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Deep Learning · Algorithms

Taekyung Lee, Jaemoo Choi, Jaewoong Choi, Myungjoo Kang

Unpaired point cloud completion is crucial for real-world applications, where ground-truth data for complete point clouds are often unavailable. By learning a completion map from unpaired incomplete and complete point cloud data, this task avoids the reliance on paired datasets. In this paper, we propose the \textit{Unbalanced Optimal Transport Map for Unpaired Point Cloud Completion (\textbf{UOT-UPC})} model, which formulates the unpaired completion task as the (Unbalanced) Optimal Transport (OT) problem. Our method employs a Neural OT model learning the UOT map using neural networks. Our model is the first attempt to leverage UOT for unpaired point cloud completion, achieving competitive or superior performance on both single-category and multi-category benchmarks. In particular, our approach is especially robust under the class imbalance problem, which is frequently encountered in real-world unpaired point cloud completion scenarios.

Deep Learning · Graph Neural Networks

Louis Airale, Antonio Longa, Mattia Rigon, Andrea Passerini, Roberto Passerone

Graph transformers extend global self-attention to graph-structured data, achieving notable success in graph learning. Recently, random walk structural encoding (RWSE) has been found to further enhance their predictive power by encoding both structural and positional information into the edge representation. However, RWSE cannot always distinguish between edges that belong to different local graph patterns, which reduces its ability to capture the full structural complexity of graphs.This work introduces Simple Path Structural Encoding (SPSE), a novel method that utilizes simple path counts for edge encoding. We show theoretically and experimentally that SPSE overcomes the limitations of RWSE, providing a richer representation of graph structures, particularly in capturing local cyclic patterns. To make SPSE computationally tractable, we propose an efficient approximate algorithm for simple path counting.SPSE demonstrates significant performance improvements over RWSE on various benchmarks, including molecular and long-range graph datasets, achieving statistically significant gains in discriminative tasks. These results pose SPSE as a powerful edge encoding alternative for enhancing the expressivity of graph transformers.

Deep Learning · Algorithms

Pedram Pad, Hadi Hammoud, Mohamad Dia, nadim maamari, Liza Dunbar

Feature selection is a critical step in data-driven applications, reducing input dimensionality to enhance learning accuracy, computational efficiency, and interpretability. Existing state-of-the-art methods often require post-selection retraining and extensive hyperparameter tuning, complicating their adoption. We introduce a novel, non-intrusive feature selection layer that, given a target feature count $k$, automatically identifies and selects the $k$ most informative features during neural network training. Our method is uniquely simple, requiring no alterations to the loss function, network architecture, or post-selection retraining. The layer is mathematically elegant and can be fully described by:\begin{align}\nonumber\tilde{x}_i = a_i x_i + (1-a_i)z_i\end{align}where $x_i$ is the input feature, $\tilde{x}_i$ the output, $z_i$ a Gaussian noise, and $a_i$ trainable gain such that $\sum_i{a_i^2}=k$.This formulation induces an automatic clustering effect, driving $k$ of the $a_i$ gains to $1$ (selecting informative features) and the rest to $0$ (discarding redundant ones) via weighted noise distortion and gain normalization. Despite its extreme simplicity, our method achieves competitive performance on standard benchmark datasets and a novel real-world dataset, often matching or exceeding existing approaches without requiring hyperparameter search for $k$ or retraining. Theoretical analysis in the context of linear regression further validates its efficacy. Our work demonstrates that simplicity and performance are not mutually exclusive, offering a powerful yet straightforward tool for feature selection in machine learning.

