论文检索

Applications · Genetics, Cell Biology, etc

Xiang Zhang, Jiaqi Wei, Zijie Qiu, Sheng Xu, Zhi Jin, ZhiQiang Gao, Nanqing Dong, Siqi Sun

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks like de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding 9-species benchmark of de novo peptide sequencing task show our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Our code is available on GitHub: https://github.com/BEAM-Labs/denovo

Computer Vision · 3D Rendering & Reconstruction

Yuqing Wang, Zhaiyu Chen, Xiaoxiang Zhu

3D shape completion methods typically assume scans are pre-aligned to a canonical frame. This leaks pose and scale cues that networks may exploit to memorize absolute positions rather than inferring intrinsic geometry. When such alignment is absent in real data, performance collapses. We argue that robust generalization demands architectural equivariance to the similarity group, SIM(3), so the model remains agnostic to pose and scale. Following this principle, we introduce the first SIM(3)-equivariant shape completion network, whose modular layers successively canonicalize features, reason over similarity-invariant geometry, and restore the original frame. Under a de-biased evaluation protocol that removes the hidden cues, our model outperforms both equivariant and augmentation baselines on the PCN benchmark. It also sets new cross-domain records on real driving and indoor scans, lowering minimal matching distance on KITTI by 17\% and Chamfer distance $\ell1$ on OmniObject3D by 14\%. Perhaps surprisingly, ours under the stricter protocol still outperforms competitors under their biased settings. These results establish full SIM(3) equivariance as an effective route to truly generalizable shape completion.

Deep Learning · Graph Neural Networks

Tianxiang Zhao, Youqing Wang, Jinlu Wang, Jiapu Wang, Mingliang Cui, Junbin Gao, Jipeng Guo

Due to its powerful capability of self-supervised representation learning and clustering, contrastive attributed graph clustering (CAGC) has achieved great success, which mainly depends on effective data augmentation and contrastive objective setting. However, most CAGC methods utilize edges as auxiliary information to obtain node-level embedding representation and only focus on node-level embedding augmentation. This approach overlooks edge-level embedding augmentation and the interactions between node-level and edge-level embedding augmentations across various granularity. Moreover, they often treat all contrastive sample pairs equally, neglecting the significant differences between hard and easy positive-negative sample pairs, which ultimately limits their discriminative capability. To tackle these issues, a novel robust attributed graph clustering (RAGC), incorporating hybrid-collaborative augmentation (HCA) and contrastive sample adaptive-differential awareness (CSADA), is proposed. First, node-level and edge-level embedding representations and augmentations are simultaneously executed to establish a more comprehensive similarity measurement criterion for subsequent contrastive learning. In turn, the discriminative similarity further consciously guides edge augmentation. Second, by leveraging pseudo-label information with high confidence, a CSADA strategy is elaborately designed, which adaptively identifies all contrastive sample pairs and differentially treats them by an innovative weight modulation function. The HCA and CSADA modules mutually reinforce each other in a beneficent cycle, thereby enhancing discriminability in representation learning. Comprehensive graph clustering evaluations over six benchmark datasets demonstrate the effectiveness of the proposed RAGC against several state-of-the-art CAGC methods. The code of RAGC could be available at https://github.com/TianxiangZhao0474/RAGC.git.

Applications · Time Series

Jialin Chen, Ziyu Zhao, Gaukhar Nurbek, Aosong Feng, Ali Maatouk, Leandros Tassiulas, Yifeng Gao, Rex Ying

