NeurIPS 2024 论文列表

We propose the first learning scheme for functional differential equations (FDEs). FDEs play a fundamental role in physics, mathematics, and optimal control. However, the numerical analysis of FDEs has faced challenges due to its unrealistic computational costs and has been a long standing problem over decades. Thus, numerical approximations of FDEs have been developed, but they often oversimplify the solutions. To tackle these two issues, we propose a hybrid approach combining physics-informed neural networks (PINNs) with the *cylindrical approximation*. The cylindrical approximation expands functions and functional derivatives with an orthonormal basis and transforms FDEs into high-dimensional PDEs. To validate the reliability of the cylindrical approximation for FDE applications, we prove the convergence theorems of approximated functional derivatives and solutions. Then, the derived high-dimensional PDEs are numerically solved with PINNs. Through the capabilities of PINNs, our approach can handle a broader class of functional derivatives more efficiently than conventional discretization-based methods, improving the scalability of the cylindrical approximation. As a proof of concept, we conduct experiments on two FDEs and demonstrate that our model can successfully achieve typical $L^1$ relative error orders of PINNs $\sim 10^{-3}$. Overall, our work provides a strong backbone for physicists, mathematicians, and machine learning experts to analyze previously challenging FDEs, thereby democratizing their numerical analysis, which has received limited attention.

Solving parametric partial differential equations (PDEs) presents significant challenges for data-driven methods due to the sensitivity of spatio-temporal dynamics to variations in PDE parameters. Machine learning approaches often struggle to capture this variability. To address this, data-driven approaches learn parametric PDEs by sampling a very large variety of trajectories with varying PDE parameters. We first show that incorporating conditioning mechanisms for learning parametric PDEs is essential and that among them, \textit{adaptive conditioning}, allows stronger generalization. As existing adaptive conditioning methods do not scale well with respect to the number of parameters to adapt in the neural solver, we propose GEPS, a simple adaptation mechanism to boost GEneralization in Pde Solvers via a first-order optimization and low-rank rapid adaptation of a small set of context parameters. We demonstrate the versatility of our approach for both fully data-driven and for physics-aware neural solvers. Validation performed on a whole range of spatio-temporal forecasting problems demonstrates excellent performance for generalizing to unseen conditions including initial conditions, PDE coefficients, forcing terms and solution domain. *Project page*: https://geps-project.github.io

In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data.

We present a method for controlling a simulated humanoid to grasp an object and move it to follow an object's trajectory. Due to the challenges in controlling a humanoid with dexterous hands, prior methods often use a disembodied hand and only consider vertical lifts or short trajectories. This limited scope hampers their applicability for object manipulation required for animation and simulation. To close this gap, we learn a controller that can pick up a large number (>1200) of objects and carry them to follow randomly generated trajectories. Our key insight is to leverage a humanoid motion representation that provides human-like motor skills and significantly speeds up training. Using only simplistic reward, state, and object representations, our method shows favorable scalability on diverse objects and trajectories. For training, we do not need a dataset of paired full-body motion and object trajectories. At test time, we only require the object mesh and desired trajectories for grasping and transporting. To demonstrate the capabilities of our method, we show state-of-the-art success rates in following object trajectories and generalizing to unseen objects. Code and models will be released.

A prevailing belief in attack and defense community is that the higher flatness of adversarial examples enables their better cross-model transferability, leading to a growing interest in employing sharpness-aware minimization and its variants. However, the theoretical relationship between the transferability of adversarial examples and their flatness has not been well established, making the belief questionable. To bridge this gap, we embark on a theoretical investigation and, for the first time, derive a theoretical bound for the transferability of adversarial examples with few practical assumptions. Our analysis challenges this belief by demonstrating that the increased flatness of adversarial examples does not necessarily guarantee improved transferability. Moreover, building upon the theoretical analysis, we propose TPA, a Theoretically Provable Attack that optimizes a surrogate of the derived bound to craft adversarial examples. Extensive experiments across widely used benchmark datasets and various real-world applications show that TPA can craft more transferable adversarial examples compared to state-of-the-art baselines. We hope that these results can recalibrate preconceived impressions within the community and facilitate the development of stronger adversarial attack and defense mechanisms.