Deep Learning · Large Language Models

Ian Magnusson, Tai Nguyen, Ben Bogin, David Heineman, Jena Hwang, Luca Soldaini, Akshita Bhagia, Jiacheng Liu, Dirk Groeneveld, Oyvind Tafjord 等

Because large language models are expensive to pretrain on different datasets, using smaller-scale experiments to decide on data is crucial for reducing costs. Which benchmarks and methods of making decisions from observed performance at small scale most accurately predict the datasets that yield the best large models? To empower open exploration of this question, we release models, data, and evaluations in DataDecide—the most extensive open suite of models over differences in data and scale. We conduct controlled pretraining experiments across 25 corpora with differing sources, deduplication, and filtering up to 100B tokens, model sizes up to 1B parameters, and 3 random seeds. We find that the ranking of models at a single, small size (e.g., 150M parameters) is a strong baseline for predicting best models at our larger target scale (1B) (∼ 80% of comparisons correct). No scaling law methods among 8 baselines exceed the compute-decision frontier of single-scale predictions, but DataDecide can measure improvement in future scaling laws. We also identify that using continuous likelihood metrics as proxies in small experiments makes benchmarks including MMLU, ARC, HellaSwag, MBPP, and HumanEval > 80% predictable at the target 1B scale with just 0.01% of the compute.

Deep Learning · Graph Neural Networks

Yoon Hyeok Lee, Jaemin Park, Taejin Paik, Doyun Kim, Bosun Hwang

Graph Transformers (GTs) have emerged as a powerful alternative to message-passing neural networks, yet their performance heavily depends on effectively embedding structural inductive biases. In this work, we introduce novel structural encodings (SEs) grounded in a rigorous analysis of random walks (RWs), leveraging Green and Martin kernels that we have carefully redefined for AI applications while preserving their mathematical essence.These kernels capture the long-term behavior of RWs on graphs and allow for enhanced representation of complex topologies, including non-aperiodic and directed acyclic substructures.Empirical evaluations across eight benchmark datasets demonstrate strong performance across diverse tasks, notably in molecular and circuit domains.We attribute this performance boost to the improved ability of our kernel-based SEs to encode intricate structural information, thereby strengthening the global attention and inductive bias within GTs.This work highlights the effectiveness of theoretically grounded kernel methods in advancing Transformer-based models for graph learning.

Optimization · Zero-order and Black-box Optimization

Zeyuan Ma, Zhiguang Cao, Zhou Jiang, Hongshu Guo, Yue-Jiao Gong

Recent progress in Meta-Black-Box-Optimization (MetaBBO) has demonstrated that using RL to learn a meta-level policy for dynamic algorithm configuration (DAC) over an optimization task distribution could significantly enhance the performance of the low-level BBO algorithm. However, the online learning paradigms in existing works makes the efficiency of MetaBBO problematic.To address this, we propose an offline learning-based MetaBBO framework in this paper, termed Q-Mamba, to attain both effectiveness and efficiency in MetaBBO. Specifically, we first transform DAC task into long-sequence decision process. This allows us further introduce an effective Q-function decomposition mechanism to reduce the learning difficulty within the intricate algorithm configuration space. Under this setting, we propose three novel designs to meta-learn DAC policy from offline data: we first propose a novel collection strategy for constructing offline DAC experiences dataset with balanced exploration and exploitation. We then establish a decomposition-based Q-loss that incorporates conservative Q-learning to promote stable offline learning from the offline dataset. To further improve the offline learning efficiency, we equip our work with a Mamba architecture which helps long-sequence learning effectiveness and efficiency by selective state model and hardware-aware parallel scan respectively. Through extensive benchmarking, we observe that Q-Mamba achieves competitive or even superior performance to prior online/offline baselines, while significantly improving the training efficiency of existing online baselines. We provide sourcecodes of Q-Mamba \href{https://github.com/MetaEvo/Q-Mamba}{online}.

