NeurIPS 2024 Papers

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%.

Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost, analogous to Moore’s Law, has led to an exponential increase in the availability of patient-level GV data. This growth poses a challenge for clinicians who must efficiently prioritize patient-specific GVs and integrate them with existing genomic databases to inform patient management. To addressing the interpretation of GVs, genomic foundation models (GFMs) have emerged. However, these models lack standardized performance assessments, leading to considerable variability in model evaluations. This poses the question: *How effectively do deep learning methods classify unknown GVs and align them with clinically-verified GVs?* We argue that representation learning, which transforms raw data into meaningful feature spaces, is an effective approach for addressing both indexing and classification challenges. We introduce a large-scale Genetic Variant dataset, named $\textsf{GV-Rep}$, featuring variable-length contexts and detailed annotations, designed for deep learning models to learn GV representations across various traits, diseases, tissue types, and experimental contexts. Our contributions are three-fold: (i) $\textbf{Construction}$ of a comprehensive dataset with 7 million records, each labeled with characteristics of the corresponding variants, alongside additional data from 17,548 gene knockout tests across 1,107 cell types, 1,808 variant combinations, and 156 unique clinically-verified GVs from real-world patients. (ii) $\textbf{Analysis}$ of the structure and properties of the dataset. (iii) $\textbf{Experimentation}$ of the dataset with pre-trained genomic foundation models (GFMs). The results highlight a significant disparity between the current capabilities of GFMs and the accurate representation of GVs. We hope this dataset will advance genomic deep learning to bridge this gap.

Diffusion-based models have achieved notable empirical successes in reinforcement learning (RL) due to their expressiveness in modeling complex distributions. Despite existing methods being promising, the key challenge of extending existing methods for broader real-world applications lies in the computational cost at inference time, i.e., sampling from a diffusion model is considerably slow as it often requires tens to hundreds of iterations to generate even one sample. To circumvent this issue, we propose to leverage the flexibility of diffusion models for RL from a representation learning perspective. In particular, by exploiting the connection between diffusion models and energy-based models, we develop Diffusion Spectral Representation (Diff-SR), a coherent algorithm framework that enables extracting sufficient representations for value functions in Markov decision processes (MDP) and partially observable Markov decision processes (POMDP). We further demonstrate how Diff-SR facilitates efficient policy optimization and practical algorithms while explicitly bypassing the difficulty and inference cost of sampling from the diffusion model. Finally, we provide comprehensive empirical studies to verify the benefits of Diff-SR in delivering robust and advantageous performance across various benchmarks with both fully and partially observable settings.

Contrastive learning methods, such as CLIP, leverage naturally paired data—for example, images and their corresponding text captions—to learn general representations that transfer efficiently to downstream tasks. While such approaches are generally applied to two modalities, domains such as robotics, healthcare, and video need to support many types of data at once. We show that the pairwise application of CLIP fails to capture joint information between modalities, thereby limiting the quality of the learned representations. To address this issue, we present Symile, a simple contrastive learning approach that captures higher-order information between any number of modalities. Symile provides a flexible, architecture-agnostic objective for learning modality-specific representations. To develop Symile's objective, we derive a lower bound on total correlation, and show that Symile representations for any set of modalities form a sufficient statistic for predicting the remaining modalities. Symile outperforms pairwise CLIP, even with modalities missing in the data, on cross-modal classification and retrieval across several experiments including on an original multilingual dataset of 33M image, text and audio samples and a clinical dataset of chest X-rays, electrocardiograms, and laboratory measurements. All datasets and code used in this work are publicly available at https://github.com/rajesh-lab/symile.

Masked Autoencoder (MAE) is a self-supervised approach for representation learning, widely applicable to a variety of downstream tasks in computer vision. In spite of its success, it is still not fully uncovered what and how MAE exactly learns. In this paper, with an in-depth analysis, we discover that MAE intrinsically learns pattern-based patch-level clustering from surprisingly early stages of pre-training. Upon this understanding, we propose self-guided masked autoencoder, which internally generates informed mask by utilizing its progress in patch clustering, substituting the naive random masking of the vanilla MAE. Our approach significantly boosts its learning process without relying on any external models or supplementary information, keeping the benefit of self-supervised nature of MAE intact. Comprehensive experiments on various downstream tasks verify the effectiveness of the proposed method.

