Daily Papers

We introduce the category of information structures, whose objects are suitable diagrams of measurable sets that encode the possible outputs of a given family of observables and their mutual relationships of refinement; they serve as mathematical models of contextuality in classical and quantum settings. Each information structure can be regarded as a ringed site with trivial topology; the structure ring is generated by the observables themselves and its multiplication corresponds to joint measurement. We extend Baudot and Bennequin's definition of information cohomology to this setting, as a derived functor in the category of modules over the structure ring, and show explicitly that the bar construction gives a projective resolution in that category, recovering in this way the cochain complexes previously considered in the literature. Finally, we study the particular case of a one-parameter family of coefficients made of functions of probability distributions. The only 1-cocycles are Shannon entropy or Tsallis alpha-entropy, depending on the value of the parameter.

Denoising diffusion models (DDMs) have attracted attention for their exceptional generation quality and diversity. This success is largely attributed to the use of class- or text-conditional diffusion guidance methods, such as classifier and classifier-free guidance. In this paper, we present a more comprehensive perspective that goes beyond the traditional guidance methods. From this generalized perspective, we introduce novel condition- and training-free strategies to enhance the quality of generated images. As a simple solution, blur guidance improves the suitability of intermediate samples for their fine-scale information and structures, enabling diffusion models to generate higher quality samples with a moderate guidance scale. Improving upon this, Self-Attention Guidance (SAG) uses the intermediate self-attention maps of diffusion models to enhance their stability and efficacy. Specifically, SAG adversarially blurs only the regions that diffusion models attend to at each iteration and guides them accordingly. Our experimental results show that our SAG improves the performance of various diffusion models, including ADM, IDDPM, Stable Diffusion, and DiT. Moreover, combining SAG with conventional guidance methods leads to further improvement.

Neural fields, which represent signals as a function parameterized by a neural network, are a promising alternative to traditional discrete vector or grid-based representations. Compared to discrete representations, neural representations both scale well with increasing resolution, are continuous, and can be many-times differentiable. However, given a dataset of signals that we would like to represent, having to optimize a separate neural field for each signal is inefficient, and cannot capitalize on shared information or structures among signals. Existing generalization methods view this as a meta-learning problem and employ gradient-based meta-learning to learn an initialization which is then fine-tuned with test-time optimization, or learn hypernetworks to produce the weights of a neural field. We instead propose a new paradigm that views the large-scale training of neural representations as a part of a partially-observed neural process framework, and leverage neural process algorithms to solve this task. We demonstrate that this approach outperforms both state-of-the-art gradient-based meta-learning approaches and hypernetwork approaches.

Unsupervised constituency parsers organize phrases within a sentence into a tree-shaped syntactic constituent structure that reflects the organization of sentence semantics. However, the traditional objective of maximizing sentence log-likelihood (LL) does not explicitly account for the close relationship between the constituent structure and the semantics, resulting in a weak correlation between LL values and parsing accuracy. In this paper, we introduce a novel objective for training unsupervised parsers: maximizing the information between constituent structures and sentence semantics (SemInfo). We introduce a bag-of-substrings model to represent the semantics and apply the probability-weighted information metric to estimate the SemInfo. Additionally, we develop a Tree Conditional Random Field (TreeCRF)-based model to apply the SemInfo maximization objective to Probabilistic Context-Free Grammar (PCFG) induction, the state-of-the-art method for unsupervised constituency parsing. Experiments demonstrate that SemInfo correlates more strongly with parsing accuracy than LL. Our algorithm significantly enhances parsing accuracy by an average of 7.85 points across five PCFG variants and in four languages, achieving new state-of-the-art results in three of the four languages.

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.

