NeurIPS 2024 Papers

Tabular data – structured, heterogeneous, spreadsheet-style data with rows and columns – is widely used in practice across many domains. However, while recent foundation models have reduced the need for developing task-specific datasets and predictors in domains such as language modeling and computer vision, this transfer learning paradigm has not had similar impact in the tabular domain. In this work, we seek to narrow this gap and present TABULA-8B, a language model for tabular prediction. We define a process for extracting a large, high-quality training dataset from the TabLib corpus, proposing methods for tabular data filtering and quality control. Using the resulting dataset, which comprises over 2.1B rows from 4.2M unique tables, we fine-tune a Llama 3-8B large language model (LLM) for tabular data prediction (classification and binned regression) using a novel packing and attention scheme for tabular prediction. Through evaluation across a test suite of 329 datasets, we find that TABULA-8B has zero-shot accuracy on unseen tables that is over 15 percentage points (pp) higher than random guessing, a feat that is not possible with existing state-of-the-art tabular prediction models (e.g. XGBoost, TabPFN). In the few-shot setting (1-32 shots), without any fine-tuning on the target datasets, TABULA-8B is 5-15 pp more accurate than XGBoost and TabPFN models that are explicitly trained on equal, or even up to 16× more data. We release our model, code, and data along with the publication of this paper.

Inverse problems describe the process of estimating the causal factors from a set of measurements or data. Mapping of often incomplete or degraded data to parameters is ill-posed, thus data-driven iterative solutions are required, for example when reconstructing clean images from poor signals. Diffusion models have shown promise as potent generative tools for solving inverse problems due to their superior reconstruction quality and their compatibility with iterative solvers. However, most existing approaches are limited to linear inverse problems represented as Stochastic Differential Equations (SDEs). This simplification falls short of addressing the challenging nature of real-world problems, leading to amplified cumulative errors and biases. We provide an explanation for this gap through the lens of measure-preserving dynamics of Random Dynamical Systems (RDS) with which we analyse Temporal Distribution Discrepancy and thus introduce a theoretical framework based on RDS for SDE diffusion models. We uncover several strategies that inherently enhance the stability and generalizability of diffusion models for inverse problems and introduce a novel score-based diffusion framework, the Dynamics-aware SDE Diffusion Generative Model (D^3GM). The Measure-preserving property can return the degraded measurement to the original state despite complex degradation with the RDS concept of stability. Our extensive experimental results corroborate the effectiveness of D^3GM across multiple benchmarks including a prominent application for inverse problems, magnetic resonance imaging.

We present a formulation of flow matching as variational inference, which we refer to as variational flow matching (VFM). We use this formulation to develop CatFlow, a flow matching method for categorical data that is easy to implement, computationally efficient, and achieves strong results on graph generation tasks. In VFM, the objective is to approximate the posterior probability path, which is a distribution over possible end points of a trajectory. VFM admits both the original flow matching objective and the CatFlow objective as special cases. We also relate VFM to score-based models, in which the dynamics are stochastic rather than deterministic, and derive a bound on the model likelihood based on a reweighted VFM objective. We evaluate CatFlow on one abstract graph generation task and two molecular generation tasks. In all cases, CatFlow exceeds or matches performance of the current state-of-the-art models.

We investigate learning the eigenfunctions of evolution operators for time-reversal invariant stochastic processes, a prime example being the Langevin equation used in molecular dynamics. Many physical or chemical processes described by this equation involve transitions between metastable states separated by high potential barriers that can hardly be crossed during a simulation. To overcome this bottleneck, data are collected via biased simulations that explore the state space more rapidly. We propose a framework for learning from biased simulations rooted in the infinitesimal generator of the process {and the associated resolvent operator}. We contrast our approach to more common ones based on the transfer operator, showing that it can provably learn the spectral properties of the unbiased system from biased data. In experiments, we highlight the advantages of our method over transfer operator approaches and recent developments based on generator learning, demonstrating its effectiveness in estimating eigenfunctions and eigenvalues. Importantly, we show that even with datasets containing only a few relevant transitions due to sub-optimal biasing, our approach recovers relevant information about the transition mechanism.

The interest in leveraging physics-based inductive bias in deep learning has resulted in recent development of _hybrid deep generative models (hybrid-DGMs)_ that integrates known physics-based mathematical expressions in neural generative models. To identify these hybrid-DGMs requires inferring parameters of the physics-based component along with their neural component. The identifiability of these hybrid-DGMs, however, has not yet been theoretically probed or established. How does the existing theory of the un-identifiability of general DGMs apply to hybrid-DGMs? What may be an effective approach to consutrct a hybrid-DGM with theoretically-proven identifiability? This paper provides the first theoretical probe into the identifiability of hybrid-DGMs, and present meta-learning as a novel solution to construct identifiable hybrid-DGMs. On synthetic and real-data benchmarks, we provide strong empirical evidence for the un-identifiability of existing hybrid-DGMs using unconditional priors, and strong identifiability results of the presented meta-formulations of hybrid-DGMs.

