NeurIPS 2024 论文列表

Can a physicist make only a finite number of errors in the eternal quest to uncover the law of nature? This millennium-old philosophical problem, known as inductive inference, lies at the heart of epistemology. Despite its significance to understanding human reasoning, a rigorous justification of inductive inference has remained elusive. At a high level, inductive inference asks whether one can make at most finite errors amidst an infinite sequence of observations, when deducing the correct hypothesis from a given hypothesis class. Historically, the only theoretical guarantee has been that if the hypothesis class is countable, inductive inference is possible, as exemplified by Solomonoff induction for learning Turing machines. In this paper, we provide a tight characterization of inductive inference by establishing a novel link to online learning theory. As our main result, we prove that inductive inference is possible if and only if the hypothesis class is a countable union of online learnable classes, potentially with an uncountable size, no matter the observations are adaptively chosen or iid sampled. Moreover, the same condition is also sufficient and necessary in the agnostic setting, where any hypothesis class meeting this criterion enjoys an $\tilde{O}(\sqrt{T})$ regret bound for any time step $T$, while others require an arbitrarily slow rate of regret. Our main technical tool is a novel non-uniform online learning framework, which may be of independent interest. Our main technical tool is a novel non-uniform online learning framework, which may be of independent interest.

Worldwide geolocalization aims to locate the precise location at the coordinate level of photos taken anywhere on the Earth. It is very challenging due to 1) the difficulty of capturing subtle location-aware visual semantics, and 2) the heterogeneous geographical distribution of image data. As a result, existing studies have clear limitations when scaled to a worldwide context. They may easily confuse distant images with similar visual contents, or cannot adapt to various locations worldwide with different amounts of relevant data. To resolve these limitations, we propose **G3**, a novel framework based on Retrieval-Augmented Generation (RAG). In particular, G3 consists of three steps, i.e., **G**eo-alignment, **G**eo-diversification, and **G**eo-verification to optimize both retrieval and generation phases of worldwide geolocalization. During Geo-alignment, our solution jointly learns expressive multi-modal representations for images, GPS and textual descriptions, which allows us to capture location-aware semantics for retrieving nearby images for a given query. During Geo-diversification, we leverage a prompt ensembling method that is robust to inconsistent retrieval performance for different image queries. Finally, we combine both retrieved and generated GPS candidates in Geo-verification for location prediction. Experiments on two well-established datasets IM2GPS3k and YFCC4k verify the superiority of G3 compared to other state-of-the-art methods. Our code is available online [https://github.com/Applied-Machine-Learning-Lab/G3](https://github.com/Applied-Machine-Learning-Lab/G3) for reproduction.

Spatio-temporal (ST) prediction has garnered a De facto attention in earth sciences, such as meteorological prediction, human mobility perception. However, the scarcity of data coupled with the high expenses involved in sensor deployment results in notable data imbalances. Furthermore, models that are excessively customized and devoid of causal connections further undermine the generalizability and interpretability. To this end, we establish a causal framework for ST predictions, termed CaPaint, which targets to identify causal regions in data and endow model with causal reasoning ability in a two-stage process. Going beyond this process, we utilize the back-door adjustment to specifically address the sub-regions identified as non-causal in the upstream phase. Specifically, we employ a novel image inpainting technique. By using a fine-tuned unconditional Diffusion Probabilistic Model (DDPM) as the generative prior, we in-fill the masks defined as environmental parts, offering the possibility of reliable extrapolation for potential data distributions. CaPaint overcomes the high complexity dilemma of optimal ST causal discovery models by reducing the data generation complexity from exponential to quasi-linear levels. Extensive experiments conducted on five real-world ST benchmarks demonstrate that integrating the CaPaint concept allows models to achieve improvements ranging from 4.3% to 77.3%. Moreover, compared to traditional mainstream ST augmenters, CaPaint underscores the potential of diffusion models in ST enhancement, offering a novel paradigm for this field. Our project is available at https://anonymous.4open.science/r/12345-DFCC.

Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computational task is to reconstruct the 3D density of the particle, along with 3D pose of the particle in each 2D image, for which the posterior pose distribution is highly multi-modal. Recent developments in cryo-EM have focused on deep learning for which amortized inference has been used to predict pose. Here, we address key problems with this approach, and propose a new semi-amortized method, cryoSPIN, in which reconstruction begins with amortized inference and then switches to a form of auto-decoding to refine poses locally using stochastic gradient descent. Through evaluation on synthetic datasets, we demonstrate that cryoSPIN is able to handle multi-modal pose distributions during the amortized inference stage, while the later, more flexible stage of direct pose optimization yields faster and more accurate convergence of poses compared to baselines. On experimental data, we show that cryoSPIN outperforms the state-of-the-art cryoAI in speed and reconstruction quality.

