NeurIPS 2024 Papers

While tabular classification has traditionally relied on from-scratch training, a recent breakthrough called prior-data fitted networks (PFNs) challenges this approach. Similar to large language models, PFNs make use of pretraining and in-context learning to achieve strong performance on new tasks in a single forward pass. However, current PFNs have limitations that prohibit their widespread adoption. Notably, TabPFN achieves very strong performance on small tabular datasets but is not designed to make predictions for datasets of size larger than 1000. In this work, we overcome these limitations and substantially improve the performance of PFNs via context optimization. We introduce TuneTables, a parameter-efficient fine-tuning strategy for PFNs that compresses large datasets into a smaller learned context. We conduct extensive experiments on nineteen algorithms over 98 datasets and find that TuneTables achieves the best performance on average, outperforming boosted trees such as CatBoost, while optimizing fewer than 5\% of TabPFN's parameters. Furthermore, we show that TuneTables can be used as an interpretability tool and can even be used to mitigate biases by optimizing a fairness objective.

Solving nonlinear partial differential equations (PDEs) with multiple solutions is essential in various fields, including physics, biology, and engineering. However, traditional numerical methods, such as finite element and finite difference methods, often face challenges when dealing with nonlinear solvers, particularly in the presence of multiple solutions. These methods can become computationally expensive, especially when relying on solvers like Newton's method, which may struggle with ill-posedness near bifurcation points. In this paper, we propose a novel approach, the Newton Informed Neural Operator, which learns the Newton solver for nonlinear PDEs. Our method integrates traditional numerical techniques with the Newton nonlinear solver, efficiently learning the nonlinear mapping at each iteration. This approach allows us to compute multiple solutions in a single learning process while requiring fewer supervised data points than existing neural network methods.

Foundation models have significantly enhanced 2D task performance, and recent works like Bridge3D have successfully applied these models to improve 3D scene understanding through knowledge distillation, marking considerable advancements. Nonetheless, challenges such as the misalignment between 2D and 3D representations and the persistent long-tail distribution in 3D datasets still restrict the effectiveness of knowledge distillation from 2D to 3D using foundation models. To tackle these issues, we introduce a novel SAM-guided tokenization method that seamlessly aligns 3D transformer structures with region-level knowledge distillation, replacing the traditional KNN-based tokenization techniques. Additionally, we implement a group-balanced re-weighting strategy to effectively address the long-tail problem in knowledge distillation. Furthermore, inspired by the recent success of masked feature prediction, our framework incorporates a two-stage masked token prediction process in which the student model predicts both the global embeddings and token-wise local embeddings derived from the teacher models trained in the first stage. Our methodology has been validated across multiple datasets, including SUN RGB-D, ScanNet, and S3DIS, for tasks like 3D object detection and semantic segmentation. The results demonstrate significant improvements over current state-of-the-art self-supervised methods, establishing new benchmarks in this field.

Gene therapies have the potential to treat disease by delivering therapeutic genetic cargo to disease-associated cells. One limitation to their widespread use is the lack of short regulatory sequences, or promoters, that differentially induce the expression of delivered genetic cargo in target cells, minimizing side effects in other cell types. Such cell-type-specific promoters are difficult to discover using existing methods, requiring either manual curation or access to large datasets of promoter-driven expression from both targeted and untargeted cells. Model-based optimization (MBO) has emerged as an effective method to design biological sequences in an automated manner, and has recently been used in promoter design methods. However, these methods have only been tested using large training datasets that are expensive to collect, and focus on designing promoters for markedly different cell types, overlooking the complexities associated with designing promoters for closely related cell types that share similar regulatory features. Therefore, we introduce a comprehensive framework for utilizing MBO to design promoters in a data-efficient manner, with an emphasis on discovering promoters for similar cell types. We use conservative objective models (COMs) for MBO and highlight practical considerations such as best practices for improving sequence diversity, getting estimates of model uncertainty, and choosing the optimal set of sequences for experimental validation. Using three leukemia cell lines (Jurkat, K562, and THP1), we show that our approach discovers many novel cell-type-specific promoters after experimentally validating the designed sequences. For K562 cells, in particular, we discover a promoter that has 75.85\% higher cell-type-specificity than the best promoter from the initial dataset used to train our models. Our code and data will be available at https://github.com/young-geng/promoter_design.

