NeurIPS 2023 Papers

In this paper we tackle the problem of Generalized Category Discovery (GCD). Specifically, given a dataset with labelled and unlabelled images, the task is to cluster all images in the unlabelled subset, whether or not they belong to the labelled categories. Our first contribution is to recognise that most existing GCD benchmarks only contain labels for a single clustering of the data, making it difficult to ascertain whether models are leveraging the available labels to solve the GCD task, or simply solving an unsupervised clustering problem. As such, we present a synthetic dataset, named 'Clevr-4', for category discovery. Clevr-4 contains four equally valid partitions of the data, i.e based on object 'shape', 'texture' or 'color' or 'count'. To solve the task, models are required to extrapolate the taxonomy specified by labelled set, rather than simply latch onto a single natural grouping of the data. We use this dataset to demonstrate the limitations of unsupervised clustering in the GCD setting, showing that even very strong unsupervised models fail on Clevr-4. We further use Clevr-4 to examine the weaknesses of existing GCD algorithms, and propose a new method which addresses these shortcomings, leveraging consistent findings from the representation learning literature to do so. Our simple solution, which is based on `Mean Teachers' and termed $\mu$GCD, substantially outperforms implemented baselines on Clevr-4. Finally, when we transfer these findings to real data on the challenging Semantic Shift Benchmark suite, we find that $\mu$GCD outperforms all prior work, setting a new state-of-the-art.

Discovering genes with similar functions across diverse biomedical contexts poses a significant challenge in gene representation learning due to data heterogeneity. In this study, we resolve this problem by introducing a novel model called Multimodal Similarity Learning Graph Neural Network, which combines Multimodal Machine Learning and Deep Graph Neural Networks to learn gene representations from single-cell sequencing and spatial transcriptomic data. Leveraging 82 training datasets from 10 tissues, three sequencing techniques, and three species, we create informative graph structures for model training and gene representations generation, while incorporating regularization with weighted similarity learning and contrastive learning to learn cross-data gene-gene relationships. This novel design ensures that we can offer gene representations containing functional similarity across different contexts in a joint space. Comprehensive benchmarking analysis shows our model's capacity to effectively capture gene function similarity across multiple modalities, outperforming state-of-the-art methods in gene representation learning by up to $\textbf{100.4}$%. Moreover, we employ bioinformatics tools in conjunction with gene representations to uncover pathway enrichment, regulation causal networks, and functions of disease-associated genes. Therefore, our model efficiently produces unified gene representations for the analysis of gene functions, tissue functions, diseases, and species evolution.

Learning object-centric representations from complex natural environments enables both humans and machines with reasoning abilities from low-level perceptual features. To capture compositional entities of the scene, we proposed cyclic walks between perceptual features extracted from vision transformers and object entities. First, a slot-attention module interfaces with these perceptual features and produces a finite set of slot representations. These slots can bind to any object entities in the scene via inter-slot competitions for attention. Next, we establish entity-feature correspondence with cyclic walks along high transition probability based on the pairwise similarity between perceptual features (aka "parts") and slot-binded object representations (aka "whole"). The whole is greater than its parts and the parts constitute the whole. The part-whole interactions form cycle consistencies, as supervisory signals, to train the slot-attention module. Our rigorous experiments on \textit{seven} image datasets in \textit{three} \textit{unsupervised} tasks demonstrate that the networks trained with our cyclic walks can disentangle foregrounds and backgrounds, discover objects, and segment semantic objects in complex scenes. In contrast to object-centric models attached with a decoder for the pixel-level or feature-level reconstructions, our cyclic walks provide strong learning signals, avoiding computation overheads and enhancing memory efficiency. Our source code and data are available at: \href{https://github.com/ZhangLab-DeepNeuroCogLab/Parts-Whole-Object-Centric-Learning/}{link}.

We have recently seen great progress in learning interpretable music representations, ranging from basic factors, such as pitch and timbre, to high-level concepts, such as chord and texture. However, most methods rely heavily on music domain knowledge. It remains an open question what general computational principles *give rise to* interpretable representations, especially low-dim factors that agree with human perception. In this study, we take inspiration from modern physics and use *physical symmetry* as a self-consistency constraint for the latent space. Specifically, it requires the prior model that characterises the dynamics of the latent states to be *equivariant* with respect to certain group transformations. We show that physical symmetry leads the model to learn a *linear* pitch factor from unlabelled monophonic music audio in a self-supervised fashion. In addition, the same methodology can be applied to computer vision, learning a 3D Cartesian space from videos of a simple moving object without labels. Furthermore, physical symmetry naturally leads to *counterfactual representation augmentation*, a new technique which improves sample efficiency.

