NeurIPS 2024 Papers

Continual learning aims to incrementally acquire new concepts in data streams while resisting forgetting previous knowledge. With the rise of powerful pre-trained models (PTMs), there is a growing interest in training incremental learning systems using these foundation models, rather than learning from scratch. Existing works often view PTMs as a strong initial point and directly apply parameter-efficient tuning (PET) in the first session for adapting to downstream tasks. In the following sessions, most methods freeze model parameters for tackling forgetting issues. However, applying PET directly to downstream data cannot fully explore the inherent knowledge in PTMs. Additionally, freezing the parameters in incremental sessions hinders models' plasticity to novel concepts not covered in the first session. To solve the above issues, we propose a Slow And Fast parameter-Efficient tuning (SAFE) framework. In particular, to inherit general knowledge from foundation models, we include a transfer loss function by measuring the correlation between the PTM and the PET-applied model. After calibrating in the first session, the slow efficient tuning parameters can capture more informative features, improving generalization to incoming classes. Moreover, to further incorporate novel concepts, we strike a balance between stability and plasticity by fixing slow efficient tuning parameters and continuously updating the fast ones. Specifically, a cross-classification loss with feature alignment is proposed to circumvent catastrophic forgetting. During inference, we introduce an entropy-based aggregation strategy to dynamically utilize the complementarity in the slow and fast learners. Extensive experiments on seven benchmark datasets verify the effectiveness of our method by significantly surpassing the state-of-the-art.

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.

We introduce DataComp for Language Models, a testbed for controlled dataset experiments with the goal of improving language models. As part of DCLM, we provide a standardized corpus of 240T tokens extracted from Common Crawl, effective pretraining recipes based on the OpenLM framework, and a broad suite of 53 downstream evaluations. Participants in the DCLM benchmark can experiment with data curation strategies such as deduplication, filtering, and data mixing at model scales ranging from 412M to 7B parameters. As a baseline for DCLM, we conduct extensive experiments and find that model-based filtering is key to assembling a high-quality training set. The resulting dataset, DCLM-Baseline, enables training a 7B parameter language model from scratch to 63% 5-shot accuracy on MMLU with 2T training tokens. Compared to MAP-Neo, the previous state-of-the-art in open-data language models, DCLM-Baseline represents a 6 percentage point improvement on MMLU while being trained with half the compute. Our results highlight the importance of dataset design for training language models and offer a starting point for further research on data curation. We release the \dclm benchmark, framework, models, and datasets at https://www.datacomp.ai/dclm/

Current research in adversarial robustness of LLMs focuses on \textit{discrete} input manipulations in the natural language space, which can be directly transferred to \textit{closed-source} models. However, this approach neglects the steady progression of \textit{open-source} models. As open-source models advance in capability, ensuring their safety becomes increasingly imperative. Yet, attacks tailored to open-source LLMs that exploit full model access remain largely unexplored. We address this research gap and propose the \textit{embedding space attack}, which directly attacks the \textit{continuous} embedding representation of input tokens. We find that embedding space attacks circumvent model alignments and trigger harmful behaviors more efficiently than discrete attacks or model fine-tuning. Additionally, we demonstrate that models compromised by embedding attacks can be used to create discrete jailbreaks in natural language. Lastly, we present a novel threat model in the context of unlearning and show that embedding space attacks can extract supposedly deleted information from unlearned LLMs across multiple datasets and models. Our findings highlight embedding space attacks as an important threat model in open-source LLMs.

Deep neural networks have long been criticized for being black-box. To unveil the inner workings of modern neural architectures, a recent work proposed an information-theoretic objective function called Sparse Rate Reduction (SRR) and interpreted its unrolled optimization as a Transformer-like model called Coding Rate Reduction Transformer (CRATE). However, the focus of the study was primarily on the basic implementation, and whether this objective is optimized in practice and its causal relationship to generalization remain elusive. Going beyond this study, we derive different implementations by analyzing layer-wise behaviors of CRATE, both theoretically and empirically. To reveal the predictive power of SRR on generalization, we collect a set of model variants induced by varied implementations and hyperparameters and evaluate SRR as a complexity measure based on its correlation with generalization. Surprisingly, we find out that SRR has a positive correlation coefficient and outperforms other baseline measures, such as path-norm and sharpness-based ones. Furthermore, we show that generalization can be improved using SRR as regularization on benchmark image classification datasets. We hope this paper can shed light on leveraging SRR to design principled models and study their generalization ability.

Assessing action quality is both imperative and challenging due to its significant impact on the quality of AI-generated videos, further complicated by the inherently ambiguous nature of actions within AI-generated video (AIGV). Current action quality assessment (AQA) algorithms predominantly focus on actions from real specific scenarios and are pre-trained with normative action features, thus rendering them inapplicable in AIGVs. To address these problems, we construct GAIA, a Generic AI-generated Action dataset, by conducting a large-scale subjective evaluation from a novel causal reasoning-based perspective, resulting in 971,244 ratings among 9,180 video-action pairs. Based on GAIA, we evaluate a suite of popular text-to-video (T2V) models on their ability to generate visually rational actions, revealing their pros and cons on different categories of actions. We also extend GAIA as a testbed to benchmark the AQA capacity of existing automatic evaluation methods. Results show that traditional AQA methods, action-related metrics in recent T2V benchmarks, and mainstream video quality methods perform poorly with an average SRCC of 0.454, 0.191, and 0.519, respectively, indicating a sizable gap between current models and human action perception patterns in AIGVs. Our findings underscore the significance of action quality as a unique perspective for studying AIGVs and can catalyze progress towards methods with enhanced capacities for AQA in AIGVs.

