NeurIPS 2024 Papers

Continual learning (CL) aims to adapt to non-stationary data distributions while retaining previously acquired knowledge. However, CL models typically face a trade-off between preserving old task knowledge and excelling in new task performance. Existing approaches often sacrifice one for the other. To overcome this limitation, orthogonal to existing approaches, we propose a novel perspective that views the CL model ability in preserving old knowledge and performing well in new task as a matter of model sensitivity to parameter updates. \textit{Excessive} parameter sensitivity can lead to two drawbacks: (1) significant forgetting of previous knowledge; and (2) overfitting to new tasks. To reduce parameter sensitivity, we optimize the model's performance based on the parameter distribution, which achieves the worst-case CL performance within a distribution neighborhood. This innovative learning paradigm offers dual benefits: (1) reduced forgetting of old knowledge by mitigating drastic changes in model predictions under small parameter updates; and (2) enhanced new task performance by preventing overfitting to new tasks. Consequently, our method achieves superior ability in retaining old knowledge and achieving excellent new task performance simultaneously. Importantly, our approach is compatible with existing CL methodologies, allowing seamless integration while delivering significant improvements in effectiveness, efficiency, and versatility with both theoretical and empirical supports.

The challenge of discovering new molecules with desired properties is crucial in domains like drug discovery and material design. Recent advances in deep learning-based generative methods have shown promise but face the issue of sample efficiency due to the computational expense of evaluating the reward function. This paper proposes a novel algorithm for sample-efficient molecular optimization by distilling a powerful genetic algorithm into deep generative policy using GFlowNets training, the off-policy method for amortized inference. This approach enables the deep generative policy to learn from domain knowledge, which has been explicitly integrated into the genetic algorithm. Our method achieves state-of-the-art performance in the official molecular optimization benchmark, significantly outperforming previous methods. It also demonstrates effectiveness in designing inhibitors against SARS-CoV-2 with substantially fewer reward calls.

Intelligent education stands as a prominent application of machine learning. Within this domain, cognitive diagnosis (CD) is a key research focus that aims to diagnose students' proficiency levels in specific knowledge concepts. As a crucial task within the field of education, cognitive diagnosis encompasses two fundamental requirements: accuracy and fairness. Existing studies have achieved significant success by primarily utilizing observed historical logs of student-exercise interactions. However, real-world scenarios often present a challenge, where a substantial number of students engage with a limited number of exercises. This data sparsity issue can lead to both inaccurate and unfair diagnoses. To this end, we introduce a monotonic data augmentation framework, CMCD, to tackle the data sparsity issue and thereby achieve accurate and fair CD results. Specifically, CMCD integrates the monotonicity assumption, a fundamental educational principle in CD, to establish two constraints for data augmentation. These constraints are general and can be applied to the majority of CD backbones. Furthermore, we provide theoretical analysis to guarantee the accuracy and convergence speed of CMCD. Finally, extensive experiments on real-world datasets showcase the efficacy of our framework in addressing the data sparsity issue with accurate and fair CD results.

With the proposal of patching technique in time series forecasting, Transformerbased models have achieved compelling performance and gained great interest from the time series community. But at the same time, we observe a new problem that the recent Transformer-based models are overly reliant on patching to achieve ideal performance, which limits their applicability to some forecasting tasks unsuitable for patching. In this paper, we intent to handle this emerging issue. Through diving into the relationship between patching and full attention (the core mechanism in Transformer-based models), we further find out the reason behind this issue is that full attention relies overly on the guidance of patching to focus on the important time points and learn non-trivial temporal representation. Based on this finding, we propose DeformableTST as an effective solution to this emerging issue. Specifically, we propose deformable attention, a sparse attention mechanism that can better focus on the important time points by itself, to get rid of the need of patching. And we also adopt a hierarchical structure to alleviate the efficiency issue caused by the removal of patching. Experimentally, our DeformableTST achieves the consistent state-of-the-art performance in a broader range of time series tasks, especially achieving promising performance in forecasting tasks unsuitable for patching, therefore successfully reducing the reliance on patching and broadening the applicability of Transformer-based models. Code is available at this repository: https://github.com/luodhhh/DeformableTST.

Semi-supervised multi-label learning (SSMLL) refers to inducing classifiers using a small number of samples with multiple labels and many unlabeled samples. The prevalent solution of SSMLL involves forming pseudo-labels for unlabeled samples and inducing classifiers using both labeled and pseudo-labeled samples in a self-training manner. Unfortunately, with the commonly used binary type of loss and negative sampling, we have empirically found that learning with labeled and pseudo-labeled samples can result in the variance bias problem between the feature distributions of positive and negative samples for each label. To alleviate this problem, we aim to balance the variance bias between positive and negative samples from the perspective of the feature angle distribution for each label. Specifically, we extend the traditional binary angular margin loss to a balanced extension with feature angle distribution transformations under the Gaussian assumption, where the distributions are iteratively updated during classifier training. We also suggest an efficient prototype-based negative sampling method to maintain high-quality negative samples for each label. With this insight, we propose a novel SSMLL method, namely Semi-Supervised Multi-Label Learning with Balanced Binary Angular Margin loss (S$^2$ML$^2$-BBAM). To evaluate the effectiveness of S$^2$ML$^2$-BBAM, we compare it with existing competitors on benchmark datasets. The experimental results validate that S$^2$ML$^2$-BBAM can achieve very competitive performance.