The ubiquity of dynamic data in domains such as weather, healthcare, and energy underscores a growing need for effective interpretation and retrieval of time-series data. These data are inherently tied to domain-specific contexts, such as clinical notes or weather narratives, making cross-modal retrieval essential not only for downstream tasks but also for developing robust time-series foundation models by retrieval-augmented generation (RAG). Despite the increasing demand, time-series retrieval remains largely underexplored. Existing methods often lack semantic grounding, struggle to align heterogeneous modalities, and have limited capacity for handling multi-channel signals. To address this gap, we propose TRACE, a generic multimodal retriever that grounds time-series embeddings in aligned textual context. TRACE enables fine-grained channel-level alignment and employs hard negative mining to facilitate semantically meaningful retrieval. It supports flexible cross-modal retrieval modes, including Text-to-Timeseries and Timeseries-to-Text, effectively linking linguistic descriptions with complex temporal patterns. By retrieving semantically relevant pairs, TRACE enriches downstream models with informative context, leading to improved predictive accuracy and interpretability. Beyond a static retrieval engine, TRACE also serves as a powerful standalone encoder, with lightweight task-specific tuning that refines context-aware representations while maintaining strong cross-modal alignment. These representations achieve state-of-the-art performance on downstream forecasting and classification tasks. Extensive experiments across multiple domains highlight its dual utility, as both an effective encoder for downstream applications and a general-purpose retriever to enhance time-series models.

General Machine Learning · Representation Learning

Hugues Van Assel, Mark Ibrahim, Tommaso Biancalani, Aviv Regev, Randall Balestriero

Reconstruction and joint-embedding have emerged as two leading paradigms in Self‑Supervised Learning (SSL). Reconstruction methods focus on recovering the original sample from a different view in input space. On the other hand, joint-embedding methods align the representations of different views in latent space. Both approaches offer compelling advantages, yet practitioners lack clear guidelines for choosing between them. In this work, we unveil the core mechanisms that distinguish each paradigm. By leveraging closed-form solutions for both approaches, we precisely characterize how the view generation process, e.g. data augmentation, impacts the learned representations. We then demonstrate that, unlike supervised learning, both SSL paradigms require a minimal alignment between augmentations and irrelevant features to achieve asymptotic optimality with increasing sample size. Our findings indicate that in scenarios where these irrelevant features have a large magnitude, joint-embedding methods are preferable because they impose a strictly weaker alignment condition compared to reconstruction-based methods. These results not only clarify the trade-offs between the two paradigms but also substantiate the empirical success of joint-embedding approaches on real-world challenging datasets.

Data-centric AI · Data augmentation

Leitian Tao, Xuefeng Du, Sharon Li

Reward modeling, crucial for aligning large language models (LLMs) with human preferences, is often bottlenecked by the high cost of preference data. Existing textual data synthesis methods are computationally expensive. We propose a novel framework LENS for synthesizing preference data directly in the LLM's latent embedding space. Our method employs a Variational Autoencoder (VAE) to learn a structured latent representation of response embeddings. By performing controlled perturbations in this latent space and decoding back to the embedding space, we efficiently generate diverse, semantically consistent synthetic preference pairs, bypassing costly text generation and annotation. We provide theoretical guarantees that our synthesized pairs approximately preserve original preference ordering and improve reward model generalization. Empirically, our latent-space synthesis significantly outperforms text-based augmentation on standard benchmarks, achieving superior results while being 18× faster in generation and using a 16,000× smaller model. Our work offers a scalable and effective alternative for enhancing reward modeling through efficient data augmentation. Code is publicly available at https://github.com/deeplearning-wisc/lens.

Data-centric AI · Data-centric AI methods and tools

Wei Wang, Fuqing Bie, Junzhe Chen, Dan Zhang, Shiyu Huang, Evgeny Kharlamov, Jie Tang