From the onset of infanthood, humans naturally develop the ability to closely observe and interpret the visual gaze of others. This skill, known as gaze following, holds significance in developmental theory as it enables us to grasp another person’s mental state, emotions, intentions, and more. In computer vision, gaze following is defined as the prediction of the pixel coordinates where a person in the image is focusing their attention. Existing methods in this research area have predominantly centered on pinpointing the gaze target by predicting a gaze heatmap or gaze point. However, a notable drawback of this approach is its limited practical value in gaze applications, as mere localization may not fully capture our primary interest — understanding the underlying semantics, such as the nature of the gaze target, rather than just its 2D pixel location. To address this gap, we extend the gaze following task, and introduce a novel architecture that simultaneously predicts the localization and semantic label of the gaze target. We devise a pseudo-annotation pipeline for the GazeFollow dataset, propose a new benchmark, develop an experimental protocol and design a suitable baseline for comparison. Our method sets a new state-of-the-art on the main GazeFollow benchmark for localization and achieves competitive results in the recognition task on both datasets compared to the baseline, with 40% fewer parameters

To train a deblurring network, an appropriate dataset with paired blurry and sharp images is essential. Existing datasets collect blurry images either synthetically by aggregating consecutive sharp frames or using sophisticated camera systems to capture real blur. However, these methods offer limited diversity in blur types (blur trajectories) or require extensive human effort to reconstruct large-scale datasets, failing to fully reflect real-world blur scenarios. To address this, we propose GS-Blur, a dataset of synthesized realistic blurry images created using a novel approach. To this end, we first reconstruct 3D scenes from multi-view images using 3D Gaussian Splatting~(3DGS), then render blurry images by moving the camera view along the randomly generated motion trajectories. By adopting various camera trajectories in reconstructing our GS-Blur, our dataset contains realistic and diverse types of blur, offering a large-scale dataset that generalizes well to real-world blur. Using GS-Blur with various deblurring methods, we demonstrate its ability to generalize effectively compared to previous synthetic or real blur datasets, showing significant improvements in deblurring performance. We will publicly release our dataset.

Spiking Transformers, which integrate Spiking Neural Networks (SNNs) with Transformer architectures, have attracted significant attention due to their potential for low energy consumption and high performance. However, there remains a substantial gap in performance between SNNs and Artificial Neural Networks (ANNs). To narrow this gap, we have developed QKFormer, a direct training spiking transformer with the following features: i) _Linear complexity and high energy efficiency_, the novel spike-form Q-K attention module efficiently models the token or channel attention through binary vectors and enables the construction of larger models. ii) _Multi-scale spiking representation_, achieved by a hierarchical structure with the different numbers of tokens across blocks. iii) _Spiking Patch Embedding with Deformed Shortcut (SPEDS)_, enhances spiking information transmission and integration, thus improving overall performance. It is shown that QKFormer achieves significantly superior performance over existing state-of-the-art SNN models on various mainstream datasets. Notably, with comparable size to Spikformer (66.34 M, 74.81\%), QKFormer (64.96 M) achieves a groundbreaking top-1 accuracy of **85.65\%** on ImageNet-1k, substantially outperforming Spikformer by **10.84\%**. To our best knowledge, this is the first time that directly training SNNs have exceeded 85\% accuracy on ImageNet-1K.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality MS/MS spectra and defines three MS/MS annotation challenges: \textit{de novo} molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at \url{https://github.com/pluskal-lab/MassSpecGym}.

Standardized benchmarks drive progress in machine learning. However, with repeated testing, the risk of overfitting grows as algorithms over-exploit benchmark idiosyncrasies. In our work, we seek to mitigate this challenge by compiling \textit{ever-expanding} large-scale benchmarks called \textit{Lifelong Benchmarks}. As exemplars of our approach, we create \textit{Lifelong-CIFAR10} and \textit{Lifelong-ImageNet}, containing (for now) 1.69M and 1.98M test samples, respectively. While reducing overfitting, lifelong benchmarks introduce a key challenge: the high cost of evaluating a growing number of models across an ever-expanding sample set. To address this challenge, we also introduce an efficient evaluation framework: \textit{Sort \& Search (S\&S)}, which reuses previously evaluated models by leveraging dynamic programming algorithms to selectively rank and sub-select test samples, enabling cost-effective lifelong benchmarking. Extensive empirical evaluations across $\sim$31,000 models demonstrate that \textit{S\&S} achieves highly-efficient approximate accuracy measurement, reducing compute cost from 180 GPU days to 5 GPU hours ($\sim$1000x reduction) on a single A100 GPU, with low approximation error. As such, lifelong benchmarks offer a robust, practical solution to the ``benchmark exhaustion'' problem.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, geographical, and size information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at https://github.com/bioscan-ml/BIOSCAN-5M.