Label distribution learning is a powerful learning paradigm to deal with label polysemy and has been widely applied in many practical tasks. A significant obstacle to the effective utilization of label distribution is the substantial expenses of accurate quantifying the label distributions. To tackle this challenge, label enhancement methods automatically infer label distributions from more easily accessible multi-label data based on binary annotations. However, the binary annotation of multi-label data requires experts to accurately assess whether each label can describe the instance, which may diminish the annotating efficiency and heighten the risk of erroneous annotation since the relationship between the label and the instance is unclear in many practical scenarios. Therefore, we propose to predict label distribution from ternary labels, allowing experts to annotate labels in a three-way annotation scheme. They can annotate the label as "$0$" indicating "uncertain relevant" if it is difficult to definitively determine whether the label can describe the instance, in addition to the binary annotation of "$1$" indicating "definitely relevant" and "$-1$" indicating "definitely irrelevant". Both the theoretical and methodological studies are conducted for the proposed learning paradigm. In the theoretical part, we conduct a quantitative comparison of approximation error between ternary and binary labels to elucidate the superiority of ternary labels over binary labels. In the methodological part, we propose a Categorical distribution with monotonicity and orderliness to model the mapping from label description degrees to ternary labels, which can serve as a loss function or as a probability distribution, allowing most existing label enhancement methods to be adapted to our task. Finally, we experimentally demonstrate the effectiveness of our proposal.

Predicting high-fidelity 3D structures of atomic systems is a fundamental yet challenging problem in scientific domains. While recent work demonstrates the advantage of generative models in this realm, the exploration of different probability paths are still insufficient, and hallucinations during sampling are persistently occurring. To address these pitfalls, we introduce FlowDPO, a novel framework that explores various probability paths with flow matching models and further suppresses hallucinations using Direct Preference Optimization (DPO) for structure generation. Our approach begins with a pre-trained flow matching model to generate multiple candidate structures for each training sample. These structures are then evaluated and ranked based on their distance to the ground truth, resulting in an automatic preference dataset. Using this dataset, we apply DPO to optimize the original model, improving its performance in generating structures closely aligned with the desired reference distribution. As confirmed by our theoretical analysis, such paradigm and objective function are compatible with arbitrary Gaussian paths, exhibiting favorable universality. Extensive experimental results on antibodies and crystals demonstrate substantial benefits of our FlowDPO, highlighting its potential to advance the field of 3D structure prediction with generative models.

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular *low displacement rank*) for integrating tensor fields defined on weighted trees. Several applications of the resulting *fast tree-field integrators* (FTFIs) are presented, including: (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) *Topological Transformers* (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as **three** extra learnable parameters per Transformer layer, leading to **1.0-1.5\%+** accuracy gains. Importantly, most of FTFIs are **exact** methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide **5.7-13x** speedups. We also provide an extensive theoretical analysis of our methods.

Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of determining their microbial compositions. In this paper, we revisit k-mer-based representations of genomes and provide a theoretical analysis of their use in representation learning. Based on the analysis, we propose a lightweight and scalable model for performing metagenomic binning at the genome read level, relying only on the k-mer compositions of the DNA fragments. We compare the model to recent genome foundation models and demonstrate that while the models are comparable in performance, the proposed model is significantly more effective in terms of scalability, a crucial aspect for performing metagenomic binning of real-world data sets.

Time series forecasting has played a pivotal role across various industries, including finance, transportation, energy, healthcare, and climate. Due to the abundant seasonal information they contain, timestamps possess the potential to offer robust global guidance for forecasting techniques. However, existing works primarily focus on local observations, with timestamps being treated merely as an optional supplement that remains underutilized. When data gathered from the real world is polluted, the absence of global information will damage the robust prediction capability of these algorithms. To address these problems, we propose a novel framework named GLAFF. Within this framework, the timestamps are modeled individually to capture the global dependencies. Working as a plugin, GLAFF adaptively adjusts the combined weights for global and local information, enabling seamless collaboration with any time series forecasting backbone. Extensive experiments conducted on nine real-world datasets demonstrate that GLAFF significantly enhances the average performance of widely used mainstream forecasting models by 12.5\%, surpassing the previous state-of-the-art method by 5.5\%.

Generating ligand molecules for specific protein targets, known as structure-based drug design, is a fundamental problem in therapeutics development and biological discovery. Recently, target-aware generative models, especially diffusion models, have shown great promise in modeling protein-ligand interactions and generating candidate drugs. However, existing models primarily focus on learning the chemical distribution of all drug candidates, which lacks effective steerability on the chemical quality of model generations. In this paper, we propose a novel and general alignment framework to align pretrained target diffusion models with preferred functional properties, named AliDiff. AliDiff shifts the target-conditioned chemical distribution towards regions with higher binding affinity and structural rationality, specified by user-defined reward functions, via the preference optimization approach. To avoid the overfitting problem in common preference optimization objectives, we further develop an improved Exact Energy Preference Optimization method to yield an exact and efficient alignment of the diffusion models, and provide the closed-form expression for the converged distribution. Empirical studies on the CrossDocked2020 benchmark show that AliDiff can generate molecules with state-of-the-art binding energies with up to -7.07 Avg. Vina Score, while maintaining strong molecular properties. Code is available at https://github.com/MinkaiXu/AliDiff.