Diffusion models are initially designed for image generation. Recent research shows that the internal signals within their backbones, named activations, can also serve as dense features for various discriminative tasks such as semantic segmentation. Given numerous activations, selecting a small yet effective subset poses a fundamental problem. To this end, the early study of this field performs a large-scale quantitative comparison of the discriminative ability of the activations. However, we find that many potential activations have not been evaluated, such as the queries and keys used to compute attention scores. Moreover, recent advancements in diffusion architectures bring many new activations, such as those within embedded ViT modules. Both combined, activation selection remains unresolved but overlooked. To tackle this issue, this paper takes a further step with a much broader range of activations evaluated. Considering the significant increase in activations, a full-scale quantitative comparison is no longer operational. Instead, we seek to understand the properties of these activations, such that the activations that are clearly inferior can be filtered out in advance via simple qualitative evaluation. After careful analysis, we discover three properties universal among diffusion models, enabling this study to go beyond specific models. On top of this, we present effective feature selection solutions for several popular diffusion models. Finally, the experiments across multiple discriminative tasks validate the superiority of our method over the SOTA competitors. Our code is available at https://github.com/Darkbblue/generic-diffusion-feature.

We introduce AlphaTablets, a novel and generic representation of 3D planes that features continuous 3D surface and precise boundary delineation. By representing 3D planes as rectangles with alpha channels, AlphaTablets combine the advantages of current 2D and 3D plane representations, enabling accurate, consistent and flexible modeling of 3D planes. We derive differentiable rasterization on top of AlphaTablets to efficiently render 3D planes into images, and propose a novel bottom-up pipeline for 3D planar reconstruction from monocular videos. Starting with 2D superpixels and geometric cues from pre-trained models, we initialize 3D planes as AlphaTablets and optimize them via differentiable rendering. An effective merging scheme is introduced to facilitate the growth and refinement of AlphaTablets. Through iterative optimization and merging, we reconstruct complete and accurate 3D planes with solid surfaces and clear boundaries. Extensive experiments on the ScanNet dataset demonstrate state-of-the-art performance in 3D planar reconstruction, underscoring the great potential of AlphaTablets as a generic 3D plane representation for various applications.

We study offline multitask representation learning in reinforcement learning (RL), where a learner is provided with an offline dataset from different tasks that share a common representation and is asked to learn the shared representation. We theoretically investigate offline multitask low-rank RL, and propose a new algorithm called MORL for offline multitask representation learning. Furthermore, we examine downstream RL in reward-free, offline and online scenarios, where a new task is introduced to the agent that shares the same representation as the upstream offline tasks. Our theoretical results demonstrate the benefits of using the learned representation from the upstream offline task instead of directly learning the representation of the low-rank model.

Model heterogeneous federated learning (MHeteroFL) enables FL clients to collaboratively train models with heterogeneous structures in a distributed fashion. However, existing MHeteroFL methods rely on training loss to transfer knowledge between the client model and the server model, resulting in limited knowledge exchange. To address this limitation, we propose the **Fed**erated model heterogeneous **M**atryoshka **R**epresentation **L**earning (**FedMRL**) approach for supervised learning tasks. It adds an auxiliary small homogeneous model shared by clients with heterogeneous local models. (1) The generalized and personalized representations extracted by the two models' feature extractors are fused by a personalized lightweight representation projector. This step enables representation fusion to adapt to local data distribution. (2) The fused representation is then used to construct Matryoshka representations with multi-dimensional and multi-granular embedded representations learned by the global homogeneous model header and the local heterogeneous model header. This step facilitates multi-perspective representation learning and improves model learning capability. Theoretical analysis shows that FedMRL achieves a $O(1/T)$ non-convex convergence rate. Extensive experiments on benchmark datasets demonstrate its superior model accuracy with low communication and computational costs compared to seven state-of-the-art baselines. It achieves up to 8.48% and 24.94% accuracy improvement compared with the state-of-the-art and the best same-category baseline, respectively.