With the emerging of huge amount of unlabeled data, unsupervised out-of-distribution (OOD) detection is vital for ensuring the reliability of graph neural networks (GNNs) by identifying OOD samples from in-distribution (ID) ones during testing, where encountering novel or unknown data is inevitable. Existing methods often suffer from compromised performance due to redundant information in graph structures, which impairs their ability to effectively differentiate between ID and OOD data. To address this challenge, we propose SEGO, an unsupervised framework that integrates structural entropy into OOD detection regarding graph classification. Specifically, within the architecture of contrastive learning, SEGO introduces an anchor view in the form of coding tree by minimizing structural entropy. The obtained coding tree effectively removes redundant information from graphs while preserving essential structural information, enabling the capture of distinct graph patterns between ID and OOD samples. Furthermore, we present a multi-grained contrastive learning scheme at local, global, and tree levels using triplet views, where coding trees with essential information serve as the anchor view. Extensive experiments on real-world datasets validate the effectiveness of SEGO, demonstrating superior performance over state-of-the-art baselines in OOD detection. Specifically, our method achieves the best performance on 9 out of 10 dataset pairs, with an average improvement of 3.7\% on OOD detection datasets, significantly surpassing the best competitor by 10.8\% on the FreeSolv/ToxCast dataset pair.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Prior work on pretrained sentence embeddings and benchmarks focus on the capabilities of stand-alone sentences. We propose DiscoEval, a test suite of tasks to evaluate whether sentence representations include broader context information. We also propose a variety of training objectives that makes use of natural annotations from Wikipedia to build sentence encoders capable of modeling discourse. We benchmark sentence encoders pretrained with our proposed training objectives, as well as other popular pretrained sentence encoders on DiscoEval and other sentence evaluation tasks. Empirically, we show that these training objectives help to encode different aspects of information in document structures. Moreover, BERT and ELMo demonstrate strong performances over DiscoEval with individual hidden layers showing different characteristics.

Superconductivity allows electrical current to flow without any energy loss, and thus making solids superconducting is a grand goal of physics, material science, and electrical engineering. More than 16 Nobel Laureates have been awarded for their contribution to superconductivity research. Superconductors are valuable for sustainable development goals (SDGs), such as climate change mitigation, affordable and clean energy, industry, innovation and infrastructure, and so on. However, a unified physics theory explaining all superconductivity mechanism is still unknown. It is believed that superconductivity is microscopically due to not only molecular compositions but also the geometric crystal structure. Hence a new dataset, S2S, containing both crystal structures and superconducting critical temperature, is built upon SuperCon and Material Project. Based on this new dataset, we propose a novel model, S2SNet, which utilizes the attention mechanism for superconductivity prediction. To overcome the shortage of data, S2SNet is pre-trained on the whole Material Project dataset with Masked-Language Modeling (MLM). S2SNet makes a new state-of-the-art, with out-of-sample accuracy of 92% and Area Under Curve (AUC) of 0.92. To the best of our knowledge, S2SNet is the first work to predict superconductivity with only information of crystal structures. This work is beneficial to superconductivity discovery and further SDGs. Code and datasets are available in https://github.com/zjuKeLiu/S2SNet

Recently, significant progress has been made applying machine learning to the problem of table structure inference and extraction from unstructured documents. However, one of the greatest challenges remains the creation of datasets with complete, unambiguous ground truth at scale. To address this, we develop a new, more comprehensive dataset for table extraction, called PubTables-1M. PubTables-1M contains nearly one million tables from scientific articles, supports multiple input modalities, and contains detailed header and location information for table structures, making it useful for a wide variety of modeling approaches. It also addresses a significant source of ground truth inconsistency observed in prior datasets called oversegmentation, using a novel canonicalization procedure. We demonstrate that these improvements lead to a significant increase in training performance and a more reliable estimate of model performance at evaluation for table structure recognition. Further, we show that transformer-based object detection models trained on PubTables-1M produce excellent results for all three tasks of detection, structure recognition, and functional analysis without the need for any special customization for these tasks. Data and code will be released at https://github.com/microsoft/table-transformer.

Due to high utility in many applications, from social networks to blockchain to power grids, deep learning on non-Euclidean objects such as graphs and manifolds, coined Geometric Deep Learning (GDL), continues to gain an ever increasing interest. We propose a new L\'evy Flights Graph Convolutional Networks (LFGCN) method for semi-supervised learning, which casts the L\'evy Flights into random walks on graphs and, as a result, allows both to accurately account for the intrinsic graph topology and to substantially improve classification performance, especially for heterogeneous graphs. Furthermore, we propose a new preferential P-DropEdge method based on the Girvan-Newman argument. That is, in contrast to uniform removing of edges as in DropEdge, following the Girvan-Newman algorithm, we detect network periphery structures using information on edge betweenness and then remove edges according to their betweenness centrality. Our experimental results on semi-supervised node classification tasks demonstrate that the LFGCN coupled with P-DropEdge accelerates the training task, increases stability and further improves predictive accuracy of learned graph topology structure. Finally, in our case studies we bring the machinery of LFGCN and other deep networks tools to analysis of power grid networks - the area where the utility of GDL remains untapped.

