NeurIPS 2024 Papers

Decision support systems based on prediction sets have proven to be effective at helping human experts solve classification tasks. Rather than providing single-label predictions, these systems provide sets of label predictions constructed using conformal prediction, namely prediction sets, and ask human experts to predict label values from these sets. In this paper, we first show that the prediction sets constructed using conformal prediction are, in general, suboptimal in terms of average accuracy. Then, we show that the problem of finding the optimal prediction sets under which the human experts achieve the highest average accuracy is NP-hard. More strongly, unless P = NP, we show that the problem is hard to approximate to any factor less than the size of the label set. However, we introduce a simple and efficient greedy algorithm that, for a large class of expert models and non-conformity scores, is guaranteed to find prediction sets that provably offer equal or greater performance than those constructed using conformal prediction. Further, using a simulation study with both synthetic and real expert predictions, we demonstrate that, in practice, our greedy algorithm finds near-optimal prediction sets offering greater performance than conformal prediction.

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation https://github.com/WillHua127/ReactZyme.

While neural networks can enjoy an outstanding flexibility and exhibit unprecedented performance, the mechanism behind their behavior is still not well-understood. To tackle this fundamental challenge, researchers have tried to restrict and manipulate some of their properties in order to gain new insights and better control on them. Especially, throughout the past few years, the concept of *bi-Lipschitzness* has been proved as a beneficial inductive bias in many areas. However, due to its complexity, the design and control of bi-Lipschitz architectures are falling behind, and a model that is precisely designed for bi-Lipschitzness realizing a direct and simple control of the constants along with solid theoretical analysis is lacking. In this work, we investigate and propose a novel framework for bi-Lipschitzness that can achieve such a clear and tight control based on convex neural networks and the Legendre-Fenchel duality. Its desirable properties are illustrated with concrete experiments to illustrate its broad range of applications.

We introduce a novel framework for incorporating human expertise into algorithmic predictions. Our approach leverages human judgment to distinguish inputs which are *algorithmically indistinguishable*, or "look the same" to predictive algorithms. We argue that this framing clarifies the problem of human-AI collaboration in prediction tasks, as experts often form judgments by drawing on information which is not encoded in an algorithm's training data. Algorithmic indistinguishability yields a natural test for assessing whether experts incorporate this kind of "side information", and further provides a simple but principled method for selectively incorporating human feedback into algorithmic predictions. We show that this method provably improves the performance of any feasible algorithmic predictor and precisely quantify this improvement. We find empirically that although algorithms often outperform their human counterparts *on average*, human judgment can improve algorithmic predictions on *specific* instances (which can be identified ex-ante). In an X-ray classification task, we find that this subset constitutes nearly 30% of the patient population. Our approach provides a natural way of uncovering this heterogeneity and thus enabling effective human-AI collaboration.

Recent insights have revealed that rate-coding is a primary form of information representation captured by surrogate-gradient-based Backpropagation Through Time (BPTT) in training deep Spiking Neural Networks (SNNs). Motivated by these findings, we propose rate-based backpropagation, a training strategy specifically designed to exploit rate-based representations to reduce the complexity of BPTT. Our method minimizes reliance on detailed temporal derivatives by focusing on averaged dynamics, streamlining the computational graph to reduce memory and computational demands of SNNs training. We substantiate the rationality of the gradient approximation between BPTT and the proposed method through both theoretical analysis and empirical observations. Comprehensive experiments on CIFAR-10, CIFAR-100, ImageNet, and CIFAR10-DVS validate that our method achieves comparable performance to BPTT counterparts, and surpasses state-of-the-art efficient training techniques. By leveraging the inherent benefits of rate-coding, this work sets the stage for more scalable and efficient SNNs training within resource-constrained environments.

