NeurIPS 2024 Papers

Deep neural networks (DNNs) have recently achieved remarkable advancements in time series forecasting (TSF) due to their powerful ability of sequence dependence modeling. To date, existing DNN-based TSF methods still suffer from unreliable predictions for real-world data due to its non-stationarity characteristics, i.e., data distribution varies quickly over time. To mitigate this issue, several normalization methods (e.g., SAN) have recently been specifically designed by normalization in a fixed period/window in the time domain. However, these methods still struggle to capture distribution variations, due to the complex time patterns of time series in the time domain. Based on the fact that wavelet transform can decompose time series into a linear combination of different frequencies, which exhibits distribution variations with time-varying periods, we propose a novel Dual-domain Dynamic Normalization (DDN) to dynamically capture distribution variations in both time and frequency domains. Specifically, our DDN tries to eliminate the non-stationarity of time series via both frequency and time domain normalization in a sliding window way. Besides, our DDN can serve as a plug-in-play module, and thus can be easily incorporated into other forecasting models. Extensive experiments on public benchmark datasets under different forecasting models demonstrate the superiority of our DDN over other normalization methods. Code will be made available following the review process.

High-quality, large-scale corpora are the cornerstone of building foundation models. In this work, we introduce MathPile, a diverse and high-quality math-centric corpus comprising about 9.5 billion tokens. Throughout its creation, we adhered to the principle of “less is more”, firmly believing in the supremacy of data quality over quantity, even in the pre-training phase. Our meticulous data collection and processing efforts included a complex suite of preprocessing, prefiltering, language identification, cleaning, filtering, and deduplication, ensuring the high quality of our corpus. Furthermore, we performed data contamination detection on downstream benchmark test sets to eliminate duplicates and conducted continual pre-training experiments, booting the performance on common mathematical reasoning benchmarks. We aim for our MathPile to boost language models’ mathematical reasoning abilities and open-source its different versions and processing scripts to advance the field.

Image fusion aims to integrate complementary information from multiple input images acquired through various sources to synthesize a new fused image. Existing methods usually employ distinct constraint designs tailored to specific scenes, forming fixed fusion paradigms. However, this data-driven fusion approach is challenging to deploy in varying scenarios, especially in rapidly changing environments. To address this issue, we propose a conditional controllable fusion (CCF) framework for general image fusion tasks without specific training. Due to the dynamic differences of different samples, our CCF employs specific fusion constraints for each individual in practice. Given the powerful generative capabilities of the denoising diffusion model, we first inject the specific constraints into the pre-trained DDPM as adaptive fusion conditions. The appropriate conditions are dynamically selected to ensure the fusion process remains responsive to the specific requirements in each reverse diffusion stage. Thus, CCF enables conditionally calibrating the fused images step by step. Extensive experiments validate our effectiveness in general fusion tasks across diverse scenarios against the competing methods without additional training. The code is publicly available.

Widely adopted in modern Vision Transformer designs, Softmax attention can effectively capture long-range visual information; however, it incurs excessive computational cost when dealing with high-resolution inputs. In contrast, linear attention naturally enjoys linear complexity and has great potential to scale up to higher-resolution images. Nonetheless, the unsatisfactory performance of linear attention greatly limits its practical application in various scenarios. In this paper, we take a step forward to close the gap between the linear and Softmax attention with novel theoretical analyses, which demystify the core factors behind the performance deviations. Specifically, we present two key perspectives to understand and alleviate the limitations of linear attention: the injective property and the local modeling ability. Firstly, we prove that linear attention is not injective, which is prone to assign identical attention weights to different query vectors, thus adding to severe semantic confusion since different queries correspond to the same outputs. Secondly, we confirm that effective local modeling is essential for the success of Softmax attention, in which linear attention falls short. The aforementioned two fundamental differences significantly contribute to the disparities between these two attention paradigms, which is demonstrated by our substantial empirical validation in the paper. In addition, more experiment results indicate that linear attention, as long as endowed with these two properties, can outperform Softmax attention across various tasks while maintaining lower computation complexity. Code is available at https://github.com/LeapLabTHU/InLine.

Smoke segmentation is of great importance in precisely identifying the smoke location, enabling timely fire rescue and gas leak detection. However, due to the visual diversity and blurry edges of the non-grid smoke, noisy labels are almost inevitable in large-scale pixel-level smoke datasets. Noisy labels significantly impact the robustness of the model and may lead to serious accidents. Nevertheless, currently, there are no specific methods for addressing noisy labels in smoke segmentation. Smoke differs from regular objects as its transparency varies, causing inconsistent features in the noisy labels. In this paper, we propose a conditional sample weighting (CoSW). CoSW utilizes a multi-prototype framework, where prototypes serve as prior information to apply different weighting criteria to the different feature clusters. A novel regularized within-prototype entropy (RWE) is introduced to achieve CoSW and stable prototype update. The experiments show that our approach achieves SOTA performance on both real-world and synthetic noisy smoke segmentation datasets.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further research of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we also evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark is open-sourced to facilitate future research and application. The code is available at \url{https://github.com/Westlake-OmicsAI/NovoBench}.

