NeurIPS 2024 Papers

The spatio-temporal relations of impacts of extreme events and their drivers in climate data are not fully understood and there is a need of machine learning approaches to identify such spatio-temporal relations from data. The task, however, is very challenging since there are time delays between extremes and their drivers, and the spatial response of such drivers is inhomogeneous. In this work, we propose a first approach and benchmarks to tackle this challenge. Our approach is trained end-to-end to predict spatio-temporally extremes and spatio-temporally drivers in the physical input variables jointly. By enforcing the network to predict extremes from spatio-temporal binary masks of identified drivers, the network successfully identifies drivers that are correlated with extremes. We evaluate our approach on three newly created synthetic benchmarks, where two of them are based on remote sensing or reanalysis climate data, and on two real-world reanalysis datasets. The source code and datasets are publicly available at the project page https://hakamshams.github.io/IDE.

Subset selection tasks, such as anomaly detection and compound selection in AI-assisted drug discovery, are crucial for a wide range of applications. Learning subset-valued functions with neural networks has achieved great success by incorporating permutation invariance symmetry into the architecture. However, existing neural set architectures often struggle to either capture comprehensive information from the superset or address complex interactions within the input. Additionally, they often fail to perform in scenarios where superset sizes surpass available memory capacity. To address these challenges, we introduce the novel concept of the Identity Property, which requires models to integrate information from the originating set, resulting in the development of neural networks that excel at performing effective subset selection from large supersets. Moreover, we present the Hierarchical Representation of Neural Subset Selection (HORSE), an attention-based method that learns complex interactions and retains information from both the input set and the optimal subset supervision signal. Specifically, HORSE enables the partitioning of the input ground set into manageable chunks that can be processed independently and then aggregated, ensuring consistent outcomes across different partitions. Through extensive experimentation, we demonstrate that HORSE significantly enhances neural subset selection performance by capturing more complex information and surpasses state-of-the-art methods in handling large-scale inputs by a margin of up to 20%.

We introduce multiple physics pretraining (MPP), an autoregressive task-agnostic pretraining approach for physical surrogate modeling of spatiotemporal systems with transformers. In MPP, rather than training one model on a specific physical system, we train a backbone model to predict the dynamics of multiple heterogeneous physical systems simultaneously in order to learn features that are broadly useful across systems and facilitate transfer. In order to learn effectively in this setting, we introduce a shared embedding and normalization strategy that projects the fields of multiple systems into a shared embedding space. We validate the efficacy of our approach on both pretraining and downstream tasks over a broad fluid mechanics-oriented benchmark. We show that a single MPP-pretrained transformer is able to match or outperform task-specific baselines on all pretraining sub-tasks without the need for finetuning. For downstream tasks, we demonstrate that finetuning MPP-trained models results in more accurate predictions across multiple time-steps on systems with previously unseen physical components or higher dimensional systems compared to training from scratch or finetuning pretrained video foundation models. We open-source our code and model weights trained at multiple scales for reproducibility.

Reward Machines provide an automaton-inspired structure for specifying instructions, safety constraints, and other temporally extended reward-worthy behaviour. By exposing the underlying structure of a reward function, they enable the decomposition of an RL task, leading to impressive gains in sample efficiency. Although Reward Machines and similar formal specifications have a rich history of application towards sequential decision-making problems, prior frameworks have traditionally ignored ambiguity and uncertainty when interpreting the domain-specific vocabulary forming the building blocks of the reward function. Such uncertainty critically arises in many real-world settings due to factors like partial observability or noisy sensors. In this work, we explore the use of Reward Machines for Deep RL in noisy and uncertain environments. We characterize this problem as a POMDP and propose a suite of RL algorithms that exploit task structure under uncertain interpretation of the domain-specific vocabulary. Through theory and experiments, we expose pitfalls in naive approaches to this problem while simultaneously demonstrating how task structure can be successfully leveraged under noisy interpretations of the vocabulary.