Mesh quality assessment (MQA) models play a critical role in the design, optimization, and evaluation of mesh operation systems in a wide variety of applications. Current MQA models, whether model-based methods using topology-aware features or projection-based approaches working on rendered 2D projections, often fail to capture the intricate interactions between texture and 3D geometry. We introduce HybridMQA, a first-of-its-kind hybrid full-reference colored MQA framework that integrates model-based and projection-based approaches, capturing complex interactions between textural information and 3D structures for enriched quality representations. Our method employs graph learning to extract detailed 3D representations, which are then projected to 2D using a novel feature rendering process that precisely aligns them with colored projections. This enables the exploration of geometry-texture interactions via cross-attention, producing comprehensive mesh quality representations. Extensive experiments demonstrate HybridMQA's superior performance across diverse datasets, highlighting its ability to effectively leverage geometry-texture interactions for a thorough understanding of mesh quality. Our implementation will be made publicly available.

Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.

Learning rotation-invariant distinctive features is a fundamental requirement for point cloud registration. Existing methods often use rotation-sensitive networks to extract features, while employing rotation augmentation to learn an approximate invariant mapping rudely. This makes networks fragile to rotations, overweight, and hinders the distinctiveness of features. To tackle these problems, we propose a novel position-aware rotation-equivariant network, for efficient, light-weighted, and robust registration. The network can provide a strong model inductive bias to learn rotation-equivariant/invariant features, thus addressing the aforementioned limitations. To further improve the distinctiveness of descriptors, we propose a position-aware convolution, which can better learn spatial information of local structures. Moreover, we also propose a feature-based hypothesis proposer. It leverages rotation-equivariant features that encode fine-grained structure orientations to generate reliable model hypotheses. Each correspondence can generate a hypothesis, thus it is more efficient than classic estimators that require multiple reliable correspondences. Accordingly, a contrastive rotation loss is presented to enhance the robustness of rotation-equivariant features against data degradation. Extensive experiments on indoor and outdoor datasets demonstrate that our method significantly outperforms the SOTA methods in terms of registration recall while being lightweight and keeping a fast speed. Moreover, experiments on rotated datasets demonstrate its robustness against rotation variations. Code is available at https://github.com/yaorz97/PARENet.

Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method Wei2022ChainOT can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at https://tianchi.aliyun.com/dataset/95414, and the source codes are open-sourced at https://github.com/michael-wzhu/text2dt.

Large language models are extensively applied across a wide range of tasks, such as customer support, content creation, educational tutoring, and providing financial guidance. However, a well-known drawback is their predisposition to generate hallucinations. This damages the trustworthiness of the information these models provide, impacting decision-making and user confidence. We propose a method to detect hallucinations by looking at the structure of the latent space and finding associations within hallucinated and non-hallucinated generations. We create a graph structure that connects generations that lie closely in the embedding space. Moreover, we employ a Graph Attention Network which utilizes message passing to aggregate information from neighboring nodes and assigns varying degrees of importance to each neighbor based on their relevance. Our findings show that 1) there exists a structure in the latent space that differentiates between hallucinated and non-hallucinated generations, 2) Graph Attention Networks can learn this structure and generalize it to unseen generations, and 3) the robustness of our method is enhanced when incorporating contrastive learning. When evaluated against evidence-based benchmarks, our model performs similarly without access to search-based methods.