Complex games have long been an important benchmark for testing the progress of artificial intelligence algorithms. AlphaGo, AlphaZero, and MuZero have defeated top human players in Go and Chess, garnering widespread societal attention towards artificial intelligence. Concurrently, large language models (LLMs) have exhibited remarkable capabilities across various tasks, raising the question of whether LLMs can achieve similar success in complex games. In this paper, we explore the potential of LLMs in mastering complex card games. We systematically assess the learning capabilities of LLMs across eight diverse card games, evaluating the impact of fine-tuning on high-quality gameplay data, and examining the models' ability to retain general capabilities while mastering these games. Our findings indicate that: (1) LLMs can approach the performance of strong game AIs through supervised fine-tuning on high-quality data, (2) LLMs can achieve a certain level of proficiency in multiple complex card games simultaneously, with performance augmentation for games with similar rules and conflicts for dissimilar ones, and (3) LLMs experience a decline in general capabilities when mastering complex games, but this decline can be mitigated by integrating a certain amount of general instruction data. The evaluation results demonstrate strong learning ability and versatility of LLMs. The code is available at https://github.com/THUDM/LLM4CardGame

Applications · Neuroscience, Cognitive Science

Lisa Schmors, Dominic Gonschorek, Jan Niklas Böhm, Yongrong Qiu, Na Zhou, Dmitry Kobak, Andreas Tolias, Fabian Sinz, Jacob Reimer, Katrin Franke 等

Modern neural recording techniques such as two-photon imaging or Neuropixel probes allow to acquire vast time-series datasets with responses of hundreds or thousands of neurons. Contrastive learning is a powerful self-supervised framework for learning representations of complex datasets. Existing applications for neural time series rely on generic data augmentations and do not exploit the multi-trial data structure inherent in many neural datasets. Here we present TRACE, a new contrastive learning framework that averages across different subsets of trials to generate positive pairs. TRACE allows to directly learn a two-dimensional embedding, combining ideas from contrastive learning and neighbor embeddings. We show that TRACE outperforms other methods, resolving fine response differences in simulated data. Further, using in vivo recordings, we show that the representations learned by TRACE capture both biologically relevant continuous variation, cell-type-related cluster structure, and can assist data quality control.

General Machine Learning · Causality

Alessandro Marchese, Jeroen Berrevoets, Sam Verboven

A central challenge in organ transplantation is the extremely low acceptance rate of donor organ offers—typically in the single digits—leading to high discard rates and suboptimal use of available grafts. Current acceptance models embedded in allocation systems are non-causal, trained on observational data, and fail to generalize to policy-relevant counterfactuals. This limits their reliability for both policy evaluation and simulator-based optimization. In this work, we reframe organ offer acceptance as a counterfactual prediction problem and propose a method to learn from routinely recorded—but often overlooked—refusal explanations. These refusal reasons act as direction-only counterfactual signals: for example, a refusal reason such as "old donor age" implies acceptance might have occurred had the donor been younger. We formalize this setting and introduce ClexNet, a novel causal model that learns policy-invariant representations via balanced training and an explanation-guided augmentation loss. On both synthetic and semi-synthetic data, ClexNet outperforms existing acceptance models in predictive performance, generalization, and calibration, offering a robust drop-in improvement for simulators and allocation policy evaluation. Beyond transplantation, our approach provides a general method for incorporating human direction-only explanations as a form of model supervision, improving performance in settings where only observational data is available.

Theory · Everything Else

XianJun, Davin Choo, Billy Jin, Yongho Shin

Online bipartite matching is a fundamental problem in online optimization, extensively studied both in its integral and fractional forms due to its theoretical significance and practical applications, such as online advertising and resource allocation. Motivated by recent progress in learning-augmented algorithms, we study online bipartite fractional matching when the algorithm is given advice in the form of a suggested matching in each iteration. We develop algorithms for both the vertex-weighted and unweighted variants that provably dominate the naive ``coin flip'' strategy of randomly choosing between the advice-following and advice-free algorithms. Moreover, our algorithm for the vertex-weighted setting extends to the AdWords problem under the small bids assumption, yielding a significant improvement over the seminal work of Mahdian, Nazerzadeh, and Saberi (EC 2007, TALG 2012). Complementing our positive results, we establish a hardness bound on the robustness-consistency tradeoff that is attainable by any algorithm. We empirically validate our algorithms through experiments on synthetic and real-world data.

