NeurIPS 2024 Papers

Visual-Language Alignment (VLA) has gained a lot of attention since CLIP's groundbreaking work. Although CLIP performs well, the typical direct latent feature alignment lacks clarity in its representation and similarity scores. On the other hand, lexical representation, a vector whose element represents the similarity between the sample and a word from the vocabulary, is a natural sparse representation and interpretable, providing exact matches for individual words. However, lexical representations are difficult to learn due to no ground-truth supervision and false-discovery issues, and thus requires complex design to train effectively. In this paper, we introduce LexVLA, a more interpretable VLA framework by learning a unified lexical representation for both modalities without complex design. We use DINOv2 as our visual model for its local-inclined features and Llama 2, a generative language model, to leverage its in-context lexical prediction ability. To avoid the false discovery, we propose an overuse penalty to refrain the lexical representation from falsely frequently activating meaningless words. We demonstrate that these two pre-trained uni-modal models can be well-aligned by fine-tuning on the modest multi-modal dataset and avoid intricate training configurations. On cross-modal retrieval benchmarks, LexVLA, trained on the CC-12M multi-modal dataset, outperforms baselines fine-tuned on larger datasets (e.g., YFCC15M) and those trained from scratch on even bigger datasets (e.g., 1.1B data, including CC-12M). We conduct extensive experiments to analyze LexVLA. Codes are available at https://github.com/Clementine24/LexVLA.

Learning the unique directed acyclic graph corresponding to an unknown causal model is a challenging task. Methods based on functional causal models can identify a unique graph, but either suffer from the curse of dimensionality or impose strong parametric assumptions. To address these challenges, we propose a novel hybrid approach for global causal discovery in observational data that leverages local causal substructures. We first present a topological sorting algorithm that leverages ancestral relationships in linear structural causal models to establish a compact top-down hierarchical ordering, encoding more causal information than linear orderings produced by existing methods. We demonstrate that this approach generalizes to nonlinear settings with arbitrary noise. We then introduce a nonparametric constraint-based algorithm that prunes spurious edges by searching for local conditioning sets, achieving greater accuracy than current methods. We provide theoretical guarantees for correctness and worst-case polynomial time complexities, with empirical validation on synthetic data.

Large Language Models (LLMs) have the potential to transform humanities and social science research, yet their history knowledge and comprehension at a graduate level remains untested. Benchmarking LLMs in history is particularly challenging, given that human knowledge of history is inherently unbalanced, with more information available on Western history and recent periods. We introduce the History Seshat Test for LLMs (HiST-LLM), based on a subset of the Seshat Global History Databank, which provides a structured representation of human historical knowledge, containing 36,000 data points across 600 historical societies and over 2,700 scholarly references. This dataset covers every major world region from the Neolithic period to the Industrial Revolution and includes information reviewed and assembled by history experts and graduate research assistants. Using this dataset, we benchmark a total of seven models from the Gemini, OpenAI, and Llama families. We find that, in a four-choice format, LLMs have a balanced accuracy ranging from 33.6% (Llama-3.1-8B) to 46% (GPT-4-Turbo), outperforming random guessing (25%) but falling short of expert comprehension. LLMs perform better on earlier historical periods. Regionally, performance is more even but still better for the Americas and lowest in Oceania and Sub-Saharan Africa for the more advanced models. Our benchmark shows that while LLMs possess some expert-level historical knowledge, there is considerable room for improvement.