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of subgraphs. While previous approaches attempted to generate smaller subsets of subgraphs through random or learnable sampling, these methods often yielded suboptimal selections or were limited to small subset sizes, ultimately compromising their effectiveness. This paper introduces a new Subgraph GNN framework to address these issues. Our approach diverges from most previous methods by associating subgraphs with node clusters rather than with individual nodes. We show that the resulting collection of subgraphs can be viewed as the product of coarsened and original graphs, unveiling a new connectivity structure on which we perform generalized message passing. Crucially, controlling the coarsening function enables meaningful selection of any number of subgraphs. In addition, we reveal novel permutation symmetries in the resulting node feature tensor, characterize associated linear equivariant layers, and integrate them into our Subgraph GNN. We also introduce novel node marking strategies and provide a theoretical analysis of their expressive power and other key aspects of our approach. Extensive experiments on multiple graph learning benchmarks demonstrate that our method is significantly more flexible than previous approaches, as it can seamlessly handle any number of subgraphs, while consistently outperforming baseline approaches. Our code is available at https://github.com/BarSGuy/Efficient-Subgraph-GNNs.

This paper presents UltraEdit, a large-scale (~ 4M editing samples), automatically generated dataset for instruction-based image editing. Our key idea is to address the drawbacks in existing image editing datasets like InstructPix2Pix and MagicBrush, and provide a *systematic* approach to producing massive and high-quality image editing samples: 1) UltraEdit includes more diverse editing instructions by combining LLM creativity and in-context editing examples by human raters; 2) UltraEdit is anchored on real images (photographs or artworks), which offers more diversity and less biases than those purely synthesized by text-to-image models; 3) UltraEdit supports region-based editing with high-quality, automatically produced region annotations. Our experiments show that canonical diffusion-based editing baselines trained on UltraEdit set new records on challenging MagicBrush and Emu-Edit benchmarks, respectively. Our analysis further confirms the crucial role of real image anchors and region-based editing data. The dataset, code, and models will be made public.

Distributionally robust offline reinforcement learning (RL), which seeks robust policy training against environment perturbation by modeling dynamics uncertainty, calls for function approximations when facing large state-action spaces. However, the consideration of dynamics uncertainty introduces essential nonlinearity and computational burden, posing unique challenges for analyzing and practically employing function approximation. Focusing on a basic setting where the nominal model and perturbed models are linearly parameterized, we propose minimax optimal and computationally efficient algorithms realizing function approximation and initiate the study on instance-dependent suboptimality analysis in the context of robust offline RL. Our results uncover that function approximation in robust offline RL is essentially distinct from and probably harder than that in standard offline RL. Our algorithms and theoretical results crucially depend on a novel function approximation mechanism incorporating variance information, a new procedure of suboptimality and estimation uncertainty decomposition, a quantification of the robust value function shrinkage, and a meticulously designed family of hard instances, which might be of independent interest.

We introduce $r$-loopy Weisfeiler-Leman ($r$-$\ell$WL), a novel hierarchy of graph isomorphism tests and a corresponding GNN framework, $r$-$\ell$MPNN, that can count cycles up to length $r{+}2$. Most notably, we show that $r$-$\ell$WL can count homomorphisms of cactus graphs. This extends 1-WL, which can only count homomorphisms of trees and, in fact, is incomparable to $k$-WL for any fixed $k$. We empirically validate the expressive and counting power of $r$-$\ell$MPNN on several synthetic datasets and demonstrate the scalability and strong performance on various real-world datasets, particularly on sparse graphs.

In speech separation, time-domain approaches have successfully replaced the time-frequency domain with latent sequence feature from a learnable encoder. Conventionally, the feature is separated into speaker-specific ones at the final stage of the network. Instead, we propose a more intuitive strategy that separates features earlier by expanding the feature sequence to the number of speakers as an extra dimension. To achieve this, an asymmetric strategy is presented in which the encoder and decoder are partitioned to perform distinct processing in separation tasks. The encoder analyzes features, and the output of the encoder is split into the number of speakers to be separated. The separated sequences are then reconstructed by the weight-shared decoder, which also performs cross-speaker processing. Without relying on speaker information, the weight-shared network in the decoder directly learns to discriminate features using a separation objective. In addition, to improve performance, traditional methods have extended the sequence length, leading to the adoption of dual-path models, which handle the much longer sequence effectively by segmenting it into chunks. To address this, we introduce global and local Transformer blocks that can directly handle long sequences more efficiently without chunking and dual-path processing. The experimental results demonstrated that this asymmetric structure is effective and that the combination of proposed global and local Transformer can sufficiently replace the role of inter- and intra-chunk processing in dual-path structure. Finally, the presented model combining both of these achieved state-of-the-art performance with much less computation in various benchmark datasets.