This paper considers the problem of learning from multiple sets of inaccurate labels, which can be easily obtained from low-cost annotators, such as rule-based annotators. Previous works typically concentrate on aggregating information from all the annotators, overlooking the significance of data refinement. This paper presents a collaborative refining approach for learning from inaccurate labels. To refine the data, we introduce the annotator agreement as an instrument, which refers to whether multiple annotators agree or disagree on the labels for a given sample. For samples where some annotators disagree, a comparative strategy is proposed to filter noise. Through theoretical analysis, the connections among multiple sets of labels, the respective models trained on them, and the true labels are uncovered to identify relatively reliable labels. For samples where all annotators agree, an aggregating strategy is designed to mitigate potential noise. Guided by theoretical bounds on loss values, a sample selection criterion is introduced and modified to be more robust against potentially problematic values. Through these two methods, all the samples are refined during training, and these refined samples are used to train a lightweight model simultaneously. Extensive experiments are conducted on benchmark and real-world datasets to demonstrate the superiority of our methods.

Uncertainty quantification (UQ) is a crucial but challenging task in many high-dimensional learning problems to increase the confidence of a given predictor. We develop a new data-driven approach for UQ in regression that applies both to classical optimization approaches such as the LASSO as well as to neural networks. One of the most notable UQ techniques is the debiased LASSO, which modifies the LASSO to allow for the construction of asymptotic confidence intervals by decomposing the estimation error into a Gaussian and an asymptotically vanishing bias component. However, in real-world problems with finite-dimensional data, the bias term is often too significant to disregard, resulting in overly narrow confidence intervals. Our work rigorously addresses this issue and derives a data-driven adjustment that corrects the confidence intervals for a large class of predictors by estimating the means and variances of the bias terms from training data, exploiting high-dimensional concentration phenomena. This gives rise to non-asymptotic confidence intervals, which can help avoid overestimating certainty in critical applications such as MRI diagnosis. Importantly, our analysis extends beyond sparse regression to data-driven predictors like neural networks, enhancing the reliability of model-based deep learning. Our findings bridge the gap between established theory and the practical applicability of such methods.

Diffusion models have demonstrated great success in text-to-video (T2V) generation. However, existing methods may face challenges when handling complex (long) video generation scenarios that involve multiple objects or dynamic changes in object numbers. To address these limitations, we propose VideoTetris, a novel framework that enables compositional T2V generation. Specifically, we propose spatio-temporal compositional diffusion to precisely follow complex textual semantics by manipulating and composing the attention maps of denoising networks spatially and temporally. Moreover, we propose a new dynamic-aware data processing pipeline and a consistency regularization method to enhance the consistency of auto-regressive video generation. Extensive experiments demonstrate that our VideoTetris achieves impressive qualitative and quantitative results in compositional T2V generation. Code is available at: https://github.com/YangLing0818/VideoTetris

Recent studies show that Large Language Models (LLMs) with safety alignment can be jail-broken by fine-tuning on a dataset mixed with harmful data. For the first time in the literature, we show that the jail-break effect can be mitigated by separating two states in the fine-tuning stage to respectively optimize over the alignment and user datasets. Unfortunately, our subsequent study shows that this simple Bi-State Optimization (BSO) solution experiences convergence instability when steps invested in its alignment state is too small, leading to downgraded alignment performance. By statistical analysis, we show that the \textit{excess drift} towards the switching iterates of the two states could be a probable reason for the instability. To remedy this issue, we propose \textbf{L}azy(\textbf{i}) \textbf{s}afety \textbf{a}lignment (\textbf{Lisa}), which introduces a proximal term to constraint the drift of each state. Theoretically, the benefit of the proximal term is supported by the convergence analysis, wherein we show that a sufficient large proximal factor is necessary to guarantee Lisa's convergence. Empirically, our results on four downstream fine-tuning tasks show that Lisa with a proximal term can significantly increase alignment performance while maintaining the LLM's accuracy on the user tasks. Code is available at https://github.com/git-disl/Lisa.

