes from --- by yielding the best recall accuracy when the graph is narrated in a language style consistent with its original domain.

Analytics on structured data is a mature field with many successful methods. However, most real world data exists in unstructured form, such as images and conversations. We investigate the potential of Large Language Models (LLMs) to enable unstructured data analytics. In particular, we propose a new Universal Query Engine (UQE) that directly interrogates and draws insights from unstructured data collections. This engine accepts queries in a Universal Query Language (UQL), a dialect of SQL that provides full natural language flexibility in specifying conditions and operators. The new engine leverages the ability of LLMs to conduct analysis of unstructured data, while also allowing us to exploit advances in sampling and optimization techniques to achieve efficient and accurate query execution. In addition, we borrow techniques from classical compiler theory to better orchestrate the workflow between sampling methods and foundation model calls. We demonstrate the efficiency of UQE on data analytics across different modalities, including images, dialogs and reviews, across a range of useful query types, including conditional aggregation, semantic retrieval and abstraction aggregation.

Large Language Models (LLMs) have shown significant problem-solving capabilities across predictive and generative tasks in chemistry. However, their proficiency in multi-step chemical reasoning remains underexplored. We introduce a new challenge: molecular structure elucidation, which involves deducing a molecule’s structure from various types of spectral data. Solving such a molecular puzzle, akin to solving crossword puzzles, poses reasoning challenges that require integrating clues from diverse sources and engaging in iterative hypothesis testing. To address this challenging problem with LLMs, we present \textbf{MolPuzzle}, a benchmark comprising 217 instances of structure elucidation, which feature over 23,000 QA samples presented in a sequential puzzle-solving process, involving three interlinked sub-tasks: molecule understanding, spectrum interpretation, and molecule construction. Our evaluation of 12 LLMs reveals that the best-performing LLM, GPT-4o, performs significantly worse than humans, with only a small portion (1.4\%) of its answers exactly matching the ground truth. However, it performs nearly perfectly in the first subtask of molecule understanding, achieving accuracy close to 100\%. This discrepancy highlights the potential of developing advanced LLMs with improved chemical reasoning capabilities in the other two sub-tasks. Our MolPuzzle dataset and evaluation code are available at this \href{https://github.com/KehanGuo2/MolPuzzle}{link}.

In human-centric applications like healthcare and education, the \textit{heterogeneity} among patients and students necessitates personalized treatments and instructional interventions. While reinforcement learning (RL) has been utilized in those tasks, off-policy selection (OPS) is pivotal to close the loop by offline evaluating and selecting policies without online interactions, yet current OPS methods often overlook the heterogeneity among participants. Our work is centered on resolving a \textit{pivotal challenge} in human-centric systems (HCSs): \textbf{\textit{how to select a policy to deploy when a new participant joining the cohort, without having access to any prior offline data collected over the participant?}} We introduce First-Glance Off-Policy Selection (FPS), a novel approach that systematically addresses participant heterogeneity through sub-group segmentation and tailored OPS criteria to each sub-group. By grouping individuals with similar traits, FPS facilitates personalized policy selection aligned with unique characteristics of each participant or group of participants. FPS is evaluated via two important but challenging applications, intelligent tutoring systems and a healthcare application for sepsis treatment and intervention. FPS presents significant advancement in enhancing learning outcomes of students and in-hospital care outcomes.

Shape from polarization (SfP) benefits from advancements like polarization cameras for single-shot normal estimation, but its performance heavily relies on light conditions. This paper proposes SfPUEL, an end-to-end SfP method to jointly estimate surface normal and material under unknown environment light. To handle this challenging light condition, we design a transformer-based framework for enhancing the perception of global context features. We further propose to integrate photometric stereo (PS) priors from pretrained models to enrich extracted features for high-quality normal predictions. As metallic and dielectric materials exhibit different BRDFs, SfPUEL additionally predicts dielectric and metallic material segmentation to further boost performance. Experimental results on synthetic and our collected real-world dataset demonstrate that SfPUEL significantly outperforms existing SfP and single-shot normal estimation methods. The code and dataset is available at https://github.com/YouweiLyu/SfPUEL.