3D object detection is fundamentally important for various emerging applications, including autonomous driving and robotics. A key requirement for training an accurate 3D object detector is the availability of a large amount of LiDAR-based point cloud data. Unfortunately, labeling point cloud data is extremely challenging, as accurate 3D bounding boxes and semantic labels are required for each potential object. This paper proposes a unified active 3D object detection framework, for greatly reducing the labeling cost of training 3D object detectors. Our framework is based on a novel formulation of submodular optimization, specifically tailored to the problem of active 3D object detection. In particular, we address two fundamental challenges associated with active 3D object detection: data imbalance and the need to cover the distribution of the data, including LiDAR-based point cloud data of varying difficulty levels. Extensive experiments demonstrate that our method achieves state-of-the-art performance with high computational efficiency compared to existing active learning methods. The code is available at [https://github.com/RuiyuM/STONE](https://github.com/RuiyuM/STONE)

Given a graph $G$ and a positive integer $k$, the Graphlet Sampling problem asks to sample a connected induced $k$-vertex subgraph of $G$ uniformly at random. Graphlet sampling enhances machine learning applications by transforming graph structures into feature vectors for tasks such as graph classification and subgraph identification, boosting neural network performance, and supporting clustered federated learning by capturing local structures and relationships. A recent work has shown that the problem admits an algorithm that preprocesses $G$ in time $O(nk^2 \log k + m)$, and draws one sample in expected time $k^{O(k)} \log n$, where $n=|V(G)|$ and $m=|E(G)|$. Such an algorithm relies on the assumption that the input graph fits into main memory and it does not seem to be straightforward to adapt it to very large graphs. We consider Graphlet Sampling in the semi-streaming setting, where we have a memory of $M = \Omega(n \log n)$ words, and $G$ can be only read through sequential passes over the edge list. We develop a semi-streaming algorithm that preprocesses $G$ in $p={O}(\log n)$ passes and samples $\Theta(M k^{-O(k)})$ independent uniform $k$-graphlets in $O(k)$ passes. For constant $k$, both phases run in time $O((n+m)\log n)$. We also show that the tradeoff between memory and number of passes of our algorithms is near-optimal. Our extensive evaluation on very large graphs shows the effectiveness of our algorithms.

One-shot Federated Learning (OFL) significantly reduces communication costs in FL by aggregating trained models only once. However, the performance of advanced OFL methods is far behind the normal FL. In this work, we provide a causal view to find that this performance drop of OFL methods comes from the isolation problem, which means that local isolatedly trained models in OFL may easily fit to spurious correlations due to the data heterogeneity. From the causal perspective, we observe that the spurious fitting can be alleviated by augmenting intermediate features from other clients. Built upon our observation, we propose a novel learning approach to endow OFL with superb performance and low communication and storage costs, termed as FuseFL. Specifically, FuseFL decomposes neural networks into several blocks, and progressively trains and fuses each block following a bottom-up manner for feature augmentation, introducing no additional communication costs. Comprehensive experiments demonstrate that FuseFL outperforms existing OFL and ensemble FL by a significant margin. We conduct comprehensive experiments to show that FuseFL supports high scalability of clients, heterogeneous model training, and low memory costs. Our work is the first attempt using causality to analyze and alleviate data heterogeneity of OFL.

Subset selection tasks, such as anomaly detection and compound selection in AI-assisted drug discovery, are crucial for a wide range of applications. Learning subset-valued functions with neural networks has achieved great success by incorporating permutation invariance symmetry into the architecture. However, existing neural set architectures often struggle to either capture comprehensive information from the superset or address complex interactions within the input. Additionally, they often fail to perform in scenarios where superset sizes surpass available memory capacity. To address these challenges, we introduce the novel concept of the Identity Property, which requires models to integrate information from the originating set, resulting in the development of neural networks that excel at performing effective subset selection from large supersets. Moreover, we present the Hierarchical Representation of Neural Subset Selection (HORSE), an attention-based method that learns complex interactions and retains information from both the input set and the optimal subset supervision signal. Specifically, HORSE enables the partitioning of the input ground set into manageable chunks that can be processed independently and then aggregated, ensuring consistent outcomes across different partitions. Through extensive experimentation, we demonstrate that HORSE significantly enhances neural subset selection performance by capturing more complex information and surpasses state-of-the-art methods in handling large-scale inputs by a margin of up to 20%.