Traditional 3D shape reconstruction techniques from multi-view images, such as structure from motion and multi-view stereo, face challenges in reconstructing transparent objects. Recent advances in neural radiance fields and its variants primarily address opaque or transparent objects, encountering difficulties to reconstruct both transparent and opaque objects simultaneously. This paper introduces $\alpha$-NeuS$\textemdash$an extension of NeuS$\textemdash$that proves NeuS is unbiased for materials from fully transparent to fully opaque. We find that transparent and opaque surfaces align with the non-negative local minima and the zero iso-surface, respectively, in the learned distance field of NeuS. Traditional iso-surfacing extraction algorithms, such as marching cubes, which rely on fixed iso-values, are ill-suited for such data. We develop a method to extract the transparent and opaque surface simultaneously based on DCUDF. To validate our approach, we construct a benchmark that includes both real-world and synthetic scenes, demonstrating its practical utility and effectiveness. Our data and code are publicly available at https://github.com/728388808/alpha-NeuS.

The standard paradigm of modeling marked point processes is by parameterizing the intensity function using an attention-based (Transformer-style) architecture. Despite the flexibility of these methods, their inference is based on the computationally intensive thinning algorithm. In this work, we propose a framework where the advantages of the attention-based architecture are maintained and the limitation of the thinning algorithm is circumvented. The framework depends on modeling the conditional distribution of inter-event times with a mixture of log-normals satisfying a Markov property and the conditional probability mass function for the marks with a Transformer-based architecture. The proposed method attains state-of-the-art performance in predicting the next event of a sequence given its history. The experiments also reveal the efficacy of the methods that do not rely on the thinning algorithm during inference over the ones they do. Finally, we test our method on the challenging long-horizon prediction task and find that it outperforms a baseline developed specifically for tackling this task; importantly, inference requires just a fraction of time compared to the thinning-based baseline.

State-space graphical models and the variational autoencoder framework provide a principled apparatus for learning dynamical systems from data. State-of-the-art probabilistic approaches are often able to scale to large problems at the cost of flexibility of the variational posterior or expressivity of the dynamics model. However, those consolidations can be detrimental if the ultimate goal is to learn a generative model capable of explaining the spatiotemporal structure of the data and making accurate forecasts. We introduce a low-rank structured variational autoencoding framework for nonlinear Gaussian state-space graphical models capable of capturing dense covariance structures that are important for learning dynamical systems with predictive capabilities. Our inference algorithm exploits the covariance structures that arise naturally from sample based approximate Gaussian message passing and low-rank amortized posterior updates -- effectively performing approximate variational smoothing with time complexity scaling linearly in the state dimensionality. In comparisons with other deep state-space model architectures our approach consistently demonstrates the ability to learn a more predictive generative model. Furthermore, when applied to neural physiological recordings, our approach is able to learn a dynamical system capable of forecasting population spiking and behavioral correlates from a small portion of single trials.

LLMs show remarkable emergent abilities, such as inferring concepts from presumably out-of-distribution prompts, known as in-context learning. Though this success is often attributed to the Transformer architecture, our systematic understanding is limited. In complex real-world data sets, even defining what is out-of-distribution is not obvious. To better understand the OOD behaviour of autoregressive LLMs, we focus on formal languages, which are defined by the intersection of rules. We define a new scenario of OOD compositional generalization, termed \textit{rule extrapolation}. Rule extrapolation describes OOD scenarios, where the prompt violates at least one rule. We evaluate rule extrapolation in formal languages with varying complexity in linear and recurrent architectures, the Transformer, and state space models to understand the architectures' influence on rule extrapolation. We also lay the first stones of a normative theory of rule extrapolation, inspired by the Solomonoff prior in algorithmic information theory.

Tokenization is widely used in large language models because it significantly improves performance. However, tokenization imposes several disadvantages, such as performance biases, increased adversarial vulnerability, decreased character-level modeling performance, and increased modeling complexity. To address these disadvantages without sacrificing performance, we propose SpaceByte, a novel byte-level decoder architecture that closes the performance gap between byte-level and subword autoregressive language modeling. SpaceByte consists of a byte-level Transformer model, but with extra larger transformer blocks inserted in the middle of the layers. We find that performance is significantly improved by applying these larger blocks only after certain bytes, such as space characters, which typically denote word boundaries. Our experiments show that for a fixed training and inference compute budget, SpaceByte outperforms other byte-level architectures and roughly matches the performance of tokenized Transformer architectures.