Motivated by the transformative capabilities of large language models (LLMs) across various natural language tasks, there has been a growing demand to deploy these models effectively across diverse real-world applications and platforms. However, the challenge of efficiently deploying LLMs has become increasingly pronounced due to the varying application-specific performance requirements and the rapid evolution of computational platforms, which feature diverse resource constraints and deployment flows. These varying requirements necessitate LLMs that can adapt their structures (depth and width) for optimal efficiency across different platforms and application specifications. To address this critical gap, we propose AmoebaLLM, a novel framework designed to enable the instant derivation of LLM subnets of arbitrary shapes, which achieve the accuracy-efficiency frontier and can be extracted immediately after a one-time fine-tuning. In this way, AmoebaLLM significantly facilitates rapid deployment tailored to various platforms and applications. Specifically, AmoebaLLM integrates three innovative components: (1) a knowledge-preserving subnet selection strategy that features a dynamic-programming approach for depth shrinking and an importance-driven method for width shrinking; (2) a shape-aware mixture of LoRAs to mitigate gradient conflicts among subnets during fine-tuning; and (3) an in-place distillation scheme with loss-magnitude balancing as the fine-tuning objective. Extensive experiments validate that AmoebaLLM not only sets new standards in LLM adaptability but also successfully delivers subnets that achieve state-of-the-art trade-offs between accuracy and efficiency.

Cryptographic problems, operating within binary variable spaces, can be routinely transformed into Boolean Satisfiability (SAT) problems regarding specific cryptographic conditions like plaintext-ciphertext matching. With the fast development of learning for discrete data, this SAT representation also facilitates the utilization of machine-learning approaches with the hope of automatically capturing patterns and strategies inherent in cryptographic structures in a data-driven manner. Existing neural SAT solvers consistently adopt conjunctive normal form (CNF) for instance representation, which in the cryptographic context can lead to scale explosion and a loss of high-level semantics. In particular, extensively used XOR operations in cryptographic problems can incur an exponential number of clauses. In this paper, we propose a graph structure based on Arithmetic Normal Form (ANF) to efficiently handle the XOR operation bottleneck. Additionally, we design an encoding method for AND operations in these ANF-based graphs, demonstrating improved efficiency over alternative general graph forms for SAT. We then propose CryptoANFNet, a graph learning approach that trains a classifier based on a message-passing scheme to predict plaintext-ciphertext satisfiability. Using ANF-based SAT instances, CryptoANFNet demonstrates superior scalability and can naturally capture higher-order operational information. Empirically, CryptoANFNet achieves a 50x speedup over heuristic solvers and outperforms SOTA learning-based SAT solver NeuroSAT, with 96\% vs. 91\% accuracy on small-scale and 72\% vs. 55\% on large-scale datasets from real encryption algorithms. We also introduce a key-solving algorithm that simplifies ANF-based SAT instances from plaintext and ciphertext, enhancing key decryption accuracy from 76.5\% to 82\% and from 72\% to 75\% for datasets generated from two real encryption algorithms.

We propose a novel approach to molecular simulations using neural network reparametrization, which offers a flexible alternative to traditional coarse-graining methods. Unlike conventional techniques that strictly reduce degrees of freedom, the complexity of the system can be adjusted in our model, sometimes increasing it to simplify the optimization process. Our approach also maintains continuous access to fine-grained modes and eliminates the need for force-matching, enhancing both the efficiency and accuracy of energy minimization. Importantly, our framework allows for the use of potentially arbitrary neural networks (e.g., Graph Neural Networks (GNN)) to perform the reparametrization, incorporating CG modes as needed. In fact, our experiments using very weak molecular forces (Lennard-Jones potential) the GNN-based model is the sole model to find the correct configuration. Similarly, in protein-folding scenarios, our GNN-based CG method consistently outperforms traditional optimization methods. It not only recovers the target structures more accurately but also achieves faster convergence to the deepest energy states. This work demonstrates significant advancements in molecular simulations by optimizing energy minimization and convergence speeds, offering a new, efficient framework for simulating complex molecular systems.

This paper introduces an approach to endow generative diffusion processes the ability to satisfy and certify compliance with constraints and physical principles. The proposed method recast the traditional sampling process of generative diffusion models as a constrained optimization problem, steering the generated data distribution to remain within a specified region to ensure adherence to the given constraints. These capabilities are validated on applications featuring both convex and challenging, non-convex, constraints as well as ordinary differential equations, in domains spanning from synthesizing new materials with precise morphometric properties, generating physics-informed motion, optimizing paths in planning scenarios, and human motion synthesis.