In the era of extensive intersection between art and Artificial Intelligence (AI), such as image generation and fiction co-creation, AI for music remains relatively nascent, particularly in music understanding. This is evident in the limited work on deep music representations, the scarcity of large-scale datasets, and the absence of a universal and community-driven benchmark. To address this issue, we introduce the Music Audio Representation Benchmark for universaL Evaluation, termed MARBLE. It aims to provide a benchmark for various Music Information Retrieval (MIR) tasks by defining a comprehensive taxonomy with four hierarchy levels, including acoustic, performance, score, and high-level description. We then establish a unified protocol based on 18 tasks on 12 public-available datasets, providing a fair and standard assessment of representations of all open-sourced pre-trained models developed on music recordings as baselines. Besides, MARBLE offers an easy-to-use, extendable, and reproducible suite for the community, with a clear statement on copyright issues on datasets. Results suggest recently proposed large-scale pre-trained musical language models perform the best in most tasks, with room for further improvement. The leaderboard and toolkit repository are published to promote future music AI research.

Representational limits of message-passing graph neural networks (MP-GNNs), e.g., in terms of the Weisfeiler-Leman (WL) test for isomorphism, are well understood. Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem. Specifically, we establish the necessary and sufficient conditions for distinguishing graphs based on the persistence of their connected components, obtained from filter functions on vertex and edge colors. Our constructions expose the limits of vertex- and edge-level PH, proving that neither category subsumes the other. Leveraging these theoretical insights, we propose RePHINE for learning topological features on graphs. RePHINE efficiently combines vertex- and edge-level PH, achieving a scheme that is provably more powerful than both. Integrating RePHINE into MP-GNNs boosts their expressive power, resulting in gains over standard PH on several benchmarks for graph classification.

Webly supervised learning has attracted increasing attention for its effectiveness in exploring publicly accessible data at scale without manual annotation. However, most existing methods of learning with web datasets are faced with challenges from label noise, and they have limited assumptions on clean samples under various noise. For instance, web images retrieved with queries of ”tiger cat“ (a cat species) and ”drumstick“ (a musical instrument) are almost dominated by images of tigers and chickens, which exacerbates the challenge of fine-grained visual concept learning. In this case, exploiting both web images and their associated texts is a requisite solution to combat real-world noise. In this paper, we propose Cross-modality Aligned Prototypes (CAPro), a unified prototypical contrastive learning framework to learn visual representations with correct semantics. For one thing, we leverage textual prototypes, which stem from the distinct concept definition of classes, to select clean images by text matching and thus disambiguate the formation of visual prototypes. For another, to handle missing and mismatched noisy texts, we resort to the visual feature space to complete and enhance individual texts and thereafter improve text matching. Such semantically aligned visual prototypes are further polished up with high-quality samples, and engaged in both cluster regularization and noise removal. Besides, we propose collective bootstrapping to encourage smoother and wiser label reference from appearance-similar instances in a manner of dictionary look-up. Extensive experiments on WebVision1k and NUS-WIDE (Web) demonstrate that CAPro well handles realistic noise under both single-label and multi-label scenarios. CAPro achieves new state-of-the-art performance and exhibits robustness to open-set recognition. Codes are available at https://github.com/yuleiqin/capro.

This paper focuses on graph-level representation learning that aims to represent graphs as vectors that can be directly utilized in downstream tasks such as graph classification. We propose a novel graph-level representation learning principle called Lovász principle, which is motivated by the Lovász number in graph theory. The Lovász number of a graph is a real number that is an upper bound for graph Shannon capacity and is strongly connected with various global characteristics of the graph. Specifically, we show that the handle vector for computing the Lovász number is potentially a suitable choice for graph representation, as it captures a graph's global properties, though a direct application of the handle vector is difficult and problematic. We propose to use neural networks to address the problems and hence provide the Lovász principle. Moreover, we propose an enhanced Lovász principle that is able to exploit the subgraph Lovász numbers directly and efficiently. The experiments demonstrate that our Lovász principles achieve competitive performance compared to the baselines in unsupervised and semi-supervised graph-level representation learning tasks. The code of our Lovász principles is publicly available on GitHub.

Geometric representation learning of molecules is challenging yet essential for applications in multiple domains. Despite the impressive breakthroughs made by geometric deep learning in various molecular representation learning tasks, effectively capturing complicated geometric features across spatial dimensions is still underexplored due to the significant difficulties in modeling efficient geometric representations and learning the inherent correlation in 3D structural modeling. These include computational inefficiency, underutilization of vectorial embeddings, and limited generalizability to integrate various geometric properties. To address the raised concerns, we introduce an efficient and effective framework, Scalable Vector Network (SaVeNet), designed to accommodate a range of geometric requirements without depending on costly embeddings. In addition, the proposed framework scales effectively with introduced direction noise. Theoretically, we analyze the desired properties (i.e., invariance and equivariant) and framework efficiency of the SaVeNet. Empirically, we conduct a comprehensive series of experiments to evaluate the efficiency and expressiveness of the proposed model. Our efficiency-focused experiments underscore the model's empirical superiority over existing methods. Experimental results on synthetic and real-world datasets demonstrate the expressiveness of our model, which achieves state-of-the-art performance across various tasks within molecular representation learning.