Monocular 3D object detection aims for precise 3D localization and identification of objects from a single-view image. Despite its recent progress, it often struggles while handling pervasive object occlusions that tend to complicate and degrade the prediction of object dimensions, depths, and orientations. We design MonoMAE, a monocular 3D detector inspired by Masked Autoencoders that addresses the object occlusion issue by masking and reconstructing objects in the feature space. MonoMAE consists of two novel designs. The first is depth-aware masking that selectively masks certain parts of non-occluded object queries in the feature space for simulating occluded object queries for network training. It masks non-occluded object queries by balancing the masked and preserved query portions adaptively according to the depth information. The second is lightweight query completion that works with the depth-aware masking to learn to reconstruct and complete the masked object queries. With the proposed feature-space occlusion and completion, MonoMAE learns enriched 3D representations that achieve superior monocular 3D detection performance qualitatively and quantitatively for both occluded and non-occluded objects. Additionally, MonoMAE learns generalizable representations that can work well in new domains.

The cortico-spinal neural pathway is fundamental for motor control and movement execution, and in humans it is typically studied using concurrent electroencephalography (EEG) and electromyography (EMG) recordings. However, current approaches for capturing high-level and contextual connectivity between these recordings have important limitations. Here, we present a novel application of statistical dependence estimators based on orthonormal decomposition of density ratios to model the relationship between cortical and muscle oscillations. Our method extends from traditional scalar-valued measures by learning eigenvalues, eigenfunctions, and projection spaces of density ratios from realizations of the signal, addressing the interpretability, scalability, and local temporal dependence of cortico-muscular connectivity. We experimentally demonstrate that eigenfunctions learned from cortico-muscular connectivity can accurately classify movements and subjects. Moreover, they reveal channel and temporal dependencies that confirm the activation of specific EEG channels during movement.

With the popularity of location-based services, human mobility prediction plays a key role in enhancing personalized navigation, optimizing recommendation systems, and facilitating urban mobility and planning. This involves predicting a user's next POI (point-of-interest) visit using their past visit history. However, the uneven distribution of visitations over time and space, namely the long-tail problem in spatial distribution, makes it difficult for AI models to predict those POIs that are less visited by humans. In light of this issue, we propose the $\underline{\bf{Lo}}$ng-$\underline{\bf{T}}$ail Adjusted $\underline{\bf{Next}}$ POI Prediction (LoTNext) framework for mobility prediction, combining a Long-Tailed Graph Adjustment module to reduce the impact of the long-tailed nodes in the user-POI interaction graph and a novel Long-Tailed Loss Adjustment module to adjust loss by logit score and sample weight adjustment strategy. Also, we employ the auxiliary prediction task to enhance generalization and accuracy. Our experiments with two real-world trajectory datasets demonstrate that LoTNext significantly surpasses existing state-of-the-art works.

We propose a method for metric-scale monocular depth estimation. Inferring depth from a single image is an ill-posed problem due to the loss of scale from perspective projection during the image formation process. Any scale chosen is a bias, typically stemming from training on a dataset; hence, existing works have instead opted to use relative (normalized, inverse) depth. Our goal is to recover metric-scaled depth maps through a linear transformation. The crux of our method lies in the observation that certain objects (e.g., cars, trees, street signs) are typically found or associated with certain types of scenes (e.g., outdoor). We explore whether language descriptions can be used to transform relative depth predictions to those in metric scale. Our method, RSA , takes as input a text caption describing objects present in an image and outputs the parameters of a linear transformation which can be applied globally to a relative depth map to yield metric-scaled depth predictions. We demonstrate our method on recent general-purpose monocular depth models on indoors (NYUv2, VOID) and outdoors (KITTI). When trained on multiple datasets, RSA can serve as a general alignment module in zero-shot settings. Our method improves over common practices in aligning relative to metric depth and results in predictions that are comparable to an upper bound of fitting relative depth to ground truth via a linear transformation. Code is available at: https://github.com/Adonis-galaxy/RSA.

Credal sets are sets of probability distributions that are considered as candidates for an imprecisely known ground-truth distribution. In machine learning, they have recently attracted attention as an appealing formalism for uncertainty representation, in particular, due to their ability to represent both the aleatoric and epistemic uncertainty in a prediction. However, the design of methods for learning credal set predictors remains a challenging problem. In this paper, we make use of conformal prediction for this purpose. More specifically, we propose a method for predicting credal sets in the classification task, given training data labeled by probability distributions. Since our method inherits the coverage guarantees of conformal prediction, our conformal credal sets are guaranteed to be valid with high probability (without any assumptions on model or distribution). We demonstrate the applicability of our method on ambiguous classification tasks for uncertainty quantification.