Graph Transformers (GTs) have recently emerged as popular alternatives to traditional message-passing Graph Neural Networks (GNNs), due to their theoretically superior expressiveness and impressive performance reported on standard node classification benchmarks, often significantly outperforming GNNs. In this paper, we conduct a thorough empirical analysis to reevaluate the performance of three classic GNN models (GCN, GAT, and GraphSAGE) against GTs. Our findings suggest that the previously reported superiority of GTs may have been overstated due to suboptimal hyperparameter configurations in GNNs. Remarkably, with slight hyperparameter tuning, these classic GNN models achieve state-of-the-art performance, matching or even exceeding that of recent GTs across 17 out of the 18 diverse datasets examined. Additionally, we conduct detailed ablation studies to investigate the influence of various GNN configurations—such as normalization, dropout, residual connections, and network depth—on node classification performance. Our study aims to promote a higher standard of empirical rigor in the field of graph machine learning, encouraging more accurate comparisons and evaluations of model capabilities. Our implementation is available at https://github.com/LUOyk1999/tunedGNN.

The Spiking Neural Network (SNN) is a biologically inspired neural network infrastructure that has recently garnered significant attention. It utilizes binary spike activations to transmit information, thereby replacing multiplications with additions and resulting in high energy efficiency. However, training an SNN directly poses a challenge due to the undefined gradient of the firing spike process. Although prior works have employed various surrogate gradient training methods that use an alternative function to replace the firing process during back-propagation, these approaches ignore an intrinsic problem: gradient vanishing. To address this issue, we propose a shortcut back-propagation method in the paper, which advocates for transmitting the gradient directly from the loss to the shallow layers. This enables us to present the gradient to the shallow layers directly, thereby significantly mitigating the gradient vanishing problem. Additionally, this method does not introduce any burden during the inference phase. To strike a balance between final accuracy and ease of training, we also propose an evolutionary training framework and implement it by inducing a balance coefficient that dynamically changes with the training epoch, which further improves the network's performance. Extensive experiments conducted over static and dynamic datasets using several popular network structures reveal that our method consistently outperforms state-of-the-art methods.

Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the molecular structure, including the presence or absence of functional groups. Chemists leverage the complementary nature of the different methods to their advantage. However, the lack of a comprehensive multimodal dataset, containing spectra from a variety of spectroscopic techniques, has limited machine-learning approaches mostly to single-modality tasks for predicting molecular structures from spectra. Here we introduce a dataset comprising simulated $^1$H-NMR, $^{13}$C-NMR, HSQC-NMR, Infrared, and Mass spectra (positive and negative ion modes) for 790k molecules extracted from chemical reactions in patent data. This dataset enables the development of foundation models for integrating information from multiple spectroscopic modalities, emulating the approach employed by human experts. Additionally, we provide benchmarks for evaluating single-modality tasks such as structure elucidation, predicting the spectra for a target molecule, and functional group predictions. This dataset has the potential automate structure elucidation, streamlining the molecular discovery pipeline from synthesis to structure determination. The dataset and code for the benchmarks can be found at https://rxn4chemistry.github.io/multimodal-spectroscopic-dataset (Available upon submission of the supporting information).

Knowledge editing technology has received widespread attention for low-cost updates of incorrect or outdated knowledge in large-scale language models. However, recent research has found that edited models often exhibit varying degrees of performance degradation. The reasons behind this phenomenon and potential solutions have not yet been provided. In order to investigate the reasons for the performance decline of the edited model and optimize the editing method, this work explores the underlying reasons from both data and model perspectives. Specifically, 1) from a data perspective, to clarify the impact of data on the performance of editing models, this paper first constructs a **M**ulti-**Q**uestion **D**ataset (**MQD**) to evaluate the impact of different types of editing data on model performance. The performance of the editing model is mainly affected by the diversity of editing targets and sequence length, as determined through experiments. 2) From a model perspective, this article explores the factors that affect the performance of editing models. The results indicate a strong correlation between the L1-norm of the editing model layer and the editing accuracy, and clarify that this is an important factor leading to the bottleneck of editing performance. Finally, in order to improve the performance of the editing model, this paper further proposes a **D**ump **for** **S**equence (**D4S**) method, which successfully overcomes the previous editing bottleneck by reducing the L1-norm of the editing layer, allowing users to perform multiple effective edits and minimizing model damage. Our code is available at https://github.com/nlpkeg/D4S.