The feasibility of variational quantum algorithms, the most popular correspondent of neural networks on noisy, near-term quantum hardware, is highly impacted by the circuit depth of the involved parametrized quantum circuits (PQCs). Higher depth increases expressivity, but also results in a detrimental accumulation of errors. Furthermore, the number of parameters involved in the PQC significantly influences the performance through the necessary number of measurements to evaluate gradients, which scales linearly with the number of parameters. Motivated by this, we look at deep equilibrium models (DEQs), which mimic an infinite-depth, weight-tied network using a fraction of the memory by employing a root solver to find the fixed points of the network. In this work, we present Quantum Deep Equilibrium Models (QDEQs): a training paradigm that learns parameters of a quantum machine learning model given by a PQC using DEQs. To our knowledge, no work has yet explored the application of DEQs to QML models. We apply QDEQs to find the parameters of a quantum circuit in two settings: the first involves classifying MNIST-4 digits with 4 qubits; the second extends it to 10 classes of MNIST, FashionMNIST and CIFAR. We find that QDEQ is not only competitive with comparable existing baseline models, but also achieves higher performance than a network with 5 times more layers. This demonstrates that the QDEQ paradigm can be used to develop significantly more shallow quantum circuits for a given task, something which is essential for the utility of near-term quantum computers. Our code is available at \url{https://github.com/martaskrt/qdeq}.

Exploring the loss landscape offers insights into the inherent principles of deep neural networks (DNNs). Recent work suggests an additional asymmetry of the valley beyond the flat and sharp ones, yet without thoroughly examining its causes or implications. Our study methodically explores the factors affecting the symmetry of DNN valleys, encompassing (1) the dataset, network architecture, initialization, and hyperparameters that influence the convergence point; and (2) the magnitude and direction of the noise for 1D visualization. Our major observation shows that the {\it degree of sign consistency} between the noise and the convergence point is a critical indicator of valley symmetry. Theoretical insights from the aspects of ReLU activation and softmax function could explain the interesting phenomenon. Our discovery propels novel understanding and applications in the scenario of Model Fusion: (1) the efficacy of interpolating separate models significantly correlates with their sign consistency ratio, and (2) imposing sign alignment during federated learning emerges as an innovative approach for model parameter alignment.

We consider the problem of recovering the ground truth ordering (ranking, top-$k$, or others) over a large number of alternatives. The wisdom of crowd is a heuristic approach based on Condorcet's Jury theorem to address this problem through collective opinions. This approach fails to recover the ground truth when the majority of the crowd is misinformed. The \emph{surprisingly popular} (SP) algorithm~\citep{prelec2017solution} is an alternative approach that is able to recover the ground truth even when experts are in minority. The SP algorithm requires the voters to predict other voters' report in the form of a full probability distribution over all rankings of alternatives. However, when the number of alternatives, $m$, is large, eliciting the prediction report or even the vote over $m$ alternatives might be too costly. In this paper, we design a scalable alternative of the SP algorithm which only requires eliciting partial preferences from the voters, and propose new variants of the SP algorithm. In particular, we propose two versions---\emph{Aggregated-SP} and \emph{Partial-SP}---that ask voters to report vote and prediction on a subset of size $k$ ($\ll m$) in terms of top alternative, partial rank, or an approval set. Through a large-scale crowdsourcing experiment on MTurk, we show that both of our approaches outperform conventional preference aggregation algorithms for the recovery of ground truth rankings, when measured in terms of Kendall-Tau distance and Spearman's $\rho$. We further analyze the collected data and demonstrate that voters' behavior in the experiment, including the minority of the experts, and the SP phenomenon, can be correctly simulated by a concentric mixtures of Mallows model. Finally, we provide theoretical bounds on the sample complexity of SP algorithms with partial rankings to demonstrate the theoretical guarantees of the proposed methods.

Geometric deep learning (GDL) has gained significant attention in scientific fields, for its proficiency in modeling data with intricate geometric structures. Yet, very few works have delved into its capability of tackling the distribution shift problem, a prevalent challenge in many applications. To bridge this gap, we propose GeSS, a comprehensive benchmark designed for evaluating the performance of GDL models in scientific scenarios with distribution shifts. Our evaluation datasets cover diverse scientific domains from particle physics, materials science to biochemistry, and encapsulate a broad spectrum of distribution shifts including conditional, covariate, and concept shifts. Furthermore, we study three levels of information access from the out-of-distribution (OOD) test data, including no OOD information, only unlabeled OOD data, and OOD data with a few labels. Overall, our benchmark results in 30 different experiment settings, and evaluates 3 GDL backbones and 11 learning algorithms in each setting. A thorough analysis of the evaluation results is provided, poised to illuminate insights for GDL researchers and domain practitioners who are to use GDL in their applications.