Anomaly detection methods typically require fully observed data for model training and inference and cannot handle incomplete data, while the missing data problem is pervasive in science and engineering, leading to challenges in many important applications such as abnormal user detection in recommendation systems and novel or anomalous cell detection in bioinformatics, where the missing rates can be higher than 30\% or even 80\%. In this work, first, we construct and evaluate a straightforward strategy, ''impute-then-detect'', via combining state-of-the-art imputation methods with unsupervised anomaly detection methods, where the training data are composed of normal samples only. We observe that such two-stage methods frequently yield imputation bias from normal data, namely, the imputation methods are inclined to make incomplete samples ''normal", where the fundamental reason is that the imputation models learned only on normal data and cannot generalize well to abnormal data in the inference stage. To address this challenge, we propose an end-to-end method that integrates data imputation with anomaly detection into a unified optimization problem. The proposed model learns to generate well-designed pseudo-abnormal samples to mitigate the imputation bias and ensure the discrimination ability of both the imputation and detection processes. Furthermore, we provide theoretical guarantees for the effectiveness of the proposed method, proving that the proposed method can correctly detect anomalies with high probability. Experimental results on datasets with manually constructed missing values and inherent missing values demonstrate that our proposed method effectively mitigates the imputation bias and surpasses the baseline methods significantly. The source code of our method is available at https://github.com/jicongfan/ImAD-Anomaly-Detection-With-Missing-Data.

Persistent homology is a popular computational tool for analyzing the topology of point clouds, such as the presence of loops or voids. However, many real-world datasets with low intrinsic dimensionality reside in an ambient space of much higher dimensionality. We show that in this case traditional persistent homology becomes very sensitive to noise and fails to detect the correct topology. The same holds true for existing refinements of persistent homology. As a remedy, we find that spectral distances on the k-nearest-neighbor graph of the data, such as diffusion distance and effective resistance, allow to detect the correct topology even in the presence of high-dimensional noise. Moreover, we derive a novel closed-form formula for effective resistance, and describe its relation to diffusion distances. Finally, we apply these methods to high-dimensional single-cell RNA-sequencing data and show that spectral distances allow robust detection of cell cycle loops.

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights. Code is available at https://github.com/qiaoqiaoLF/MxDNA.

The success of machine learning models relies heavily on effectively representing high-dimensional data. However, ensuring data representations capture human-understandable concepts remains difficult, often requiring the incorporation of prior knowledge and decomposition of data into multiple subspaces. Traditional linear methods fall short in modeling more than one space, while more expressive deep learning approaches lack interpretability. Here, we introduce Supervised Independent Subspace Principal Component Analysis ($\texttt{sisPCA}$), a PCA extension designed for multi-subspace learning. Leveraging the Hilbert-Schmidt Independence Criterion (HSIC), $\texttt{sisPCA}$ incorporates supervision and simultaneously ensures subspace disentanglement. We demonstrate $\texttt{sisPCA}$'s connections with autoencoders and regularized linear regression and showcase its ability to identify and separate hidden data structures through extensive applications, including breast cancer diagnosis from image features, learning aging-associated DNA methylation changes, and single-cell analysis of malaria infection. Our results reveal distinct functional pathways associated with malaria colonization, underscoring the essentiality of explainable representation in high-dimensional data analysis.

The application of reinforcement learning in traffic signal control (TSC) has been extensively researched and yielded notable achievements. However, most existing works for TSC assume that traffic data from all surrounding intersections is fully and continuously available through sensors. In real-world applications, this assumption often fails due to sensor malfunctions or data loss, making TSC with missing data a critical challenge. To meet the needs of practical applications, we introduce DiffLight, a novel conditional diffusion model for TSC under data-missing scenarios in the offline setting. Specifically, we integrate two essential sub-tasks, i.e., traffic data imputation and decision-making, by leveraging a Partial Rewards Conditioned Diffusion (PRCD) model to prevent missing rewards from interfering with the learning process. Meanwhile, to effectively capture the spatial-temporal dependencies among intersections, we design a Spatial-Temporal transFormer (STFormer) architecture. In addition, we propose a Diffusion Communication Mechanism (DCM) to promote better communication and control performance under data-missing scenarios. Extensive experiments on five datasets with various data-missing scenarios demonstrate that DiffLight is an effective controller to address TSC with missing data. The code of DiffLight is released at https://github.com/lokol5579/DiffLight-release.