Although transformer-based methods have achieved great success in multi-scale temporal pattern interaction modeling, two key challenges limit their further development: (1) Individual time points contain less semantic information, and leveraging attention to model pair-wise interactions may cause the information utilization bottleneck. (2) Multiple inherent temporal variations (e.g., rising, falling, and fluctuating) entangled in temporal patterns. To this end, we propose Adaptive Multi-Scale Hypergraph Transformer (Ada-MSHyper) for time series forecasting. Specifically, an adaptive hypergraph learning module is designed to provide foundations for modeling group-wise interactions, then a multi-scale interaction module is introduced to promote more comprehensive pattern interactions at different scales. In addition, a node and hyperedge constraint mechanism is introduced to cluster nodes with similar semantic information and differentiate the temporal variations within each scales. Extensive experiments on 11 real-world datasets demonstrate that Ada-MSHyper achieves state-of-the-art performance, reducing prediction errors by an average of 4.56%, 10.38%, and 4.97% in MSE for long-range, short-range, and ultra-long-range time series forecasting, respectively. Code is available at https://github.com/shangzongjiang/Ada-MSHyper.

Modern image generation (IG) models have been shown to capture rich semantics valuable for image understanding (IU) tasks. However, the potential of IU models to improve IG performance remains uncharted. We address this issue using a token-based IG framework, which relies on effective tokenizers to project images into token sequences. Currently, **pixel reconstruction** (e.g., VQGAN) dominates the training objective for image tokenizers. In contrast, our approach adopts the **feature reconstruction** objective, where tokenizers are trained by distilling knowledge from pretrained IU encoders. Comprehensive comparisons indicate that tokenizers with strong IU capabilities achieve superior IG performance across a variety of metrics, datasets, tasks, and proposal networks. Notably, VQ-KD CLIP achieves $4.10$ FID on ImageNet-1k (IN-1k). Visualization suggests that the superiority of VQ-KD can be partly attributed to the rich semantics within the VQ-KD codebook. We further introduce a straightforward pipeline to directly transform IU encoders into tokenizers, demonstrating exceptional effectiveness for IG tasks. These discoveries may energize further exploration into image tokenizer research and inspire the community to reassess the relationship between IU and IG. The code is released at https://github.com/magic-research/vector_quantization.

Efficient fine-tuning of large language models for task-specific applications is imperative, yet the vast number of parameters in these models makes their training increasingly challenging. Despite numerous proposals for effective methods, a substantial memory overhead remains for gradient computations during updates. \thm{Can we fine-tune a series of task-specific small models and transfer their knowledge directly to a much larger model without additional training?} In this paper, we explore weak-to-strong specialization using logit arithmetic, facilitating a direct answer to this question. Existing weak-to-strong methods often employ a static knowledge transfer ratio and a single small model for transferring complex knowledge, which leads to suboptimal performance. To surmount these limitations, we propose a dynamic logit fusion approach that works with a series of task-specific small models, each specialized in a different task. This method adaptively allocates weights among these models at each decoding step, learning the weights through Kullback-Leibler divergence constrained optimization problems. We conduct extensive experiments across various benchmarks in both single-task and multi-task settings, achieving leading results. By transferring expertise from the 7B model to the 13B model, our method closes the performance gap by 96.4\% in single-task scenarios and by 86.3\% in multi-task scenarios compared to full fine-tuning of the 13B model. Notably, we achieve surpassing performance on unseen tasks. Moreover, we further demonstrate that our method can effortlessly integrate in-context learning for single tasks and task arithmetic for multi-task scenarios.

Deep learning algorithms have recently gained significant attention due to their impressive performance. However, their high complexity and un-interpretable mode of operation hinders their confident deployment in real-world safety-critical tasks. This work targets ante hoc interpretability, and specifically Concept Bottleneck Models (CBMs). Our goal is to design a framework that admits a highly interpretable decision making process with respect to human understandable concepts, on two levels of granularity. To this end, we propose a novel two-level concept discovery formulation leveraging: (i) recent advances in vision-language models, and (ii) an innovative formulation for coarse-to-fine concept selection via data-driven and sparsity inducing Bayesian arguments. Within this framework, concept information does not solely rely on the similarity between the whole image and general unstructured concepts; instead, we introduce the notion of concept hierarchy to uncover and exploit more granular concept information residing in patch-specific regions of the image scene. As we experimentally show, the proposed construction not only outperforms recent CBM approaches, but also yields a principled framework towards interpetability.

Tuning scientific and probabilistic machine learning models - for example, partial differential equations, Gaussian processes, or Bayesian neural networks - often relies on evaluating functions of matrices whose size grows with the data set or the number of parameters. While the state-of-the-art for _evaluating_ these quantities is almost always based on Lanczos and Arnoldi iterations, the present work is the first to explain how to _differentiate_ these workhorses of numerical linear algebra efficiently. To get there, we derive previously unknown adjoint systems for Lanczos and Arnoldi iterations, implement them in JAX, and show that the resulting code can compete with Diffrax when it comes to differentiating PDEs, GPyTorch for selecting Gaussian process models and beats standard factorisation methods for calibrating Bayesian neural networks. All this is achieved without any problem-specific code optimisation. Find the code at [link redacted] and install the library with *pip install [redacted]*.