Despite the advanced intelligence abilities of large language models (LLMs) in various applications, they still face significant computational and storage demands. Knowledge Distillation (KD) has emerged as an effective strategy to improve the performance of a smaller LLM (i.e., the student model) by transferring knowledge from a high-performing LLM (i.e., the teacher model). Prevailing techniques in LLM distillation typically use a black-box model API to generate high-quality pretrained and aligned datasets, or utilize white-box distillation by altering the loss function to better transfer knowledge from the teacher LLM. However, these methods ignore the knowledge differences between the student and teacher LLMs across domains. This results in excessive focus on domains with minimal performance gaps and insufficient attention to domains with large gaps, reducing overall performance. In this paper, we introduce a new LLM distillation framework called DDK, which dynamically adjusts the composition of the distillation dataset in a smooth manner according to the domain performance differences between the teacher and student models, making the distillation process more stable and effective. Extensive evaluations show that DDK significantly improves the performance of student models, outperforming both continuously pretrained baselines and existing knowledge distillation methods by a large margin.

Natural images captured by mobile devices often suffer from multiple types of degradation, such as noise, blur, and low light. Traditional image restoration methods require manual selection of specific tasks, algorithms, and execution sequences, which is time-consuming and may yield suboptimal results. All-in-one models, though capable of handling multiple tasks, typically support only a limited range and often produce overly smooth, low-fidelity outcomes due to their broad data distribution fitting. To address these challenges, we first define a new pipeline for restoring images with multiple degradations, and then introduce RestoreAgent, an intelligent image restoration system leveraging multimodal large language models. RestoreAgent autonomously assesses the type and extent of degradation in input images and performs restoration through (1) determining the appropriate restoration tasks, (2) optimizing the task sequence, (3) selecting the most suitable models, and (4) executing the restoration. Experimental results demonstrate the superior performance of RestoreAgent in handling complex degradation, surpassing human experts. Furthermore, the system’s modular design facilitates the fast integration of new tasks and models.

Federated graph learning (FedGL) is an emerging learning paradigm to collaboratively train graph data from various clients. However, during the development and deployment of FedGL models, they are susceptible to illegal copying and model theft. Backdoor-based watermarking is a well-known method for mitigating these attacks, as it offers ownership verification to the model owner. We take the first step to protect the ownership of FedGL models via backdoor-based watermarking. Existing techniques have challenges in achieving the goal: 1) they either cannot be directly applied or yield unsatisfactory performance; 2) they are vulnerable to watermark removal attacks; and 3) they lack of formal guarantees. To address all the challenges, we propose FedGMark, the first certified robust backdoor-based watermarking for FedGL. FedGMark leverages the unique graph structure and client information in FedGL to learn customized and diverse watermarks. It also designs a novel GL architecture that facilitates defending against both the empirical and theoretically worst-case watermark removal attacks. Extensive experiments validate the promising empirical and provable watermarking performance of FedGMark. Source code is available at: https://github.com/Yuxin104/FedGMark.

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation https://github.com/WillHua127/ReactZyme.

We measure the out-of-domain uncertainty in the prediction of Neural Networks using a statistical notion called "Lens Depth'' (LD) combined with Fermat Distance, which is able to capture precisely the "depth'' of a point with respect to a distribution in feature space, without any distributional assumption. Our method also has no trainable parameter. The method is applied directly in the feature space at test time and does not intervene in training process. As such, it does not impact the performance of the original model. The proposed method gives excellent qualitative results on toy datasets and can give competitive or better uncertainty estimation on standard deep learning datasets compared to strong baseline methods.