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.

It is vital to infer a signed distance function (SDF) for multi-view based surface reconstruction. 3D Gaussian splatting (3DGS) provides a novel perspective for volume rendering, and shows advantages in rendering efficiency and quality. Although 3DGS provides a promising neural rendering option, it is still hard to infer SDFs for surface reconstruction with 3DGS due to the discreteness, the sparseness, and the off-surface drift of 3D Gaussians. To resolve these issues, we propose a method that seamlessly merge 3DGS with the learning of neural SDFs. Our key idea is to more effectively constrain the SDF inference with the multi-view consistency. To this end, we dynamically align 3D Gaussians on the zero-level set of the neural SDF, and then render the aligned 3D Gaussians through the differentiable rasterization. Meanwhile, we update the neural SDF by pulling neighboring space to the pulled 3D Gaussians, which progressively refine the signed distance field near the surface. With both differentiable pulling and splatting, we jointly optimize 3D Gaussians and the neural SDF with both RGB and geometry constraints, which recovers more accurate, smooth, and complete surfaces with more geometry details. Our numerical and visual comparisons show our superiority over the state-of-the-art results on the widely used benchmarks.

A wide array of sequence models are built on a framework modeled after Transformers, comprising alternating sequence mixer and channel mixer layers. This paper studies a unifying *matrix mixer* view of sequence mixers that can be conceptualized as a linear map on the input sequence. This framework encompasses a broad range of well-known sequence models, including the self-attention of Transformers as well as recent strong alternatives such as structured state space models (SSMs), and allows understanding downstream characteristics such as efficiency and expressivity through properties of their structured matrix class. We identify a key axis of matrix parameterizations termed *sequence alignment*, which increases the flexibility and performance of matrix mixers, providing insights into the strong performance of Transformers and recent SSMs such as Mamba. Furthermore, the matrix mixer framework offers a systematic approach to developing sequence mixers with desired properties, allowing us to develop several new sub-quadratic sequence models. In particular, we propose a natural bidirectional extension of the Mamba model (**Hydra**), parameterized as a *quasiseparable matrix mixer*, which demonstrates superior performance over other sequence models including Transformers on non-causal tasks. As a drop-in replacement for attention layers, \name outperforms BERT by 0.8 points on the GLUE benchmark and ViT by 2% Top-1 accuracy on ImageNet.

The ability to perform different skills can encourage agents to explore. In this work, we aim to construct a set of diverse skills that uniformly cover the state space. We propose a formalization of this search for diverse skills, building on a previous definition based on the mutual information between states and skills. We consider the distribution of states reached by a policy conditioned on each skill and leverage the successor state representation to maximize the difference between these skill distributions. We call this approach LEADS: Learning Diverse Skills through Successor State Representations. We demonstrate our approach on a set of maze navigation and robotic control tasks which show that our method is capable of constructing a diverse set of skills which exhaustively cover the state space without relying on reward or exploration bonuses. Our findings demonstrate that this new formalization promotes more robust and efficient exploration by combining mutual information maximization and exploration bonuses.

Determining the 3D orientations of an object in an image, known as single-image pose estimation, is a crucial task in 3D vision applications. Existing methods typically learn 3D rotations parametrized in the spatial domain using Euler angles or quaternions, but these representations often introduce discontinuities and singularities. SO(3)-equivariant networks enable the structured capture of pose patterns with data-efficient learning, but the parametrizations in spatial domain are incompatible with their architecture, particularly spherical CNNs, which operate in the frequency domain to enhance computational efficiency. To overcome these issues, we propose a frequency-domain approach that directly predicts Wigner-D coefficients for 3D rotation regression, aligning with the operations of spherical CNNs. Our SO(3)-equivariant pose harmonics predictor overcomes the limitations of spatial parameterizations, ensuring consistent pose estimation under arbitrary rotations. Trained with a frequency-domain regression loss, our method achieves state-of-the-art results on benchmarks such as ModelNet10-SO(3) and PASCAL3D+, with significant improvements in accuracy, robustness, and data efficiency.