Neural radiance fields (NeRFs) have gained popularity with multiple works showing promising results across various applications. However, to the best of our knowledge, existing works do not explicitly model the distribution of training camera poses, or consequently the triangulation quality, a key factor affecting reconstruction quality dating back to classical vision literature. We close this gap with ProvNeRF, an approach that models the provenance for each point -- i.e., the locations where it is likely visible -- of NeRFs as a stochastic field. We achieve this by extending implicit maximum likelihood estimation (IMLE) to functional space with an optimizable objective. We show that modeling per-point provenance during the NeRF optimization enriches the model with information on triangulation leading to improvements in novel view synthesis and uncertainty estimation under the challenging sparse, unconstrained view setting against competitive baselines. The code will be available at https://github.com/georgeNakayama/ProvNeRF.

Learners sharing similar implicit cognitive states often display comparable observable problem-solving performances. Leveraging collaborative connections among such similar learners proves valuable in comprehending human learning. Motivated by the success of collaborative modeling in various domains, such as recommender systems, we aim to investigate how collaborative signals among learners contribute to the diagnosis of human cognitive states (i.e., knowledge proficiency) in the context of intelligent education. The primary challenges lie in identifying implicit collaborative connections and disentangling the entangled cognitive factors of learners for improved explainability and controllability in learner Cognitive Diagnosis (CD). However, there has been no work on CD capable of simultaneously modeling collaborative and disentangled cognitive states. To address this gap, we present Coral, a $\underline{Co}$llabo$\underline{ra}$tive cognitive diagnosis model with disentang$\underline{l}$ed representation learning. Specifically, Coral first introduces a disentangled state encoder to achieve the initial disentanglement of learners' states. Subsequently, a meticulously designed collaborative representation learning procedure captures collaborative signals. It dynamically constructs a collaborative graph of learners by iteratively searching for optimal neighbors in a context-aware manner. Using the constructed graph, collaborative information is extracted through node representation learning. Finally, a decoding process aligns the initial cognitive states and collaborative states, achieving co-disentanglement with practice performance reconstructions. Extensive experiments demonstrate the superior performance of Coral, showcasing significant improvements over state-of-the-art methods across several real-world datasets. Our code is available at https://github.com/bigdata-ustc/Coral.

We study learning-based approaches to semantic route planning, which concerns producing routes in response to rich queries that specify various criteria and preferences. Semantic routing is already widely found in industry applications, especially navigational services like Google Maps; however, existing implementations only support limited route criteria and narrow query sets as they rely on repurposing classical route optimization algorithms. We argue for a learning-based approach to semantic routing as a more scalable and general alternative. To foster interest in this important application of graph learning, we are releasing a large-scale publicly-licensed benchmark for semantic routing consisting of real-world multi-objective navigation problems---expressed via natural language queries---on the richly annotated road networks of US cities. In addition to being intractable with existing approaches to semantic routing, our benchmark poses a significant scaling challenge for graph learning methods. As a proof-of-concept, we show that---at scale---even a standard transformer network is a powerful semantic routing system and achieves non-trivial performance on our benchmark. In the process, we demonstrate a simple solution to the challenge of scaling up graph learning: an autoregressive approach that decomposes semantic routing into smaller ``next-edge'' prediction problems.

Effectively designing molecular geometries is essential to advancing pharmaceutical innovations, a domain, which has experienced great attention through the success of generative models and, in particular, diffusion models. However, current molecular diffusion models are tailored towards a specific downstream task and lack adaptability. We introduce UniGuide, a framework for controlled geometric guidance of unconditional diffusion models that allows flexible conditioning during inference without the requirement of extra training or networks. We show how applications such as structure-based, fragment-based, and ligand-based drug design are formulated in the UniGuide framework and demonstrate on-par or superior performance compared to specialised models. Offering a more versatile approach, UniGuide has the potential to streamline the development of molecular generative models, allowing them to be readily used in diverse application scenarios.

Contrastive Learning (CL) plays a crucial role in molecular representation learning, enabling unsupervised learning from large scale unlabeled molecule datasets. It has inspired various applications in molecular property prediction and drug design. However, existing molecular representation learning methods often introduce potential false positive and false negative pairs through conventional graph augmentations like node masking and subgraph removal. The issue can lead to suboptimal performance when applying standard contrastive learning techniques to molecular datasets. To address the issue of false positive and negative pairs in molecular representation learning, we propose a novel probability-based contrastive learning (CL) framework. Unlike conventional methods, our approach introduces a learnable weight distribution via Bayesian modeling to automatically identify and mitigate false positive and negative pairs. This method is particularly effective because it dynamically adjusts to the data, improving the accuracy of the learned representations. Our model is learned by a stochastic expectation-maximization process, which optimizes the model by iteratively refining the probability estimates of sample weights and updating the model parameters. Experimental results indicate that our method outperforms existing approaches in 13 out of 15 molecular property prediction benchmarks in MoleculeNet dataset and 8 out of 12 benchmarks in the QM9 benchmark, achieving new state-of-the-art results on average.