Applications · Language, Speech and Dialog

Xin Su, Sungduk Yu, Phillip Howard, Steven Bethard

Time normalization is the task of converting natural language temporal expressions into machine-readable representations. It underpins many downstream applications in information retrieval, question answering, and clinical decision-making. Traditional systems based on the ISO-TimeML schema limit expressivity and struggle with complex constructs such as compositional, event-relative, and multi-span time expressions. In this work, we introduce a novel formulation of time normalization as a code generation task grounded in the SCATE framework, which defines temporal semantics through symbolic and compositional operators. We implement a fully executable SCATE Python library and demonstrate that large language models (LLMs) can generate executable SCATE code. Leveraging this capability, we develop an automatic data augmentation pipeline using LLMs to synthesize large-scale annotated data with code-level validation. Our experiments show that small, locally deployable models trained on this augmented data can achieve strong performance, outperforming even their LLM parents and enabling practical, accurate, and interpretable time normalization.

Deep Learning · Generative Models and Autoencoders

Mohamed Amine Ketata, David Lüdke, Leo Schwinn, Stephan Günnemann

Building generative models for relational databases (RDBs) is important for many applications, such as privacy-preserving data release and augmenting real datasets. However, most prior works either focus on single-table generation or adapt single-table models to the multi-table setting by relying on autoregressive factorizations and sequential generation. These approaches limit parallelism, restrict flexibility in downstream applications, and compound errors due to commonly made conditional independence assumptions. In this paper, we propose a fundamentally different approach: jointly modeling all tables in an RDB without imposing any table order. By using a natural graph representation of RDBs, we propose the Graph-Conditional Relational Diffusion Model (GRDM), which leverages a graph neural network to jointly denoise row attributes and capture complex inter-table dependencies. Extensive experiments on six real-world RDBs demonstrate that our approach substantially outperforms autoregressive baselines in modeling multi-hop inter-table correlations and achieves state-of-the-art performance on single-table fidelity metrics. Our code is available at https://github.com/ketatam/rdb-diffusion.

Deep Learning · Everything Else

Longquan Dai, Xiaolu Wei, wang he, Shaomeng Wang, Jinhui Tang

Text-to-image diffusion models are typically trained on large-scale web data, often resulting in outputs that misalign with human preferences. Inspired by preference learning in large language models, we propose ABC (Alignment by Classification), a simple yet effective framework for aligning diffusion models with human preferences. In contrast to prior DPO-based methods that depend on suboptimal supervised fine-tuned (SFT) reference models, ABC assumes access to an ideal reference model perfectly aligned with human intent and reformulates alignment as a classification problem. Under this view, we recognize that preference data naturally forms a semi-supervised classification setting. To address this, we propose a data augmentation strategy that transforms preference comparisons into fully supervised training signals. We then introduce a classification-based ABC loss to guide alignment. Our alignment by classification approach could effectively steer the diffusion model toward the behavior of the ideal reference. Experiments on various diffusion models show that our ABC consistently outperforms existing baselines, offering a scalable and robust solution for preference-based text-to-image fine-tuning.

Wanjia Zhao, Mert Yuksekgonul, Shirley Wu, James Zou

Multi-agent AI systems powered by large language models (LLMs) are increasingly applied to solve complex tasks. However, these systems often rely on fragile, manually designed prompts and heuristics, making optimization difficult. A key challenge in optimizing multi-agent systems is acquiring suitable training data for specialized agents. We introduce SiriuS, a self-improving, reasoning-driven optimization framework for multi-agent systems. Central to our approach is the construction of an experience library: a repository of high-quality reasoning trajectories. The library is built by retaining reasoning steps that lead to successful outcomes, providing a robust training set for optimizing multi-agent system. Additionally, we introduce a library augmentation procedure that refines unsuccessful trajectories, further enriching the library. SiriuS boosts performance by 2.86% to 21.88% on reasoning and biomedical QA and enhances agent negotiation in competitive settings. Our results show that SiriuS enhances multi-agent performance while generating reusable data for self-correction and self-play enhancement in the future.