We present a novel method for symbolic regression (SR), the task of searching for compact programmatic hypotheses that best explain a dataset. The problem is commonly solved using genetic algorithms; we show that we can enhance such methods by inducing a library of abstract textual concepts. Our algorithm, called LaSR, uses zero-shot queries to a large language model (LLM) to discover and evolve concepts occurring in known high-performing hypotheses. We discover new hypotheses using a mix of standard evolutionary steps and LLM-guided steps (obtained through zero-shot LLM queries) conditioned on discovered concepts. Once discovered, hypotheses are used in a new round of concept abstraction and evolution. We validate LaSR on the Feynman equations, a popular SR benchmark, as well as a set of synthetic tasks. On these benchmarks, LaSR substantially outperforms a variety of state-of-the-art SR approaches based on deep learning and evolutionary algorithms. Moreover, we show that LASR can be used to discover a new and powerful scaling law for LLMs.

Intelligent education stands as a prominent application of machine learning. Within this domain, cognitive diagnosis (CD) is a key research focus that aims to diagnose students' proficiency levels in specific knowledge concepts. As a crucial task within the field of education, cognitive diagnosis encompasses two fundamental requirements: accuracy and fairness. Existing studies have achieved significant success by primarily utilizing observed historical logs of student-exercise interactions. However, real-world scenarios often present a challenge, where a substantial number of students engage with a limited number of exercises. This data sparsity issue can lead to both inaccurate and unfair diagnoses. To this end, we introduce a monotonic data augmentation framework, CMCD, to tackle the data sparsity issue and thereby achieve accurate and fair CD results. Specifically, CMCD integrates the monotonicity assumption, a fundamental educational principle in CD, to establish two constraints for data augmentation. These constraints are general and can be applied to the majority of CD backbones. Furthermore, we provide theoretical analysis to guarantee the accuracy and convergence speed of CMCD. Finally, extensive experiments on real-world datasets showcase the efficacy of our framework in addressing the data sparsity issue with accurate and fair CD results.

We present AROMA (Attentive Reduced Order Model with Attention), a framework designed to enhance the modeling of partial differential equations (PDEs) using local neural fields. Our flexible encoder-decoder architecture can obtain smooth latent representations of spatial physical fields from a variety of data types, including irregular-grid inputs and point clouds. This versatility eliminates the need for patching and allows efficient processing of diverse geometries. The sequential nature of our latent representation can be interpreted spatially and permits the use of a conditional transformer for modeling the temporal dynamics of PDEs. By employing a diffusion-based formulation, we achieve greater stability and enable longer rollouts compared to conventional MSE training. AROMA's superior performance in simulating 1D and 2D equations underscores the efficacy of our approach in capturing complex dynamical behaviors.

The generation of equilibrium samples of molecular systems has been a long-standing problem in statistical physics. Boltzmann Generators are a generative machine learning method that addresses this issue by learning a transformation via a normalizing flow from a simple prior distribution to the target Boltzmann distribution of interest. Recently, flow matching has been employed to train Boltzmann Generators for small molecular systems in Cartesian coordinates. We extend this work and propose a first framework for Boltzmann Generators that are transferable across chemical space, such that they predict zero-shot Boltzmann distributions for test molecules without being retraining for these systems. These transferable Boltzmann Generators allow approximate sampling from the target distribution of unseen systems, as well as efficient reweighting to the target Boltzmann distribution. The transferability of the proposed framework is evaluated on dipeptides, where we show that it generalizes efficiently to unseen systems. Furthermore, we demonstrate that our proposed architecture enhances the efficiency of Boltzmann Generators trained on single molecular systems.

The concept of probabilistic values, such as Beta Shapley values and weighted Banzhaf values, has gained recent attention in applications like feature attribution and data valuation. However, exact computation of these values is often exponentially expensive, necessitating approximation techniques. Prior research has shown that the choice of probabilistic values significantly impacts downstream performance, with no universally superior option. Consequently, one may have to approximate multiple candidates and select the best-performing one. Although there have been many efforts to develop efficient estimators, none are intended to approximate all probabilistic values both simultaneously and efficiently. In this work, we embark on the first exploration of achieving this goal. Adhering to the principle of maximum sample reuse and avoiding amplifying factors, we propose a one-sample-fits-all framework parameterized by a sampling vector to approximate intermediate terms that can be converted to any probabilistic value. Leveraging the concept of $ (\epsilon, \delta) $-approximation, we theoretically identify a key formula that effectively determines the convergence rate of our framework. By optimizing the sampling vector using this formula, we obtain i) a one-for-all estimator that achieves the currently best time complexity for all probabilistic values on average, and ii) a faster generic estimator with the sampling vector optimally tuned for each probabilistic value. Particularly, our one-for-all estimator achieves the fastest convergence rate on Beta Shapley values, including the well-known Shapley value, both theoretically and empirically. Finally, we establish a connection between probabilistic values and the least square regression used in (regularized) datamodels, showing that our one-for-all estimator can solve a family of datamodels simultaneously. Our code is available at https://github.com/watml/one-for-all.