Applications · Health / Medicine

Justin Lee, Behnaz Moradi-Jamei, Heman Shakeri

Modeling the evolution of high-dimensional systems from limited snapshot observations at irregular time points poses a significant challenge in quantitative biology and related fields. Traditional approaches often rely on dimensionality reduction techniques, which can oversimplify the dynamics and fail to capture critical transient behaviors in non-equilibrium systems. We present Multi-Marginal Stochastic Flow Matching (MMSFM), a novel extension of simulation-free score and flow matching methods to the multi-marginal setting, enabling the alignment of high-dimensional data measured at non-equidistant time points without reducing dimensionality. The use of measure-valued splines enhances robustness to irregular snapshot timing, and score matching prevents overfitting in high-dimensional spaces. We validate our framework on several synthetic and benchmark datasets and apply it to single-cell perturbation data from melanoma cell lines and gene expression data collected at uneven time points.

Applications · Computer Vision

Yuanhuiyi Lyu, Xu Zheng, Lutao Jiang, Yibo Yan, Xin Zou, Huiyu Zhou, Linfeng Zhang, Xuming Hu

Recent text-to-image generative models, e.g., Stable Diffusion V3 and Flux, have achieved notable progress. However, these models are strongly restricted to their limited knowledge, a.k.a., their own fixed parameters, that are trained with closed datasets. This leads to significant hallucinations or distortions when facing fine-grained and unseen novel real-world objects, e.g., the appearance of the Tesla Cybertruck. To this end, we present **the first** real-object-based retrieval-augmented generation framework (**RealRAG**), which augments fine-grained and unseen novel object generation by learning and retrieving real-world images to overcome the knowledge gaps of generative models. Specifically, to integrate missing memory for unseen novel object generation, we train a reflective retriever by **self-reflective contrastive learning**, which injects the generator's knowledge into the sef-reflective negatives, ensuring that the retrieved augmented images compensate for the model's missing knowledge. Furthermore, the real-object-based framework integrates fine-grained visual knowledge for the generative models, tackling the distortion problem and improving the realism for fine-grained object generation. Our Real-RAG is superior in its modular application to **all types** of state-of-the-art text-to-image generative models and also delivers **remarkable** performance boosts with all of them, such as a **gain of *16.18\%* FID score** with the auto-regressive model on the Stanford Car benchmark.

Applications · Computer Vision

Yu Zhou, Bingxuan Li, Mohan Tang, Xiaomeng Jin, Te-Lin Wu, Kuan-Hao Huang, Heng Ji, Kai-Wei Chang, Nanyun Peng

Large multimodal models (LMMs) often struggle to recognize novel concepts, as they rely on pre-trained knowledge and have limited ability to capture subtle visual details. Domain-specific knowledge gaps in training also make them prone to confusing visually similar, commonly misrepresented, or low-resource concepts. To help LMMs better align nuanced visual features with language, improving their ability to recognize and reason about novel or rare concepts, we propose a Contrastive visual Data Augmentation (CoDA) strategy. CoDA extracts key contrastive textual and visual features of target concepts against the known concepts they are misrecognized as, and then uses multimodal generative models to produce targeted synthetic data. Automatic filtering of extracted features and augmented images is implemented to guarantee their quality, as verified by human annotators. We show the effectiveness and efficiency of CoDA on low-resource concept and diverse scene recognition datasets including INaturalist and SUN. We additionally collect NovelSpecies, a benchmark dataset consisting of newly discovered animal species that are guaranteed to be unseen by LMMs. LLaVA-1.6 1-shot updating results on these three datasets show CoDA significantly improves SOTA visual data augmentation strategies by 12.3% (NovelSpecies), 5.1% (SUN), and 6.0% (iNat) absolute gains in accuracy.

Deep Learning · Sequential Models, Time series

Mehmet Yiğit Balık, Maksim Sinelnikov, Priscilla Ong, Harri Lähdesmäki

High-dimensional time-series datasets are common in domains such as healthcare and economics. Variational autoencoder (VAE) models, where latent variables are modeled with a Gaussian process (GP) prior, have become a prominent model class to analyze such correlated datasets. However, their applications are challenged by the inherent cubic time complexity that requires specific GP approximation techniques, as well as the general challenge of modeling both shared and individual-specific correlations across time. Though inducing points enhance GP prior VAE scalability, optimizing them remains challenging, especially since discrete covariates resist gradient‑based methods. In this work, we propose a scalable basis function approximation technique for GP prior VAEs that mitigates these challenges and results in linear time complexity, with a global parametrization that eliminates the need for amortized variational inference and the associated amortization gap, making it well-suited for conditional generation tasks where accuracy and efficiency are crucial. Empirical evaluations on synthetic and real-world benchmark datasets demonstrate that our approach not only improves scalability and interpretability but also drastically enhances predictive performance.