To predict future trajectories, the normalizing flow with a standard Gaussian prior suffers from weak diversity. The ineffectiveness comes from the conflict between the fact of asymmetric and multi-modal distribution of likely outcomes and symmetric and single-modal original distribution and supervision losses. Instead, we propose constructing a mixed Gaussian prior for a normalizing flow model for trajectory prediction. The prior is constructed by analyzing the trajectory patterns in the training samples without requiring extra annotations while showing better expressiveness and being multi-modal and asymmetric. Besides diversity, it also provides better controllability for probabilistic trajectory generation. We name our method Mixed Gaussian Flow (MGF). It achieves state-of-the-art performance in the evaluation of both trajectory alignment and diversity on the popular UCY/ETH and SDD datasets. Code is available at https://github.com/mulplue/MGF.

When solving partial differential equations (PDEs), classical numerical methods often require fine mesh grids and small time stepping to meet stability, consistency, and convergence conditions, leading to high computational cost. Recently, machine learning has been increasingly utilized to solve PDE problems, but they often encounter challenges related to interpretability, generalizability, and strong dependency on rich labeled data. Hence, we introduce a new PDE-Preserved Coarse Correction Network (P$^2$C$^2$Net) to efficiently solve spatiotemporal PDE problems on coarse mesh grids in small data regimes. The model consists of two synergistic modules: (1) a trainable PDE block that learns to update the coarse solution (i.e., the system state), based on a high-order numerical scheme with boundary condition encoding, and (2) a neural network block that consistently corrects the solution on the fly. In particular, we propose a learnable symmetric Conv filter, with weights shared over the entire model, to accurately estimate the spatial derivatives of PDE based on the neural-corrected system state. The resulting physics-encoded model is capable of handling limited training data (e.g., 3--5 trajectories) and accelerates the prediction of PDE solutions on coarse spatiotemporal grids while maintaining a high accuracy. P$^2$C$^2$Net achieves consistent state-of-the-art performance with over 50\% gain (e.g., in terms of relative prediction error) across four datasets covering complex reaction-diffusion processes and turbulent flows.

Feature attributions attempt to highlight what inputs drive predictive power. Good attributions or explanations are thus those that produce inputs that retain this predictive power; accordingly, evaluations of explanations score their quality of prediction. However, evaluations produce scores better than what appears possible from the values in the explanation for a class of explanations, called encoding explanations. Probing for encoding remains a challenge because there is no general characterization of what gives the extra predictive power. We develop a definition of encoding that identifies this extra predictive power via conditional dependence and show that the definition fits existing examples of encoding. This definition implies, in contrast to encoding explanations, that non-encoding explanations contain all the informative inputs used to produce the explanation, giving them a “what you see is what you get” property, which makes them transparent and simple to use. Next, we prove that existing scores (ROAR, FRESH, EVAL-X) do not rank non-encoding explanations above encoding ones, and develop STRIPE-X which ranks them correctly. After empirically demonstrating the theoretical insights, we use STRIPE-X to show that despite prompting an LLM to produce non-encoding explanations for a sentiment analysis task, the LLM-generated explanations encode.

Reinforcement learning (RL) algorithms are typically based on optimizing a Markov Decision Process (MDP) using the optimal Bellman equation. Recent studies have revealed that focusing the optimization of Bellman equations solely on in-sample actions tends to result in more stable optimization, especially in the presence of function approximation. Upon on these findings, in this paper, we propose an Empirical MDP Iteration (EMIT) framework. EMIT constructs a sequence of empirical MDPs using data from the growing replay memory. For each of these empirical MDPs, it learns an estimated Q-function denoted as $\widehat{Q}$. The key strength is that by restricting the Bellman update to in-sample bootstrapping, each empirical MDP converges to a unique optimal $\widehat{Q}$ function. Furthermore, gradually expanding from the empirical MDPs to the original MDP induces a monotonic policy improvement. Instead of creating entirely new algorithms, we demonstrate that EMIT can be seamlessly integrated with existing online RL algorithms, effectively acting as a regularizer for contemporary Q-learning methods. We show this by implementing EMIT for two representative RL algorithms, DQN and TD3. Experimental results on Atari and MuJoCo benchmarks show that EMIT significantly reduces estimation errors and substantially improves the performance of both algorithms.