Data-centric AI · Data augmentation

Seong-Hyeon Hwang, Soyoung Choi, Steven Whang

Multimodal models often over-rely on dominant modalities, failing to achieve optimal performance. While prior work focuses on modifying training objectives or optimization procedures, data-centric solutions remain underexplored. We propose MIDAS, a novel data augmentation strategy that generates misaligned samples with semantically inconsistent cross-modal information, labeled using unimodal confidence scores to compel learning from contradictory signals. However, this confidence-based labeling can still favor the more confident modality. To address this within our misaligned samples, we introduce weak-modality weighting, which dynamically increases the loss weight of the least confident modality, thereby helping the model fully utilize weaker modality. Furthermore, when misaligned features exhibit greater similarity to the aligned features, these misaligned samples pose a greater challenge, thereby enabling the model to better distinguish between classes. To leverage this, we propose hard-sample weighting, which prioritizes such semantically ambiguous misaligned samples. Experiments on multiple multimodal classification benchmarks demonstrate that MIDAS significantly outperforms related baselines in addressing modality imbalance.

Deep Learning · Generative Models and Autoencoders

Mihir Prabhudesai, Mengning Wu, Amir Zadeh, Katerina Fragkiadaki, Deepak Pathak

Autoregressive (AR) models have long dominated the landscape of large language models, driving progress across a wide range of tasks. Recently, diffusion-based language models have emerged as a promising alternative, though their advantages over AR models remain underexplored. In this paper, we systematically study masked diffusion models in data-constrained settings—where training involves repeated passes over limited data—and find that they significantly outperform AR models when compute is abundant but data is scarce. Diffusion models make better use of repeated data, achieving lower validation loss and superior downstream performance. We find new scaling laws for diffusion models and derive a closed-form expression for the critical compute threshold at which diffusion begins to outperform AR. Finally, we explain why diffusion models excel in this regime: their randomized masking objective implicitly trains over a rich distribution of token orderings, acting as an implicit data augmentation that AR’s fixed left-to-right factorization lacks. Our results suggest that when data, not compute, is the bottleneck, diffusion models offer a compelling alternative to the standard AR paradigm. Our code is available at: https://diffusion-scaling.github.io

Applications · Everything Else

Runyang You, Yongqi Li, Xinyu Lin, Xin Zhang, Wenjie Wang, Wenjie Li, Liqiang Nie

Large recommender models have extended LLMs as powerful recommenders via encoding or item generation, and recent breakthroughs in LLM reasoning synchronously motivate the exploration of reasoning in recommendation. In this work, we propose R$^2$ec, a unified large recommender model with intrinsic reasoning capability. R$^2$ec introduces a dual-head architecture that supports both reasoning chain generation and efficient item prediction in a single model, significantly reducing inference latency. To overcome the lack of annotated reasoning data, we design RecPO, a reinforcement learning framework that optimizes reasoning and recommendation jointly with a novel fused reward mechanism. Extensive experiments on three datasets demonstrate that R$^2$ec outperforms traditional, LLM-based, and reasoning-augmented recommender baselines, while further analyses validate its competitive efficiency among conventional LLM-based recommender baselines and strong adaptability to diverse recommendation scenarios. Code and checkpoints available at https://github.com/YRYangang/RRec.