We introduce multiple physics pretraining (MPP), an autoregressive task-agnostic pretraining approach for physical surrogate modeling of spatiotemporal systems with transformers. In MPP, rather than training one model on a specific physical system, we train a backbone model to predict the dynamics of multiple heterogeneous physical systems simultaneously in order to learn features that are broadly useful across systems and facilitate transfer. In order to learn effectively in this setting, we introduce a shared embedding and normalization strategy that projects the fields of multiple systems into a shared embedding space. We validate the efficacy of our approach on both pretraining and downstream tasks over a broad fluid mechanics-oriented benchmark. We show that a single MPP-pretrained transformer is able to match or outperform task-specific baselines on all pretraining sub-tasks without the need for finetuning. For downstream tasks, we demonstrate that finetuning MPP-trained models results in more accurate predictions across multiple time-steps on systems with previously unseen physical components or higher dimensional systems compared to training from scratch or finetuning pretrained video foundation models. We open-source our code and model weights trained at multiple scales for reproducibility.

Deep learning models like AlphaFold2 have revolutionized protein structure prediction, achieving unprecedented accuracy. However, the dependence on robust multiple sequence alignments (MSAs) continues to pose a challenge, especially for proteins that lack a wealth of homologous sequences. To overcome this limitation, we introduce MSA-Generator, a self-supervised generative protein language model. Trained on a sequence-to-sequence task using an automatically constructed dataset, MSA-Generator employs protein-specific attention mechanisms to harness large-scale protein databases, generating virtual MSAs that enrich existing ones and boost prediction accuracy. Our experiments on CASP14 and CASP15 benchmarks reveal significant improvements in LDDT scores, particularly for complex and challenging sequences, enhancing the performance of both AlphaFold2 and RoseTTAFold. The code is released at \url{https://github.com/lezhang7/MSAGen}.

While ensembling deep neural networks has shown promise in improving generalization performance, scaling current ensemble methods for large models remains challenging. Given that recent progress in deep learning is largely driven by the scale, exemplified by the widespread adoption of large-scale neural network architectures, scalability emerges an increasingly critical issue for machine learning algorithms in the era of large-scale models. In this work, we first showcase the potential of low precision ensembling, where ensemble members are derived from a single model within low precision number systems in a training-free manner. Our empirical analysis demonstrates the effectiveness of our proposed low precision ensembling method compared to existing ensemble approaches.

Hyperparameter optimization is crucial for obtaining peak performance of machine learning models. The standard protocol evaluates various hyperparameter configurations using a resampling estimate of the generalization error to guide optimization and select a final hyperparameter configuration. Without much evidence, paired resampling splits, i.e., either a fixed train-validation split or a fixed cross-validation scheme, are often recommended. We show that, surprisingly, reshuffling the splits for every configuration often improves the final model's generalization performance on unseen data. Our theoretical analysis explains how reshuffling affects the asymptotic behavior of the validation loss surface and provides a bound on the expected regret in the limiting regime. This bound connects the potential benefits of reshuffling to the signal and noise characteristics of the underlying optimization problem. We confirm our theoretical results in a controlled simulation study and demonstrate the practical usefulness of reshuffling in a large-scale, realistic hyperparameter optimization experiment. While reshuffling leads to test performances that are competitive with using fixed splits, it drastically improves results for a single train-validation holdout protocol and can often make holdout become competitive with standard CV while being computationally cheaper.

Large language models (LLMs) have the potential to generate texts that pose risks of misuse, such as plagiarism, planting fake reviews on e-commerce platforms, or creating inflammatory false tweets. Consequently, detecting whether a text is generated by LLMs has become increasingly important. Existing high-quality detection methods usually require access to the interior of the model to extract the intrinsic characteristics. However, since we do not have access to the interior of the black-box model, we must resort to surrogate models, which impacts detection quality. In order to achieve high-quality detection of black-box models, we would like to extract deep intrinsic characteristics of the black-box model generated texts. We view the generation process as a coupled process of prompt and intrinsic characteristics of the generative model. Based on this insight, we propose to decouple prompt and intrinsic characteristics (DPIC) for LLM-generated text detection method. Specifically, given a candidate text, DPIC employs an auxiliary LLM to reconstruct the prompt corresponding to the candidate text, then uses the prompt to regenerate text by the auxiliary LLM, which makes the candidate text and the regenerated text align with their prompts, respectively. Then, the similarity between the candidate text and the regenerated text is used as a detection feature, thus eliminating the prompt in the detection process, which allows the detector to focus on the intrinsic characteristics of the generative model. Compared to the baselines, DPIC has achieved an average improvement of 6.76\% and 2.91\% in detecting texts from different domains generated by GPT4 and Claude3, respectively.