Diffusion models have garnered considerable interest in the field of text generation. Several studies have explored text diffusion models with different structures and applied them to various tasks, including named entity recognition and summarization. However, there exists a notable disparity between the "easy-first" text generation process of current diffusion models and the "keyword-first" natural text generation process of humans, which has received limited attention. To bridge this gap, we propose InfoDiffusion, a non-autoregressive text diffusion model. Our approach introduces a "keyinfo-first" generation strategy and incorporates a noise schedule based on the amount of text information. In addition, InfoDiffusion combines self-conditioning with a newly proposed partially noising model structure. Experimental results show that InfoDiffusion outperforms the baseline model in terms of generation quality and diversity, as well as exhibiting higher sampling efficiency.

In this paper, we present a conceptual model game to examine the dynamics of asymmetric interactions in games with imperfect information. The game involves two agents with starkly contrasting capabilities: one agent can take actions but has no information of the state of the game, whereas the other agent has perfect information of the state but cannot act or observe the other agent's actions. This duality manifests an extreme form of asymmetry, and how differing abilities influence the possibility of attaining common knowledge. Using Kripke structures and epistemic logic we demonstrate that, under these conditions, common knowledge of the current game state becomes unattainable. Our findings advance the discussion on the strategic limitations of knowledge in environments where information and action are unevenly distributed.

Language exhibits a fractal structure in its information-theoretic complexity (i.e. bits per token), with self-similarity across scales and long-range dependence (LRD). In this work, we investigate whether large language models (LLMs) can replicate such fractal characteristics and identify conditions-such as temperature setting and prompting method-under which they may fail. Moreover, we find that the fractal parameters observed in natural language are contained within a narrow range, whereas those of LLMs' output vary widely, suggesting that fractal parameters might prove helpful in detecting a non-trivial portion of LLM-generated texts. Notably, these findings, and many others reported in this work, are robust to the choice of the architecture; e.g. Gemini 1.0 Pro, Mistral-7B and Gemma-2B. We also release a dataset comprising of over 240,000 articles generated by various LLMs (both pretrained and instruction-tuned) with different decoding temperatures and prompting methods, along with their corresponding human-generated texts. We hope that this work highlights the complex interplay between fractal properties, prompting, and statistical mimicry in LLMs, offering insights for generating, evaluating and detecting synthetic texts.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Information extraction suffers from its varying targets, heterogeneous structures, and demand-specific schemas. In this paper, we propose a unified text-to-structure generation framework, namely UIE, which can universally model different IE tasks, adaptively generate targeted structures, and collaboratively learn general IE abilities from different knowledge sources. Specifically, UIE uniformly encodes different extraction structures via a structured extraction language, adaptively generates target extractions via a schema-based prompt mechanism - structural schema instructor, and captures the common IE abilities via a large-scale pre-trained text-to-structure model. Experiments show that UIE achieved the state-of-the-art performance on 4 IE tasks, 13 datasets, and on all supervised, low-resource, and few-shot settings for a wide range of entity, relation, event and sentiment extraction tasks and their unification. These results verified the effectiveness, universality, and transferability of UIE.

System logs record detailed runtime information of software systems and are used as the main data source for many tasks around software engineering. As modern software systems are evolving into large scale and complex structures, logs have become one type of fast-growing big data in industry. In particular, such logs often need to be stored for a long time in practice (e.g., a year), in order to analyze recurrent problems or track security issues. However, archiving logs consumes a large amount of storage space and computing resources, which in turn incurs high operational cost. Data compression is essential to reduce the cost of log storage. Traditional compression tools (e.g., gzip) work well for general texts, but are not tailed for system logs. In this paper, we propose a novel and effective log compression method, namely logzip. Logzip is capable of extracting hidden structures from raw logs via fast iterative clustering and further generating coherent intermediate representations that allow for more effective compression. We evaluate logzip on five large log datasets of different system types, with a total of 63.6 GB in size. The results show that logzip can save about half of the storage space on average over traditional compression tools. Meanwhile, the design of logzip is highly parallel and only incurs negligible overhead. In addition, we share our industrial experience of applying logzip to Huawei's real products.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

Programming language processing (similar to natural language processing) is a hot research topic in the field of software engineering; it has also aroused growing interest in the artificial intelligence community. However, different from a natural language sentence, a program contains rich, explicit, and complicated structural information. Hence, traditional NLP models may be inappropriate for programs. In this paper, we propose a novel tree-based convolutional neural network (TBCNN) for programming language processing, in which a convolution kernel is designed over programs' abstract syntax trees to capture structural information. TBCNN is a generic architecture for programming language processing; our experiments show its effectiveness in two different program analysis tasks: classifying programs according to functionality, and detecting code snippets of certain patterns. TBCNN outperforms baseline methods, including several neural models for NLP.