Computer Vision · 3D Rendering & Reconstruction

Dekai Zhu, Yixuan Hu, Youquan Liu, Dongyue Lu, Lingdong Kong, Slobodan Ilic

Leveraging diffusion models, 3D LiDAR scene generation has achieved great success in both range-view and voxel-based representations. While recent voxel-based approaches can generate both geometric structures and semantic labels, existing range-view methods are limited to producing unlabeled LiDAR scenes. Relying on pretrained segmentation models to predict the semantic maps often results in suboptimal cross-modal consistency. To address this limitation while preserving the advantages of range-view representations, such as computational efficiency and simplified network design, we propose Spiral, a novel range-view LiDAR diffusion model that simultaneously generates depth, reflectance images, and semantic maps. Furthermore, we introduce novel semantic-aware metrics to evaluate the quality of the generated labeled range-view data. Experiments on SemanticKITTI and nuScenes datasets demonstrate that Spiral achieves state-of-the-art performance with the smallest parameter size, outperforming two-step methods that combine the best available generative and segmentation models. Additionally, we validate that Spiral’s generated range images can be effectively used for synthetic data augmentation in the downstream segmentation training, significantly reducing the labeling effort on LiDAR data.

General Machine Learning · Everything Else

Reza Ramezanpour, Victor Manuel Tenorio Gomez, Antonio G. Marques, Ashutosh Sabharwal, Santiago Segarra

Graphons, as limit objects of dense graph sequences, play a central role in the statistical analysis of network data. However, existing graphon estimation methods often struggle with scalability to large networks and resolution-independent approximation, due to their reliance on estimating latent variables or costly metrics such as the Gromov-Wasserstein distance. In this work, we propose a novel, scalable graphon estimator that directly recovers the graphon via moment matching, leveraging implicit neural representations (INRs). Our approach avoids latent variable modeling by training an INR--mapping coordinates to graphon values--to match empirical subgraph counts (i.e., moments) from observed graphs. This direct estimation mechanism yields a polynomial-time solution and crucially sidesteps the combinatorial complexity of Gromov-Wasserstein optimization. Building on foundational results, we establish a theoretical guarantee: when the observed subgraph motifs sufficiently represent those of the true graphon (a condition met with sufficiently large or numerous graph samples), the estimated graphon achieves a provable upper bound in cut distance from the ground truth. Additionally, we introduce MomentMixup, a data augmentation technique that performs mixup in the moment space to enhance graphon-based learning. Our graphon estimation method achieves strong empirical performance--demonstrating high accuracy on small graphs and superior computational efficiency on large graphs--outperforming state-of-the-art scalable estimators in 75\% of benchmark settings and matching them in the remaining cases. Furthermore, MomentMixup demonstrated improved graph classification accuracy on the majority of our benchmarks.

General Machine Learning · Representation Learning

Miaomiao Huang, Yuhai Zhao, Daniel Zhengkui Wang, Fenglong Ma, Yejiang Wang, Meixia Wang, Xingwei Wang

Graph self-supervised learning aims to learn the intrinsic graph representations from unlabeled data, with broad applicability in areas such as computing networks. Although graph contrastive learning (GCL) has achieved remarkable progress by generating perturbed views via data augmentation and optimizing sample similarity, it performs poorly in heterophilic graph scenarios (where connected nodes are likely to belong to different classes or exhibit dissimilar features). In heterophilic graphs, existing methods typically rely on random or carefully designed augmentation strategies (e.g., edge dropping) for contrastive views. However, such graph structures exhibit intricate edge relationships, where topological perturbations may completely alter the semantics of neighborhoods. Moreover, most methods focus solely on local contrastive signals while neglecting global structural constraints. To address these limitations, inspired by graph coloring, we propose a novel Coloring learning for heterophilic graph Representation framework, CoRep, which: 1) Pioneers a coloring classifier to generate coloring labels, explicitly minimizing the discrepancy between homophilic nodes while maximizing that of heterophilic nodes. A global positive sample set is constructed using multi-hop same-color nodes to capture global semantic consistency. 2) Introduces a learnable edge evaluator to guide the coloring learning dynamically and utilizes the edges' triplet relations to enhance its robustness. 3) Leverages Gumbel-Softmax to differentially discretize color distributions, suppressing noise via a redundancy constraint and enhancing intra-class compactness. Experimental results on 14 benchmark datasets demonstrate that CoRep significantly outperforms current state-of-the-art methods.