Attention-based transformers have been remarkably successful at modeling generative processes across various domains and modalities. In this paper, we study the behavior of transformers on data drawn from $k^{\text{th}}$-order Markov processes, where the conditional distribution of the next symbol in a sequence depends on the previous $k$ symbols observed. We observe a surprising phenomenon empirically which contradicts previous findings: when trained for sufficiently long, a transformer with a fixed depth and $1$ head per layer is able to achieve low test loss on sequences drawn from $k^{\text{th}}$-order Markov sources, even as $k$ grows. Furthermore, this low test loss is achieved by the transformer’s ability to represent and learn the in-context conditional empirical distribution. On the theoretical side, we prove that a transformer with $O(\log_2(k))$ layers can represent the in-context conditional empirical distribution by composing induction heads to track the previous $k$ symbols in the sequence. Surprisingly, with the addition of layer normalization, we show that a transformer with a constant number of layers can represent the in-context conditional empirical distribution, concurring with our empirical observations. This result provides more insight into the benefit of soft-attention and non-linearities in the transformer architecture.

The human brain encodes stimuli from the environment into representations that form a sensory perception of the world. Despite recent advances in understanding visual and auditory perception, olfactory perception remains an under-explored topic in the machine learning community due to the lack of large-scale datasets annotated with labels of human olfactory perception. In this work, we ask the question of whether pre-trained transformer models of chemical structures encode representations that are aligned with human olfactory perception, i.e., can transformers smell like humans? We demonstrate that representations encoded from transformers pre-trained on general chemical structures are highly aligned with human olfactory perception. We use multiple datasets and different types of perceptual representations to show that the representations encoded by transformer models are able to predict: (i) labels associated with odorants‌‌ provided by experts; (ii) continuous ratings provided by human participants with respect to pre-defined descriptors; and (iii) similarity ratings between odorants provided by human participants. Finally, we evaluate the extent to which this alignment is associated with physicochemical features of odorants known to be relevant for olfactory decoding.

Learning from previously collected data via behavioral cloning or offline reinforcement learning (RL) is a powerful recipe for scaling generalist agents by avoiding the need for expensive online learning. Despite strong generalization in some respects, agents are often remarkably brittle to minor visual variations in control-irrelevant factors such as the background or camera viewpoint. In this paper, we present theDeepMind Control Visual Benchmark (DMC-VB), a dataset collected in the DeepMind Control Suite to evaluate the robustness of offline RL agents for solving continuous control tasks from visual input in the presence of visual distractors. In contrast to prior works, our dataset (a) combines locomotion and navigation tasks of varying difficulties, (b) includes static and dynamic visual variations, (c) considers data generated by policies with different skill levels, (d) systematically returns pairs of state and pixel observation, (e) is an order of magnitude larger, and (f) includes tasks with hidden goals. Accompanying our dataset, we propose three benchmarks to evaluate representation learning methods for pretraining, and carry out experiments on several recently proposed methods. First, we find that pretrained representations do not help policy learning on DMC-VB, and we highlight a large representation gap between policies learned on pixel observations and on states. Second, we demonstrate when expert data is limited, policy learning can benefit from representations pretrained on (a) suboptimal data, and (b) tasks with stochastic hidden goals. Our dataset and benchmark code to train and evaluate agents are available at https://github.com/google-deepmind/dmc_vision_benchmark.

This paper introduces CoFie, a novel local geometry-aware neural surface representation. CoFie is motivated by the theoretical analysis of local SDFs with quadratic approximation. We find that local shapes are highly compressive in an aligned coordinate frame defined by the normal and tangent directions of local shapes. Accordingly, we introduce Coordinate Field, which is a composition of coordinate frames of all local shapes. The Coordinate Field is optimizable and is used to transform the local shapes from the world coordinate frame to the aligned shape coordinate frame. It largely reduces the complexity of local shapes and benefits the learning of MLP-based implicit representations. Moreover, we introduce quadratic layers into the MLP to enhance expressiveness concerning local shape geometry. CoFie is a generalizable surface representation. It is trained on a curated set of 3D shapes and works on novel shape instances during testing. When using the same amount of parameters with prior works, CoFie reduces the shape error by 48% and 56% on novel instances of both training and unseen shape categories. Moreover, CoFie demonstrates comparable performance to prior works when using even 70% fewer parameters. Code and model can be found here: https://hwjiang1510.github.io/CoFie/