Targeted opinion word extraction (TOWE) is a sub-task of aspect based sentiment analysis (ABSA) which aims to find the opinion words for a given aspect-term in a sentence. Despite their success for TOWE, the current deep learning models fail to exploit the syntactic information of the sentences that have been proved to be useful for TOWE in the prior research. In this work, we propose to incorporate the syntactic structures of the sentences into the deep learning models for TOWE, leveraging the syntax-based opinion possibility scores and the syntactic connections between the words. We also introduce a novel regularization technique to improve the performance of the deep learning models based on the representation distinctions between the words in TOWE. The proposed model is extensively analyzed and achieves the state-of-the-art performance on four benchmark datasets.

A major outstanding challenge in cosmology is the persistent discrepancy between the Hubble constant obtained from early and late universe measurements -- the Hubble tension. Examining cosmological evolution through the lens of information growth within a black hole we show the appearence of two fractal growing processes characterizing the early and late ages. These fractals induce space growth rates of 62.79pm5.59 km/s/Mpc and 70.07pm0.09 km/s/Mpc; close to the current values of the Hubble constants involved in the tension. These results strongly suggest that the Hubble tension is not given by unexpected large-scale structures or multiple, unrelated errors but by innate properties underlying the universe dynamics.

Recently, much attention has been drawn to learning the underlying 3D structures of a scene from monocular videos in a fully self-supervised fashion. One of the most challenging aspects of this task is handling the independently moving objects as they break the rigid-scene assumption. For the first time, we show that pixel positional information can be exploited to learn SVDE (Single View Depth Estimation) from videos. Our proposed moving object (MO) masks, which are induced by shifted positional information (SPI) and referred to as `SPIMO' masks, are very robust and consistently remove the independently moving objects in the scenes, allowing for better learning of SVDE from videos. Additionally, we introduce a new adaptive quantization scheme that assigns the best per-pixel quantization curve for our depth discretization. Finally, we employ existing boosting techniques in a new way to further self-supervise the depth of the moving objects. With these features, our pipeline is robust against moving objects and generalizes well to high-resolution images, even when trained with small patches, yielding state-of-the-art (SOTA) results with almost 8.5x fewer parameters than the previous works that learn from videos. We present extensive experiments on KITTI and CityScapes that show the effectiveness of our method.

Transformer-based Language Models are widely used in Natural Language Processing related tasks. Thanks to their pre-training, they have been successfully adapted to Information Extraction in business documents. However, most pre-training tasks proposed in the literature for business documents are too generic and not sufficient to learn more complex structures. In this paper, we use LayoutLM, a language model pre-trained on a collection of business documents, and introduce two new pre-training tasks that further improve its capacity to extract relevant information. The first is aimed at better understanding the complex layout of documents, and the second focuses on numeric values and their order of magnitude. These tasks force the model to learn better-contextualized representations of the scanned documents. We further introduce a new post-processing algorithm to decode BIESO tags in Information Extraction that performs better with complex entities. Our method significantly improves extraction performance on both public (from 93.88 to 95.50 F1 score) and private (from 84.35 to 84.84 F1 score) datasets composed of expense receipts, invoices, and purchase orders.

The challenge of information extraction (IE) lies in the diversity of label schemas and the heterogeneity of structures. Traditional methods require task-specific model design and rely heavily on expensive supervision, making them difficult to generalize to new schemas. In this paper, we decouple IE into two basic abilities, structuring and conceptualizing, which are shared by different tasks and schemas. Based on this paradigm, we propose to universally model various IE tasks with Unified Semantic Matching (USM) framework, which introduces three unified token linking operations to model the abilities of structuring and conceptualizing. In this way, USM can jointly encode schema and input text, uniformly extract substructures in parallel, and controllably decode target structures on demand. Empirical evaluation on 4 IE tasks shows that the proposed method achieves state-of-the-art performance under the supervised experiments and shows strong generalization ability in zero/few-shot transfer settings.