This work addresses the fundamental linear inverse problem in compressive sensing (CS) by introducing a new type of regularizing generative prior. Our proposed method utilizes ideas from classical dictionary-based CS and, in particular, sparse Bayesian learning (SBL), to integrate a strong regularization towards sparse solutions. At the same time, by leveraging the notion of conditional Gaussianity, it also incorporates the adaptability from generative models to training data. However, unlike most state-of-the-art generative models, it is able to learn from a few compressed and noisy data samples and requires no optimization algorithm for solving the inverse problem. Additionally, similar to Dirichlet prior networks, our model parameterizes a conjugate prior enabling its application for uncertainty quantification. We support our approach theoretically through the concept of variational inference and validate it empirically using different types of compressible signals.

Despite Flow Matching and diffusion models having emerged as powerful generative paradigms for continuous variables such as images and videos, their application to high-dimensional discrete data, such as language, is still limited. In this work, we present Discrete Flow Matching, a novel discrete flow paradigm designed specifically for generating discrete data. Discrete Flow Matching offers several key contributions: (i) it works with a general family of probability paths interpolating between source and target distributions; (ii) it allows for a generic formula for sampling from these probability paths using learned posteriors such as the probability denoiser ($x$-prediction) and noise-prediction ($\epsilon$-prediction); (iii) practically, focusing on specific probability paths defined with different schedulers improves generative perplexity compared to previous discrete diffusion and flow models; and (iv) by scaling Discrete Flow Matching models up to 1.7B parameters, we reach 6.7% Pass@1 and 13.4% Pass@10 on HumanEval and 6.7% Pass@1 and 20.6% Pass@10 on 1-shot MBPP coding benchmarks. Our approach is capable of generating high-quality discrete data in a non-autoregressive fashion, significantly closing the gap between autoregressive models and discrete flow models.

With the emergence of various molecular tasks and massive datasets, how to perform efficient training has become an urgent yet under-explored issue in the area. Data pruning (DP), as an oft-stated approach to saving training burdens, filters out less influential samples to form a coreset for training. However, the increasing reliance on pretrained models for molecular tasks renders traditional in-domain DP methods incompatible. Therefore, we propose a **Mol**ecular data **P**runing framework for **e**nhanced **G**eneralization (**MolPeg**), which focuses on the source-free data pruning scenario, where data pruning is applied with pretrained models. By maintaining two models with different updating paces during training, we introduce a novel scoring function to measure the informativeness of samples based on the loss discrepancy. As a plug-and-play framework, MolPeg realizes the perception of both source and target domain and consistently outperforms existing DP methods across four downstream tasks. Remarkably, it can surpass the performance obtained from full-dataset training, even when pruning up to 60-70% of the data on HIV and PCBA dataset. Our work suggests that the discovery of effective data-pruning metrics could provide a viable path to both enhanced efficiency and superior generalization in transfer learning.

Neural collapse ($\mathcal{NC}$) is a phenomenon observed in classification tasks where top-layer representations collapse into their class means, which become equinorm, equiangular and aligned with the classifiers. These behaviors -- associated with generalization and robustness -- would manifest under specific conditions: models are trained towards zero loss, with noise-free labels belonging to balanced classes, which do not outnumber the model's hidden dimension. Recent studies have explored $\mathcal{NC}$ in the absence of one or more of these conditions to extend and capitalize on the associated benefits of ideal geometries. Language modeling presents a curious frontier, as \textit{training by token prediction} constitutes a classification task where none of the conditions exist: the vocabulary is imbalanced and exceeds the embedding dimension; different tokens might correspond to similar contextual embeddings; and large language models (LLMs) in particular are typically only trained for a few epochs. This paper empirically investigates the impact of scaling the architectures and training of causal language models (CLMs) on their progression towards $\mathcal{NC}$. We find that $\mathcal{NC}$ properties that develop with scale (and regularization) are linked to generalization. Moreover, there is evidence of some relationship between $\mathcal{NC}$ and generalization independent of scale. Our work thereby underscores the generality of $\mathcal{NC}$ as it extends to the novel and more challenging setting of language modeling. Downstream, we seek to inspire further research on the phenomenon to deepen our understanding of LLMs -- and neural networks at large -- and improve existing architectures based on $\mathcal{NC}$-related properties. Our code is hosted on GitHub: [`https://github.com/rhubarbwu/linguistic-collapse`](https://github.com/rhubarbwu/linguistic-collapse).