Masked (or absorbing) diffusion is actively explored as an alternative to autoregressive models for generative modeling of discrete data. However, existing work in this area has been hindered by unnecessarily complex model formulations and unclear relationships between different perspectives, leading to suboptimal parameterization, training objectives, and ad hoc adjustments to counteract these issues. In this work, we aim to provide a simple and general framework that unlocks the full potential of masked diffusion models. We show that the continuous-time variational objective of masked diffusion models is a simple weighted integral of cross-entropy losses. Our framework also enables training generalized masked diffusion models with state-dependent masking schedules. When evaluated by perplexity, our models trained on OpenWebText surpass prior diffusion language models at GPT-2 scale and demonstrate superior performance on 4 out of 5 zero-shot language modeling tasks. Furthermore, our models vastly outperform previous discrete diffusion models on pixel-level image modeling, achieving 2.75 (CIFAR-10) and 3.40 (ImageNet 64x64) bits per dimension that are better than autoregressive models of similar sizes.

Social relation reasoning aims to identify relation categories such as friends, spouses, and colleagues from images. While current methods adopt the paradigm of training a dedicated network end-to-end using labeled image data, they are limited in terms of generalizability and interpretability. To address these issues, we first present a simple yet well-crafted framework named SocialGPT, which combines the perception capability of Vision Foundation Models (VFMs) and the reasoning capability of Large Language Models (LLMs) within a modular framework, providing a strong baseline for social relation recognition. Specifically, we instruct VFMs to translate image content into a textual social story, and then utilize LLMs for text-based reasoning. SocialGPT introduces systematic design principles to adapt VFMs and LLMs separately and bridge their gaps. Without additional model training, it achieves competitive zero-shot results on two databases while offering interpretable answers, as LLMs can generate language-based explanations for the decisions. The manual prompt design process for LLMs at the reasoning phase is tedious and an automated prompt optimization method is desired. As we essentially convert a visual classification task into a generative task of LLMs, automatic prompt optimization encounters a unique long prompt optimization issue. To address this issue, we further propose the Greedy Segment Prompt Optimization (GSPO), which performs a greedy search by utilizing gradient information at the segment level. Experimental results show that GSPO significantly improves performance, and our method also generalizes to different image styles. The code is available at https://github.com/Mengzibin/SocialGPT.

Multiple clustering aims to discover various latent structures of data from different aspects. Deep multiple clustering methods have achieved remarkable performance by exploiting complex patterns and relationships in data. However, existing works struggle to flexibly adapt to diverse user-specific needs in data grouping, which may require manual understanding of each clustering. To address these limitations, we introduce Multi-Sub, a novel end-to-end multiple clustering approach that incorporates a multi-modal subspace proxy learning framework in this work. Utilizing the synergistic capabilities of CLIP and GPT-4, Multi-Sub aligns textual prompts expressing user preferences with their corresponding visual representations. This is achieved by automatically generating proxy words from large language models that act as subspace bases, thus allowing for the customized representation of data in terms specific to the user’s interests. Our method consistently outperforms existing baselines across a broad set of datasets in visual multiple clustering tasks. Our code is available at https://github.com/Alexander-Yao/Multi-Sub.

How do brain circuits learn to generate behaviour? While significant strides have been made in understanding learning in artificial neural networks, applying this knowledge to biological networks remains challenging. For instance, while backpropagation is known to perform accurate credit assignment of error in artificial neural networks, how a similarly powerful process can be realized within the constraints of biological circuits remains largely unclear. One of the major challenges is that the brain's extensive recurrent connectivity requires the propagation of error through both space and time, a problem that is notoriously difficult to solve in vanilla recurrent neural networks. Moreover, the extensive feedback connections in the brain are known to influence forward network activity, but the interaction between feedback-driven activity changes and local, synaptic plasticity-based learning is not fully understood. Building on our previous work modelling motor learning, this work investigates the mechanistic properties of pre-trained networks with feedback control on a standard motor task. We show that feedback control of the ongoing recurrent network dynamics approximates the optimal first-order gradient with respect to the network activities, allowing for rapid, ongoing movement correction. Moreover, we show that trial-by-trial adaptation to a persistent perturbation using a local, biologically plausible learning rule that integrates recent activity and error feedback is both more accurate and more efficient with feedback control during learning, due to the decoupling of the recurrent network dynamics and the injection of an adaptive, second-order gradient into the network dynamics. Thus, our results suggest that feedback control may guide credit assignment in biological recurrent neural networks, enabling both rapid and efficient learning in the brain.