Deep Learning · Generative Models and Autoencoders

Christopher Wewer, Bartlomiej Pogodzinski, Bernt Schiele, Jan Eric Lenssen

We introduce Spatial Reasoning Models (SRMs), a framework to perform reasoning over sets of continuous variables via denoising generative models. SRMs infer continuous representations on a set of unobserved variables, given observations on observed variables. Current generative models on spatial domains, such as diffusion and flow matching models, often collapse to hallucination in case of complex distributions. To measure this, we introduce a set of benchmark tasks that test the quality of complex reasoning in generative models and can quantify hallucination. The SRM framework allows to report key findings about importance of sequentialization in generation, the associated order, as well as the sampling strategies during training. It demonstrates, for the first time, that order of generation can successfully be predicted by the denoising network itself. Using these findings, we can increase the accuracy of specific reasoning tasks from <1% to >50%. Our [project website](https://geometric-rl.mpi-inf.mpg.de/srm/) provides additional videos, code, and the benchmark datasets.

General Machine Learning · Supervised Learning

Dixian Zhu, Tianbao Yang, Livnat Jerby

Regression is a fundamental task in machine learning that has garnered extensive attention over the past decades. The conventional approach for regression involves employing loss functions that primarily concentrate on aligning model prediction with the ground truth for each individual data sample. Recent research endeavors have introduced novel perspectives by incorporating label similarity into regression through the imposition of additional pairwise regularization or contrastive learning on the latent feature space, demonstrating their effectiveness. However, there are two drawbacks to these approaches: (i) their pairwise operations in the latent feature space are computationally more expensive than conventional regression losses; (ii) they lack theoretical insights behind these methods. In this work, we propose GAR (Gradient Aligned Regression) as a competitive alternative method in label space, which is constituted by a conventional regression loss and two pairwise label difference losses for gradient alignment including magnitude and direction. GAR enjoys: i) the same level efficiency as conventional regression loss because the quadratic complexity for the proposed pairwise losses can be reduced to linear complexity; ii) theoretical insights from learning the pairwise label difference to learning the gradient of the ground truth function. We limit our current scope as regression on the clean data setting without noises, outliers or distributional shifts, etc. We demonstrate the effectiveness of the proposed method practically on two synthetic datasets and on eight extensive real-world tasks from six benchmark datasets with other eight competitive baselines. Running time experiments demonstrate the superior efficiency of the proposed GAR compared to existing methods with pairwise regularization or contrastive learning in the latent feature space. Additionally, ablation studies confirm the effectiveness of each component of GAR. The code is open sourced at https://github.com/DixianZhu/GAR.

Position · Methodology

Marta An Kimmel, Mueed Rehman, Yonatan Bisk, Gary Fedder

In this paper, we examine the manufacturability gap in state-of-the-art generative models for 3D object representations. Many models for generating 3D assets focus on rendering virtual content and do not consider the constraints of real-world manufacturing, such as milling, casting, or injection molding. We demonstrate that existing generative models for computer-aided design representation do not generalize outside of their training datasets or to unmodified real, human-created objects. We identify limitations with the current approaches, including missing manufacturing-readable semantics, the inability to decompose complex shapes into parameterized segments appropriate for computer-aided manufacturing, and a lack of appropriate scoring metrics to assess the generated output versus the true reconstruction. The academic community could greatly impact real-world manufacturing by rallying around pathways to solve these challenges. We offer revised, more realistic datasets and baseline benchmarks as a step in targeting the challenge. In evaluating these datasets, we find that existing models are severely overfit to simpler data.