Accurately predicting the future fluid is vital to extensive areas such as meteorology, oceanology, and aerodynamics. However, since the fluid is usually observed from the Eulerian perspective, its moving and intricate dynamics are seriously obscured and confounded in static grids, bringing thorny challenges to the prediction. This paper introduces a new Lagrangian-Eulerian combined paradigm to tackle the tanglesome fluid dynamics. Instead of solely predicting the future based on Eulerian observations, we propose DeepLag to discover hidden Lagrangian dynamics within the fluid by tracking the movements of adaptively sampled key particles. Further, DeepLag presents a new paradigm for fluid prediction, where the Lagrangian movement of the tracked particles is inferred from Eulerian observations, and their accumulated Lagrangian dynamics information is incorporated into global Eulerian evolving features to guide future prediction respectively. Tracking key particles not only provides a transparent and interpretable clue for fluid dynamics but also makes our model free from modeling complex correlations among massive grids for better efficiency. Experimentally, DeepLag excels in three challenging fluid prediction tasks covering 2D and 3D, simulated and real-world fluids. Code is available at this repository: https://github.com/thuml/DeepLag.

Eliciting a high-dimensional probability distribution from an expert via noisy judgments is notoriously challenging, yet useful for many applications, such as prior elicitation and reward modeling. We introduce a method for eliciting the expert's belief density as a normalizing flow based solely on preferential questions such as comparing or ranking alternatives. This allows eliciting in principle arbitrarily flexible densities, but flow estimation is susceptible to the challenge of collapsing or diverging probability mass that makes it difficult in practice. We tackle this problem by introducing a novel functional prior for the flow, motivated by a decision-theoretic argument, and show empirically that the belief density can be inferred as the function-space maximum a posteriori estimate. We demonstrate our method by eliciting multivariate belief densities of simulated experts, including the prior belief of a general-purpose large language model over a real-world dataset.

Dynamical systems theory (DST) is fundamental for many areas of science and engineering. It can provide deep insights into the behavior of systems evolving in time, as typically described by differential or recursive equations. A common approach to facilitate mathematical tractability and interpretability of DS models involves decomposing nonlinear DS into multiple linear DS combined by switching manifolds, i.e. piecewise linear (PWL) systems. PWL models are popular in engineering and a frequent choice in mathematics for analyzing the topological properties of DS. However, hand-crafting such models is tedious and only possible for very low-dimensional scenarios, while inferring them from data usually gives rise to unnecessarily complex representations with very many linear subregions. Here we introduce Almost-Linear Recurrent Neural Networks (AL-RNNs) which automatically and robustly produce most parsimonious PWL representations of DS from time series data, using as few PWL nonlinearities as possible. AL-RNNs can be efficiently trained with any SOTA algorithm for dynamical systems reconstruction (DSR), and naturally give rise to a symbolic encoding of the underlying DS that provably preserves important topological properties. We show that for the Lorenz and Rössler systems, AL-RNNs derive, in a purely data-driven way, the known topologically minimal PWL representations of the corresponding chaotic attractors. We further illustrate on two challenging empirical datasets that interpretable symbolic encodings of the dynamics can be achieved, tremendously facilitating mathematical and computational analysis of the underlying systems.

Accurate prediction of climate in the subseasonal-to-seasonal scale is crucial for disaster preparedness and robust decision making amidst climate change. Yet, forecasting beyond the weather timescale is challenging because it deals with problems other than initial condition, including boundary interaction, butterfly effect, and our inherent lack of physical understanding. At present, existing benchmarks tend to have shorter forecasting range of up-to 15 days, do not include a wide range of operational baselines, and lack physics-based constraints for explainability. Thus, we propose ChaosBench, a challenging benchmark to extend the predictability range of data-driven weather emulators to S2S timescale. First, ChaosBench is comprised of variables beyond the typical surface-atmospheric ERA5 to also include ocean, ice, and land reanalysis products that span over 45 years to allow for full Earth system emulation that respects boundary conditions. We also propose physics-based, in addition to deterministic and probabilistic metrics, to ensure a physically-consistent ensemble that accounts for butterfly effect. Furthermore, we evaluate on a diverse set of physics-based forecasts from four national weather agencies as baselines to our data-driven counterpart such as ViT/ClimaX, PanguWeather, GraphCast, and FourCastNetV2. Overall, we find methods originally developed for weather-scale applications fail on S2S task: their performance simply collapse to an unskilled climatology. Nonetheless, we outline and demonstrate several strategies that can extend the predictability range of existing weather emulators, including the use of ensembles, robust control of error propagation, and the use of physics-informed models. Our benchmark, datasets, and instructions are available at https://leap-stc.github.io/ChaosBench.