Data collection is often difficult in critical fields such as medicine, physics, and chemistry, yielding typically only small tabular datasets. However, classification methods tend to struggle with these small datasets, leading to poor predictive performance. Increasing the training set with additional synthetic data, similar to data augmentation in images, is commonly believed to improve downstream tabular classification performance. However, current tabular generative methods that learn either the joint distribution $ p(\mathbf{x}, y) $ or the class-conditional distribution $ p(\mathbf{x} \mid y) $ often overfit on small datasets, resulting in poor-quality synthetic data, usually worsening classification performance compared to using real data alone. To solve these challenges, we introduce TabEBM, a novel class-conditional generative method using Energy-Based Models (EBMs). Unlike existing tabular methods that use a shared model to approximate all class-conditional densities, our key innovation is to create distinct EBM generative models for each class, each modelling its class-specific data distribution individually. This approach creates robust energy landscapes, even in ambiguous class distributions. Our experiments show that TabEBM generates synthetic data with higher quality and better statistical fidelity than existing methods. When used for data augmentation, our synthetic data consistently leads to improved classification performance across diverse datasets of various sizes, especially small ones. Code is available at https://github.com/andreimargeloiu/TabEBM.

The Neural Tangent Kernel (NTK) viewpoint is widely employed to analyze the training dynamics of overparameterized Physics-Informed Neural Networks (PINNs). However, unlike the case of linear Partial Differential Equations (PDEs), we show how the NTK perspective falls short in the nonlinear scenario. Specifically, we establish that the NTK yields a random matrix at initialization that is not constant during training, contrary to conventional belief. Another significant difference from the linear regime is that, even in the idealistic infinite-width limit, the Hessian does not vanish and hence it cannot be disregarded during training. This motivates the adoption of second-order optimization methods. We explore the convergence guarantees of such methods in both linear and nonlinear cases, addressing challenges such as spectral bias and slow convergence. Every theoretical result is supported by numerical examples with both linear and nonlinear PDEs, and we highlight the benefits of second-order methods in benchmark test cases.

This paper introduces AutoSurvey, a speedy and well-organized methodology for automating the creation of comprehensive literature surveys in rapidly evolving fields like artificial intelligence. Traditional survey paper creation faces challenges due to the vast volume and complexity of information, prompting the need for efficient survey methods. While large language models (LLMs) offer promise in automating this process, challenges such as context window limitations, parametric knowledge constraints, and the lack of evaluation benchmarks remain. AutoSurvey addresses these challenges through a systematic approach that involves initial retrieval and outline generation, subsection drafting by specialized LLMs, integration and refinement, and rigorous evaluation and iteration. Our contributions include a comprehensive solution to the survey problem, a reliable evaluation method, and experimental validation demonstrating AutoSurvey's effectiveness.

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.

Many zeroth-order (ZO) optimization algorithms have been developed to solve nonconvex minimax problems in machine learning and computer vision areas. However, existing ZO minimax algorithms have high complexity and rely on some strict restrictive conditions for ZO estimations. To address these issues, we design a new unified ZO gradient descent extragradient ascent (ZO-GDEGA) algorithm, which reduces the overall complexity to $\mathcal{O}(d\epsilon^{-6})$ to find an $\epsilon$-stationary point of the function $\psi$ for nonconvex-concave (NC-C) problems, where $d$ is the variable dimension. To the best of our knowledge, ZO-GDEGA is the first ZO algorithm with complexity guarantees to solve stochastic NC-C problems. Moreover, ZO-GDEGA requires weaker conditions on the ZO estimations and achieves more robust theoretical results. As a by-product, ZO-GDEGA has advantages on the condition number for the NC-strongly concave case. Experimentally, ZO-GDEGA can generate more effective poisoning attack data with an average accuracy reduction of 5\%. The improved AUC performance also verifies the robustness of gradient estimations.

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.

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called $\nabla^2$DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level ($\omega$B97X-D/def2-SVP) for each conformation. Moreover, $\nabla^2$DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

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.

We present the `Multimodal Universe`, a large-scale multimodal dataset of scientific astronomical data, compiled specifically to facilitate machine learning research. Overall, our dataset contains hundreds of millions of astronomical observations, constituting 100TB of multi-channel and hyper-spectral images, spectra, multivariate time series, as well as a wide variety of associated scientific measurements and metadata. In addition, we include a range of benchmark tasks representative of standard practices for machine learning methods in astrophysics. This massive dataset will enable the development of large multi-modal models specifically targeted towards scientific applications. All codes used to compile the dataset, and a description of how to access the data is available at https://github.com/MultimodalUniverse/MultimodalUniverse