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights. Code is available at https://github.com/qiaoqiaoLF/MxDNA.

Despite the widespread success of Transformers across various domains, their optimization guarantees in large-scale model settings are not well-understood. This paper rigorously analyzes the convergence properties of gradient flow in training Transformers with weight decay regularization. First, we construct the mean-field limit of large-scale Transformers, showing that as the model width and depth go to infinity, gradient flow converges to the Wasserstein gradient flow, which is represented by a partial differential equation. Then, we demonstrate that the gradient flow reaches a global minimum consistent with the PDE solution when the weight decay regularization parameter is sufficiently small. Our analysis is based on a series of novel mean-field techniques that adapt to Transformers. Compared with existing tools for deep networks (Lu et al., 2020) that demand homogeneity and global Lipschitz smoothness, we utilize a refined analysis assuming only $\textit{partial homogeneity}$ and $\textit{local Lipschitz smoothness}$. These new techniques may be of independent interest.

Parallel-in-time (PinT) techniques have been proposed to solve systems of time-dependent differential equations by parallelizing the temporal domain. Among them, Parareal computes the solution sequentially using an inaccurate (fast) solver, and then ``corrects'' it using an accurate (slow) integrator that runs in parallel across temporal subintervals. This work introduces RandNet-Parareal, a novel method to learn the discrepancy between the coarse and fine solutions using random neural networks (RandNets). RandNet-Parareal achieves speed gains up to x125 and x22 compared to the fine solver run serially and Parareal, respectively. Beyond theoretical guarantees of RandNets as universal approximators, these models are quick to train, allowing the PinT solution of partial differential equations on a spatial mesh of up to $10^5$ points with minimal overhead, dramatically increasing the scalability of existing PinT approaches. RandNet-Parareal's numerical performance is illustrated on systems of real-world significance, such as the viscous Burgers' equation, the Diffusion-Reaction equation, the two- and three-dimensional Brusselator, and the shallow water equation.

The study of modern machine learning models often necessitates storing vast quantities of gradients or Hessian vector products (HVPs). Traditional sketching methods struggle to scale under these memory constraints. We present a novel framework for scalable gradient and HVP sketching, tailored for modern hardware. We provide theoretical guarantees and demonstrate the power of our methods in applications like training data attribution, Hessian spectrum analysis, and intrinsic dimension computation for pre-trained language models. Our work sheds new light on the behavior of pre-trained language models, challenging assumptions about their intrinsic dimensionality and Hessian properties.

Quantization is a fundamental optimization for many machine learning (ML) use cases, including compressing gradients, model weights and activations, and datasets. The most accurate form of quantization is adaptive, where the error is minimized with respect to a given input rather than optimizing for the worst case. However, optimal adaptive quantization methods are considered infeasible in terms of both their runtime and memory requirements. We revisit the Adaptive Stochastic Quantization (ASQ) problem and present algorithms that find optimal solutions with asymptotically improved time and space complexities. Our experiments indicate that our algorithms may open the door to using ASQ more extensively in a variety of ML applications. We also present an even faster approximation algorithm for quantizing large inputs on the fly.

Student cognitive modeling (SCM) is a fundamental task in intelligent education, with applications ranging from personalized learning to educational resource allocation. By exploiting students' response logs, SCM aims to predict their exercise performance as well as estimate knowledge proficiency in a subject. Data mining approaches such as matrix factorization can obtain high accuracy in predicting student performance on exercises, but the knowledge proficiency is unknown or poorly estimated. The situation is further exacerbated if only sparse interactions exist between exercises and students (or knowledge concepts). To solve this dilemma, we root monotonicity (a fundamental psychometric theory on educational assessments) in a co-factorization framework and present an autoencoder-like nonnegative matrix co-factorization (AE-NMCF), which improves the accuracy of estimating the student's knowledge proficiency via an encoder-decoder learning pipeline. The resulting estimation problem is nonconvex with nonnegative constraints. We introduce a projected gradient method based on block coordinate descent with Lipschitz constants and guarantee the method's theoretical convergence. Experiments on several real-world data sets demonstrate the efficacy of our approach in terms of both performance prediction accuracy and knowledge estimation ability, when compared with existing student cognitive models.