Deep Learning · Robustness

Bing Sun, Jun Sun, Wei Zhao

Despite their advances and success, real-world deep neural networks are known to be vulnerable to adversarial attacks. Universal adversarial perturbation, an input-agnostic attack, poses a serious threat for them to be deployed in security-sensitive systems. In this case, a single universal adversarial perturbation deceives the model on a range of clean inputs without requiring input-specific optimization, which makes it particularly threatening. In this work, we observe that universal adversarial perturbations usually lead to abnormal entropy spectrum in hidden layers, which suggests that the prediction is dominated by a small number of ``feature'' in such cases (rather than democratically by many features). Inspired by this, we propose an efficient yet effective defense method for mitigating UAPs called \emph{Democratic Training} by performing entropy-based model enhancement to suppress the effect of the universal adversarial perturbations in a given model. \emph{Democratic Training} is evaluated with 7 neural networks trained on 5 benchmark datasets and 5 types of state-of-the-art universal adversarial attack methods. The results show that it effectively reduces the attack success rate, improves model robustness and preserves the model accuracy on clean samples.

Deep Learning · Large Language Models

Ziyue Li, Tianyi Zhou

While large language models (LLMs) excel on generation tasks, their decoder-only architecture often limits their potential as embedding models if no further representation finetuning is applied. Does this contradict their claim of generalists? To answer the question, we take a closer look at Mixture-of-Experts (MoE) LLMs. Our study shows that the expert routers in MoE LLMs can serve as an off-the-shelf embedding model with promising performance on a diverse class of embedding-focused tasks, without requiring any finetuning. Moreover, our extensive analysis shows that the MoE routing weights (RW) is complementary to the hidden state (HS) of LLMs, a widely-used embedding. Compared to HS, we find that RW is more robust to the choice of prompts and focuses on high-level semantics. Motivated by the analysis, we propose MoEE combining RW and HS, which achieves better performance than using either separately. Our exploration of their combination and prompting strategy shed several novel insights, e.g., a weighted sum of RW and HS similarities outperforms the similarity on their concatenation. Our experiments are conducted on 6 embedding tasks with 20 datasets from the Massive Text Embedding Benchmark (MTEB). The results demonstrate the significant improvement brought by MoEE to LLM-based embedding without further finetuning.

Applications · Computer Vision

Itsumi Saito, Haruto Yoshida, Keisuke Sakaguchi

We address the challenge of automatically generating high-quality vector diagrams from hand-drawn sketches. Vector diagrams are essential for communicating complex ideas across various fields, offering flexibility and scalability. While recent research has progressed in generating diagrams from text descriptions, converting hand-drawn sketches into vector diagrams remains largely unexplored due to the lack of suitable datasets. To address this gap, we introduce SketikZ, a dataset comprising 3,231 pairs of hand-drawn sketches and thier corresponding TikZ codes as well as reference diagrams.Our evaluations reveal the limitations of state-of-the-art vision and language models (VLMs), positioning SketikZ as a key benchmark for future research in sketch-to-diagram conversion.Along with SketikZ, we present ImgTikZ, an image-to-TikZ model that integrates a 6.7B parameter code-specialized open-source large language model (LLM) with a pre-trained vision encoder. Despite its relatively compact size, ImgTikZ performs comparably to GPT-4o.This success is driven by using our two data augmentation techniques and a multi-candidate inference strategy.Our findings open promising directions for future research in sketch-to-diagram conversion and broader image-to-code generation tasks. SketikZ is publicly available.