Priority queues are one of the most fundamental and widely used data structures in computer science. Their primary objective is to efficiently support the insertion of new elements with assigned priorities and the extraction of the highest priority element. In this study, we investigate the design of priority queues within the learning-augmented framework, where algorithms use potentially inaccurate predictions to enhance their worst-case performance. We examine three prediction models spanning different use cases, and we show how the predictions can be leveraged to enhance the performance of priority queue operations. Moreover, we demonstrate the optimality of our solution and discuss some possible applications.

We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic invariance and may not lead to unique sequence representations for a given crystal structure. Here, we propose a novel method, known as Mat2Seq, to tackle this challenge. Mat2Seq converts 3D crystal structures into 1D sequences and ensures that different mathematical descriptions of the same crystal are represented in a single unique sequence, thereby provably achieving SE(3) and periodic invariance. Experimental results show that, with language models, Mat2Seq achieves promising performance in crystal structure generation as compared with prior methods.

Data valuation is a class of techniques for quantitatively assessing the value of data for applications like pricing in data marketplaces. Existing data valuation methods define a value for a discrete dataset. However, in many use cases, users are interested in not only the value of the dataset, but that of the distribution from which the dataset was sampled. For example, consider a buyer trying to evaluate whether to purchase data from different vendors. The buyer may observe (and compare) only a small preview sample from each vendor, to decide which vendor's data distribution is most useful to the buyer and purchase. The core question is how should we compare the values of data distributions from their samples? Under a Huber characterization of the data heterogeneity across vendors, we propose a maximum mean discrepancy (MMD)-based valuation method which enables theoretically principled and actionable policies for comparing data distributions from samples. We empirically demonstrate that our method is sample-efficient and effective in identifying valuable data distributions against several existing baselines, on multiple real-world datasets (e.g., network intrusion detection, credit card fraud detection) and downstream applications (classification, regression).

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Despite the development of several deep learning methods for predicting amino acid sequences (peptides) responsible for generating the observed mass spectra, training data biases hinder further advancements of \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with Post-Translational Modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in unsatisfactory peptide sequencing performance. Secondly, various noise and missing peaks in mass spectra reduce the reliability of training data (Peptide-Spectrum Matches, PSMs). To address these challenges, we propose AdaNovo, a novel and domain knowledge-inspired framework that calculates Conditional Mutual Information (CMI) between the mass spectra and amino acids or peptides, using CMI for robust training against above biases. Extensive experiments indicate that AdaNovo outperforms previous competitors on the widely-used 9-species benchmark, meanwhile yielding 3.6\% - 9.4\% improvements in PTMs identification. The supplements contain the code.

Protein representation learning is indispensable for various downstream applications of artificial intelligence for bio-medicine research, such as drug design and function prediction. However, achieving effective representation learning for proteins poses challenges due to the diversity of data modalities involved, including sequence, structure, and function annotations. Despite the impressive capabilities of large language models in biomedical text modelling, there remains a pressing need for a framework that seamlessly integrates these diverse modalities, particularly focusing on the three critical aspects of protein information: sequence, structure, and function. Moreover, addressing the inherent data scale differences among these modalities is essential. To tackle these challenges, we introduce ProtGO, a unified model that harnesses a teacher network equipped with a customized graph neural network (GNN) and a Gene Ontology (GO) encoder to learn hybrid embeddings. Notably, our approach eliminates the need for additional functions as input for the student network, which shares the same GNN module. Importantly, we utilize a domain adaptation method to facilitate distribution approximation for guiding the training of the teacher-student framework. This approach leverages distributions learned from latent representations to avoid the alignment of individual samples. Benchmark experiments highlight that ProtGO significantly outperforms state-of-the-art baselines, clearly demonstrating the advantages of the proposed unified framework.

Location-based services (LBS) have accumulated extensive human mobility data on diverse behaviors through check-in sequences. These sequences offer valuable insights into users’ intentions and preferences. Yet, existing models analyzing check-in sequences fail to consider the semantics contained in these sequences, which closely reflect human visiting intentions and travel preferences, leading to an incomplete comprehension. Drawing inspiration from the exceptional semantic understanding and contextual information processing capabilities of large language models (LLMs) across various domains, we present Mobility-LLM, a novel framework that leverages LLMs to analyze check-in sequences for multiple tasks. Since LLMs cannot directly interpret check-ins, we reprogram these sequences to help LLMs comprehensively understand the semantics of human visiting intentions and travel preferences. Specifically, we introduce a visiting intention memory network (VIMN) to capture the visiting intentions at each record, along with a shared pool of human travel preference prompts (HTPP) to guide the LLM in understanding users’ travel preferences. These components enhance the model’s ability to extract and leverage semantic information from human mobility data effectively. Extensive experiments on four benchmark datasets and three downstream tasks demonstrate that our approach significantly outperforms existing models, underscoring the effectiveness of Mobility-LLM in advancing our understanding of human mobility data within LBS contexts.