Unsupervised Multiplex Graph Learning (UMGL) aims to learn node representations on various edge types without manual labeling. However, existing research overlooks a key factor: the reliability of the graph structure. Real-world data often exhibit a complex nature and contain abundant task-irrelevant noise, severely compromising UMGL's performance. Moreover, existing methods primarily rely on contrastive learning to maximize mutual information across different graphs, limiting them to multiplex graph redundant scenarios and failing to capture view-unique task-relevant information. In this paper, we focus on a more realistic and challenging task: to unsupervisedly learn a fused graph from multiple graphs that preserve sufficient task-relevant information while removing task-irrelevant noise. Specifically, our proposed Information-aware Unsupervised Multiplex Graph Fusion framework (InfoMGF) uses graph structure refinement to eliminate irrelevant noise and simultaneously maximizes view-shared and view-unique task-relevant information, thereby tackling the frontier of non-redundant multiplex graph. Theoretical analyses further guarantee the effectiveness of InfoMGF. Comprehensive experiments against various baselines on different downstream tasks demonstrate its superior performance and robustness. Surprisingly, our unsupervised method even beats the sophisticated supervised approaches. The source code and datasets are available at https://github.com/zxlearningdeep/InfoMGF.

We study the differences arising from merging predictors in the causal and anticausal directions using the same data. In particular we study the asymmetries that arise in a simple model where we merge the predictors using one binary variable as target and two continuous variables as predictors. We use Causal Maximum Entropy (CMAXENT) as inductive bias to merge the predictors, however, we expect similar differences to hold also when we use other merging methods that take into account asymmetries between cause and effect. We show that if we observe all bivariate distributions, the CMAXENT solution reduces to a logistic regression in the causal direction and Linear Discriminant Analysis (LDA) in the anticausal direction. Furthermore, we study how the decision boundaries of these two solutions differ whenever we observe only some of the bivariate distributions implications for Out-Of-Variable (OOV) generalisation.

Instruction tuning is a supervised fine-tuning approach that significantly improves the ability of large language models (LLMs) to follow human instructions. For programming tasks, most models are finetuned with costly human-annotated instruction-response pairs or those generated by large, proprietary LLMs, which may not be permitted. We propose SelfCodeAlign, the first fully transparent and permissive pipeline for self-aligning code LLMs without extensive human annotations or distillation. SelfCodeAlign employs the same base model for inference throughout the data generation process. It first extracts diverse coding concepts from high-quality seed snippets to generate new tasks. It then samples multiple responses per task, pairs each with test cases, and validates them in a sandbox environment. Finally, passing examples are selected for instruction tuning. In our primary experiments, we use SelfCodeAlign with CodeQwen1.5-7B to generate a dataset of 74k instruction-response pairs. Finetuning on this dataset leads to a model that achieves a 67.1 pass@1 on HumanEval+, surpassing CodeLlama-70B-Instruct despite being ten times smaller. Across all benchmarks, this finetuned model consistently outperforms the original version trained with OctoPack, the previous state-of-the-art method for instruction tuning without human annotations or distillation. Additionally, we show that SelfCodeAlign is effective across LLMs of various sizes, from 3B to 33B, and that the base models can benefit more from alignment with their own data distribution. We further validate each component’s effectiveness in our pipeline, showing that SelfCodeAlign outperforms both direct distillation from GPT-4o and leading GPT-3.5-based distillation methods, such as OSS-Instruct and Evol-Instruct. SelfCodeAlign has also led to the creation of StarCoder2-Instruct, the first fully transparent, permissively licensed, and self-aligned code LLM that achieves state-of-the-art coding performance. Overall, SelfCodeAlign shows for the first time that a strong instruction-tuned code LLM can result from self-alignment rather than distillation.