Empirical data can often be considered as samples from a set of probability distributions. Kernel methods have emerged as a natural approach for learning to classify these distributions. Although numerous kernels between distributions have been proposed, applying kernel methods to distribution regression tasks remains challenging, primarily because selecting a suitable kernel is not straightforward. Surprisingly, the question of learning a data-dependent distribution kernel has received little attention. In this paper, we propose a novel objective for the unsupervised learning of data-dependent distribution kernel, based on the principle of entropy maximization in the space of probability measure embeddings. We examine the theoretical properties of the latent embedding space induced by our objective, demonstrating that its geometric structure is well-suited for solving downstream discriminative tasks. Finally, we demonstrate the performance of the learned kernel across different modalities.

Counterfactual explanations provide ways of achieving a favorable model outcome with minimum input perturbation. However, counterfactual explanations can also be leveraged to reconstruct the model by strategically training a surrogate model to give similar predictions as the original (target) model. In this work, we analyze how model reconstruction using counterfactuals can be improved by further leveraging the fact that the counterfactuals also lie quite close to the decision boundary. Our main contribution is to derive novel theoretical relationships between the error in model reconstruction and the number of counterfactual queries required using polytope theory. Our theoretical analysis leads us to propose a strategy for model reconstruction that we call Counterfactual Clamping Attack (CCA) which trains a surrogate model using a unique loss function that treats counterfactuals differently than ordinary instances. Our approach also alleviates the related problem of decision boundary shift that arises in existing model reconstruction approaches when counterfactuals are treated as ordinary instances. Experimental results demonstrate that our strategy improves fidelity between the target and surrogate model predictions on several datasets.

Auto-labeling is an important family of techniques that produce labeled training sets with minimum manual annotation. A prominent variant, threshold-based auto-labeling (TBAL), works by finding thresholds on a model's confidence scores above which it can accurately automatically label unlabeled data. However, many models are known to produce overconfident scores, leading to poor TBAL performance. While a natural idea is to apply off-the-shelf calibration methods to alleviate the overconfidence issue, we show that such methods fall short. Rather than experimenting with ad-hoc choices of confidence functions, we propose a framework for studying the optimal TBAL confidence function. We develop a tractable version of the framework to obtain Colander (Confidence functions for Efficient and Reliable Auto-labeling), a new post-hoc method specifically designed to maximize performance in TBAL systems. We perform an extensive empirical evaluation of Colander and compare it against methods designed for calibration. Colander achieves up to 60% improvement on coverage over the baselines while maintaining error level below 5% and using the same amount of labeled data.

Autoformalization, the task of automatically translating natural language descriptions into a formal language, poses a significant challenge across various domains, especially in mathematics. Recent advancements in large language models (LLMs) have unveiled their promising capabilities to formalize even competition-level math problems. However, we observe a considerable discrepancy between pass@1 and pass@k accuracies in LLM-generated formalizations. To address this gap, we introduce a novel framework that scores and selects the best result from k autoformalization candidates based on two complementary self-consistency methods: symbolic equivalence and semantic consistency. Elaborately, symbolic equivalence identifies the logical homogeneity among autoformalization candidates using automated theorem provers, and semantic consistency evaluates the preservation of the original meaning by informalizing the candidates and computing the similarity between the embeddings of the original and informalized texts. Our extensive experiments on the MATH and miniF2F datasets demonstrate that our approach significantly enhances autoformalization accuracy, achieving up to 0.22-1.35x relative improvements across various LLMs and baseline methods.

Student cognitive modeling (SCM) is a fundamental task in intelligent education, with applications ranging from personalized learning to educational resource allocation. By exploiting students' response logs, SCM aims to predict their exercise performance as well as estimate knowledge proficiency in a subject. Data mining approaches such as matrix factorization can obtain high accuracy in predicting student performance on exercises, but the knowledge proficiency is unknown or poorly estimated. The situation is further exacerbated if only sparse interactions exist between exercises and students (or knowledge concepts). To solve this dilemma, we root monotonicity (a fundamental psychometric theory on educational assessments) in a co-factorization framework and present an autoencoder-like nonnegative matrix co-factorization (AE-NMCF), which improves the accuracy of estimating the student's knowledge proficiency via an encoder-decoder learning pipeline. The resulting estimation problem is nonconvex with nonnegative constraints. We introduce a projected gradient method based on block coordinate descent with Lipschitz constants and guarantee the method's theoretical convergence. Experiments on several real-world data sets demonstrate the efficacy of our approach in terms of both performance prediction accuracy and knowledge estimation ability, when compared with existing student cognitive models.