Ricardo Buitrago Ruiz, Tanya Marwah, Albert Gu, Andrej Risteski

Data-driven techniques have emerged as a promising alternative to traditional numerical methods for solving PDEs. For time-dependent PDEs, many approaches are Markovian---the evolution of the trained system only depends on the current state, and not the past states. In this work, we investigate the benefits of using memory for modeling time-dependent PDEs: that is, when past states are explicitly used to predict the future. Motivated by the Mori-Zwanzig theory of model reduction, we theoretically exhibit examples of simple (even linear) PDEs, in which a solution that uses memory is arbitrarily better than a Markovian solution. Additionally, we introduce Memory Neural Operator (MemNO), a neural operator architecture that combines recent state space models (specifically, S4) and Fourier Neural Operators (FNOs) to effectively model memory. We empirically demonstrate that when the PDEs are supplied in low resolution or contain observation noise at train and test time, MemNO significantly outperforms the baselines without memory---with up to $6 \times$ reduction in test error. Furthermore, we show that this benefit is particularly pronounced when the PDE solutions have significant high-frequency Fourier modes (e.g., low-viscosity fluid dynamics) and we construct a challenging benchmark dataset consisting of such PDEs.

Deep Learning · Graph Neural Networks

Tongzhou Liao, Barnabás Póczos

Graph Neural Networks (GNNs) have become important tools for machine learning on graph-structured data. In this paper, we explore the synergistic combination of graph encoding, graph rewiring, and graph attention, by introducing Graph Attention with Stochastic Structures (GRASS), a novel GNN architecture. GRASS utilizes relative random walk probabilities (RRWP) encoding and a novel decomposed variant (D-RRWP) to efficiently capture structural information. It rewires the input graph by superimposing a random regular graph to enhance long-range information propagation. It also employs a novel additive attention mechanism tailored for graph-structured data. Our empirical evaluations demonstrate that GRASS achieves state-of-the-art performance on multiple benchmark datasets, including a 20.3% reduction in mean absolute error on the ZINC dataset.

Deep Learning · Large Language Models

Linda He, Jue Wang, Maurice Weber, Shang Zhu, Ben Athiwaratkun, Ce Zhang

Large Language Models (LLMs) struggle with long-context reasoning, not only due to the quadratic scaling of computational complexity with sequence length but also because of the scarcity and expense of annotating long-context data. There has been barely any open-source work that systematically ablates long-context data, nor is there any openly available instruction tuning dataset with contexts surpassing 100K tokens. To bridge this gap, we introduce a novel post-training synthetic data generation strategy designed to efficiently extend the context window of LLMs while preserving their general task performance. Our approach scalably extends to arbitrarily long context lengths, unconstrained by the length of available real-world data, which effectively addresses the scarcity of raw long-context data. Through a step-by-step rotary position embedding (RoPE) scaling training strategy, we demonstrate that our model, with a context length of up to 1M tokens, performs well on the RULER benchmark and InfiniteBench and maintains robust performance on general language tasks.

Social Aspects · Privacy-preserving Statistics and Machine Learning

XiaoHua Feng, Yuyuan Li, Chaochao Chen, Li Zhang, Li, JUN ZHOU, Xiaolin Zheng

While generative models have made significant advancements in recent years, they also raise concerns such as privacy breaches and biases. Machine unlearning has emerged as a viable solution, aiming to remove specific training data, e.g., containing private information and bias, from models. In this paper, we study the machine unlearning problem in Image-to-Image (I2I) generative models. Previous studies mainly treat it as a single objective optimization problem, offering a solitary solution, thereby neglecting the varied user expectations towards the trade-off between complete unlearning and model utility. To address this issue, we propose a controllable unlearning framework that uses a control coefficient $\epsilon$ to control the trade-off. We reformulate the I2I generative model unlearning problem into a $\epsilon$-constrained optimization problem and solve it with a gradient-based method to find optimal solutions for unlearning boundaries. These boundaries define the valid range for the control coefficient. Within this range, every yielded solution is theoretically guaranteed with Pareto optimality. We also analyze the convergence rate of our framework under various control functions. Extensive experiments on two benchmark datasets across three mainstream I2I models demonstrate the effectiveness of our controllable unlearning framework.