Learning effective representations is imperative for comprehending proteins and deciphering their biological functions. Recent strides in language models and graph neural networks have empowered protein models to harness primary or tertiary structure information for representation learning. Nevertheless, the absence of practical methodologies to appropriately model intricate inter-dependencies between protein sequences and structures has resulted in embeddings that exhibit low performance on tasks such as protein function prediction. In this study, we introduce CoupleNet, a novel framework designed to interlink protein sequences and structures to derive informative protein representations. CoupleNet integrates multiple levels and scales of features in proteins, encompassing residue identities and positions for sequences, as well as geometric representations for tertiary structures from both local and global perspectives. A two-type dynamic graph is constructed to capture adjacent and distant sequential features and structural geometries, achieving completeness at the amino acid and backbone levels. Additionally, convolutions are executed on nodes and edges simultaneously to generate comprehensive protein embeddings. Experimental results on benchmark datasets showcase that CoupleNet outperforms state-of-the-art methods, exhibiting particularly superior performance in low-sequence similarities scenarios, adeptly identifying infrequently encountered functions and effectively capturing remote homology relationships in proteins.

A method to prove generalization results for a class of stochastic learning algorithms is presented. It applies whenever the algorithm generates a distribution, which is absolutely continuous distribution relative to some a-priori measure, and the logarithm of its density is exponentially concentrated about its mean. Applications include bounds for the Gibbs algorithm and randomizations of stable deterministic algorithms, combinations thereof and PAC-Bayesian bounds with data-dependent priors.

Deep learning approaches have been widely adopted for precipitation nowcasting in recent years. Previous studies mainly focus on proposing new model architectures to improve pixel-wise metrics. However, they frequently result in blurry predictions which provide limited utility to forecasting operations. In this work, we propose a new Fourier Amplitude and Correlation Loss (FACL) which consists of two novel loss terms: Fourier Amplitude Loss (FAL) and Fourier Correlation Loss (FCL). FAL regularizes the Fourier amplitude of the model prediction and FCL complements the missing phase information. The two loss terms work together to replace the traditional L2 losses such as MSE and weighted MSE for the spatiotemporal prediction problem on signal-based data. Our method is generic, parameter-free and efficient. Extensive experiments using one synthetic dataset and three radar echo datasets demonstrate that our method improves perceptual metrics and meteorology skill scores, with a small trade-off to pixel-wise accuracy and structural similarity. Moreover, to improve the error margin in meteorological skill scores such as Critical Success Index (CSI) and Fractions Skill Score (FSS), we propose and adopt the Regional Histogram Divergence (RHD), a distance metric that considers the patch-wise similarity between signal-based imagery patterns with tolerance to local transforms.

Machine learning based surrogate models offer researchers powerful tools for accelerating simulation-based workflows. However, as standard datasets in this space often cover small classes of physical behavior, it can be difficult to evaluate the efficacy of new approaches. To address this gap, we introduce the Well: a large-scale collection of datasets containing numerical simulations of a wide variety of spatiotemporal physical systems. The Well draws from domain experts and numerical software developers to provide 15TB of data across 16 datasets covering diverse domains such as biological systems, fluid dynamics, acoustic scattering, as well as magneto-hydrodynamic simulations of extra-galactic fluids or supernova explosions. These datasets can be used individually or as part of a broader benchmark suite. To facilitate usage of the Well, we provide a unified PyTorch interface for training and evaluating models. We demonstrate the function of this library by introducing example baselines that highlight the new challenges posed by the complex dynamics of the Well. The code and data is available at https://github.com/PolymathicAI/the_well.

Many empirical studies have provided evidence for the emergence of algorithmic mechanisms (abilities) in the learning of language models, that lead to qualitative improvements of the model capabilities. Yet, a theoretical characterization of how such mechanisms emerge remains elusive. In this paper, we take a step in this direction by providing a tight theoretical analysis of the emergence of semantic attention in a solvable model of dot-product attention. More precisely, we consider a non-linear self-attention layer with trainable tied and low-rank query and key matrices. In the asymptotic limit of high-dimensional data and a comparably large number of training samples we provide a tight closed-form characterization of the global minimum of the non-convex empirical loss landscape. We show that this minimum corresponds to either a positional attention mechanism (with tokens attending to each other based on their respective positions) or a semantic attention mechanism (with tokens attending to each other based on their meaning), and evidence an emergent phase transition from the former to the latter with increasing sample complexity. Finally, we compare the dot-product attention layer to a linear positional baseline, and show that it outperforms the latter using the semantic mechanism provided it has access to sufficient data.