Neural functional networks (NFNs) have recently gained significant attention due to their diverse applications, ranging from predicting network generalization and network editing to classifying implicit neural representation. Previous NFN designs often depend on permutation symmetries in neural networks' weights, which traditionally arise from the unordered arrangement of neurons in hidden layers. However, these designs do not take into account the weight scaling symmetries of $\operatorname{ReLU}$ networks, and the weight sign flipping symmetries of $\operatorname{sin}$ or $\operatorname{Tanh}$ networks. In this paper, we extend the study of the group action on the network weights from the group of permutation matrices to the group of monomial matrices by incorporating scaling/sign-flipping symmetries. Particularly, we encode these scaling/sign-flipping symmetries by designing our corresponding equivariant and invariant layers. We name our new family of NFNs the Monomial Matrix Group Equivariant Neural Functional Networks (Monomial-NFN). Because of the expansion of the symmetries, Monomial-NFN has much fewer independent trainable parameters compared to the baseline NFNs in the literature, thus enhancing the model's efficiency. Moreover, for fully connected and convolutional neural networks, we theoretically prove that all groups that leave these networks invariant while acting on their weight spaces are some subgroups of the monomial matrix group. We provide empirical evidences to demonstrate the advantages of our model over existing baselines, achieving competitive performance and efficiency. The code is publicly available at https://github.com/MathematicalAI-NUS/Monomial-NFN.

This paper presents a new gradient flow dissipation geometry over non-negative and probability measures. This is motivated by a principled construction that combines the unbalanced optimal transport and interaction forces modeled by reproducing kernels. Using a precise connection between the Hellinger geometry and the maximum mean discrepancy (MMD), we propose the interaction-force transport (IFT) gradient flows and its spherical variant via an infimal convolution of the Wasserstein and spherical MMD tensors. We then develop a particle-based optimization algorithm based on the JKO-splitting scheme of the mass-preserving spherical IFT gradient flows. Finally, we provide both theoretical global exponential convergence guarantees and improved empirical simulation results for applying the IFT gradient flows to the sampling task of MMD-minimization. Furthermore, we prove that the spherical IFT gradient flow enjoys the best of both worlds by providing the global exponential convergence guarantee for both the MMD and KL energy.

We consider the problem of learning the dynamics in the topology of time-evolving point clouds, the prevalent spatiotemporal model for systems exhibiting collective behavior, such as swarms of insects and birds or particles in physics. In such systems, patterns emerge from (local) interactions among self-propelled entities. While several well-understood governing equations for motion and interaction exist, they are notoriously difficult to fit to data, as most prior work requires knowledge about individual motion trajectories, i.e., a requirement that is challenging to satisfy with an increasing number of entities. To evade such confounding factors, we investigate collective behavior from a _topological perspective_, but instead of summarizing entire observation sequences (as done previously), we propose learning a latent dynamical model from topological features _per time point_. The latter is then used to formulate a downstream regression task to predict the parametrization of some a priori specified governing equation. We implement this idea based on a latent ODE learned from vectorized (static) persistence diagrams and show that a combination of recent stability results for persistent homology justifies this modeling choice. Various (ablation) experiments not only demonstrate the relevance of each model component but provide compelling empirical evidence that our proposed model -- _Neural Persistence Dynamics_ -- substantially outperforms the state-of-the-art across a diverse set of parameter regression tasks.

The aim of this work is to learn models of population dynamics of physical systems that feature stochastic and mean-field effects and that depend on physics parameters. The learned models can act as surrogates of classical numerical models to efficiently predict the system behavior over the physics parameters. Building on the Benamou-Brenier formula from optimal transport and action matching, we use a variational problem to infer parameter- and time-dependent gradient fields that represent approximations of the population dynamics. The inferred gradient fields can then be used to rapidly generate sample trajectories that mimic the dynamics of the physical system on a population level over varying physics parameters. We show that combining Monte Carlo sampling with higher-order quadrature rules is critical for accurately estimating the training objective from sample data and for stabilizing the training process. We demonstrate on Vlasov-Poisson instabilities as well as on high-dimensional particle and chaotic systems that our approach accurately predicts population dynamics over a wide range of parameters and outperforms state-of-the-art diffusion-based and flow-based modeling that simply condition on time and physics parameters.