Large language models (LLMs) have achieved impressive success on many benchmarks for mathematical reasoning. However, there is growing concern that some of this performance actually reflects dataset contamination, where data closely resembling benchmark questions leaks into the training data, instead of true reasoning ability. To investigate this claim rigorously, we commission Grade School Math 1000 (GSM1k). GSM1k is designed to mirror the style and complexity of the established GSM8k benchmark, the gold standard for measuring elementary mathematical reasoning. We ensure that the two benchmarks are comparable across important metrics such as human solve rates, number of steps in solution, answer magnitude, and more. When evaluating leading open- and closed-source LLMs on GSM1k, we observe accuracy drops of up to 8%, with several families of models showing evidence of systematic overfitting across almost all model sizes. Further analysis suggests a positive relationship (Spearman's r^2=0.36) between a model's probability of generating an example from GSM8k and its performance gap between GSM8k and GSM1k, suggesting that some models may have partially memorized GSM8k. Nevertheless, many models, especially those on the frontier, show minimal signs of overfitting, and all models broadly demonstrate generalization to novel math problems guaranteed to not be in their training data.

Optimizing discrete black-box functions is key in several domains, e.g. protein engineering and drug design. Due to the lack of gradient information and the need for sample efficiency, Bayesian optimization is an ideal candidate for these tasks. Several methods for high-dimensional continuous and categorical Bayesian optimization have been proposed recently. However, our survey of the field reveals highly heterogeneous experimental set-ups across methods and technical barriers for the replicability and application of published algorithms to real-world tasks. To address these issues, we develop a unified framework to test a vast array of high-dimensional Bayesian optimization methods and a collection of standardized black-box functions representing real-world application domains in chemistry and biology. These two components of the benchmark are each supported by flexible, scalable, and easily extendable software libraries (poli and poli-baselines), allowing practitioners to readily incorporate new optimization objectives or discrete optimizers. Project website: https://machinelearninglifescience.github.io/hdbo_benchmark.

Out-of-distribution (OOD) generalization issue is a well-known challenge within deep learning tasks. In dynamic graphs, the change of temporal environments is regarded as the main cause of data distribution shift. While numerous OOD studies focusing on environment factors have achieved remarkable performance, they still fail to systematically solve the two issue of environment inference and utilization. In this work, we propose a novel dynamic graph learning model named EpoD based on prompt learning and structural causal model to comprehensively enhance both environment inference and utilization. Inspired by the superior performance of prompt learning in understanding underlying semantic and causal associations, we first design a self-prompted learning mechanism to infer unseen environment factors. We then rethink the role of environment variable within spatio-temporal causal structure model, and introduce a novel causal pathway where dynamic subgraphs serve as mediating variables. The extracted dynamic subgraph can effectively capture the data distribution shift by incorporating the inferred environment variables into the node-wise dependencies. Theoretical discussions and intuitive analysis support the generalizability and interpretability of EpoD. Extensive experiments on seven real-world datasets across domains showcase the superiority of EpoD against baselines, and toy example experiments further verify the powerful interpretability and rationality of our EpoD.

Neural Collapse (NC) was a recently discovered phenomenon that the output features and the classifier weights of the neural network converge to optimal geometric structures at the Terminal Phase of Training (TPT) under various losses. However, the relationship between these optimal structures at TPT and the classification performance remains elusive, especially in imbalanced learning. Even though it is noticed that fixing the classifier to an optimal structure can mitigate the minority collapse problem, the performance is still not comparable to the classical imbalanced learning methods with a learnable classifier. In this work, we find that the optimal structure can be designed to represent a better classification rule, and thus achieve better performance. In particular, we justify that, to achieve better classification, the features from the minor classes should align with more directions. This justification then yields a decision rule called the Generalized Classification Rule (GCR) and we also term these directions as the centers of the classes. Then we study the NC under an MSE-type loss via the Unconstrained Features Model (UFM) framework where (1) the features from a class tend to collapse to the mean of the corresponding centers of that class (named Neural Collapse to Multiple Centers (NCMC)) at the global optimum, and (2) the original classifier approximates a surrogate to GCR when NCMC occurs. Based on the analysis, we develop a strategy for determining the number of centers and propose a Cosine Loss function for the fixed classifier that induces NCMC. Our experiments have shown that the Cosine Loss can induce NCMC and has performance on long-tail classification comparable to the classical imbalanced learning methods.