Information theory, introduced by Shannon, has been extremely successful and influential as a mathematical theory of communication. Shannon's notion of information does not consider the meaning of the messages being communicated but only their probability. Even so, computational approaches regularly appeal to "information processing" to study how meaning is encoded and decoded in natural and artificial systems. Here, we contrast Shannon information theory with integrated information theory (IIT), which was developed to account for the presence and properties of consciousness. IIT considers meaning as integrated information and characterizes it as a structure, rather than as a message or code. In principle, IIT's axioms and postulates allow one to "unfold" a cause-effect structure from a substrate in a state, a structure that fully defines the intrinsic meaning of an experience and its contents. It follows that, for the communication of meaning, the cause-effect structures of sender and receiver must be similar.

Multimodal information extraction (MIE) gains significant attention as the popularity of multimedia content increases. However, current MIE methods often resort to using task-specific model structures, which results in limited generalizability across tasks and underutilizes shared knowledge across MIE tasks. To address these issues, we propose UMIE, a unified multimodal information extractor to unify three MIE tasks as a generation problem using instruction tuning, being able to effectively extract both textual and visual mentions. Extensive experiments show that our single UMIE outperforms various state-of-the-art (SoTA) methods across six MIE datasets on three tasks. Furthermore, in-depth analysis demonstrates UMIE's strong generalization in the zero-shot setting, robustness to instruction variants, and interpretability. Our research serves as an initial step towards a unified MIE model and initiates the exploration into both instruction tuning and large language models within the MIE domain. Our code, data, and model are available at https://github.com/ZUCC-AI/UMIE

In orchard automation, dense foliage during the canopy season severely occludes tree structures, minimizing visibility to various canopy parts such as trunks and branches, which limits the ability of a machine vision system. However, canopy structure is more open and visible during the dormant season when trees are defoliated. In this work, we present an information fusion framework that integrates multi-seasonal structural data to support robotic and automated crop load management during the entire growing season. The framework combines high-resolution RGB-D imagery from both dormant and canopy periods using YOLOv9-Seg for instance segmentation, Kinect Fusion for 3D reconstruction, and Fast Generalized Iterative Closest Point (Fast GICP) for model alignment. Segmentation outputs from YOLOv9-Seg were used to extract depth-informed masks, which enabled accurate 3D point cloud reconstruction via Kinect Fusion; these reconstructed models from each season were subsequently aligned using Fast GICP to achieve spatially coherent multi-season fusion. The YOLOv9-Seg model, trained on manually annotated images, achieved a mean squared error (MSE) of 0.0047 and segmentation mAP@50 scores up to 0.78 for trunks in dormant season dataset. Kinect Fusion enabled accurate reconstruction of tree geometry, validated with field measurements resulting in root mean square errors (RMSE) of 5.23 mm for trunk diameter, 4.50 mm for branch diameter, and 13.72 mm for branch spacing. Fast GICP achieved precise cross-seasonal registration with a minimum fitness score of 0.00197, allowing integrated, comprehensive tree structure modeling despite heavy occlusions during the growing season. This fused structural representation enables robotic systems to access otherwise obscured architectural information, improving the precision of pruning, thinning, and other automated orchard operations.

Time series clustering promises to uncover hidden structural patterns in data with applications across healthcare, finance, industrial systems, and other critical domains. However, without validated ground truth information, researchers cannot objectively assess clustering quality or determine whether poor results stem from absent structures in the data, algorithmic limitations, or inappropriate validation methods, raising the question whether clustering is "more art than science" (Guyon et al., 2009). To address these challenges, we introduce CSTS (Correlation Structures in Time Series), a synthetic benchmark for evaluating the discovery of correlation structures in multivariate time series data. CSTS provides a clean benchmark that enables researchers to isolate and identify specific causes of clustering failures by differentiating between correlation structure deterioration and limitations of clustering algorithms and validation methods. Our contributions are: (1) a comprehensive benchmark for correlation structure discovery with distinct correlation structures, systematically varied data conditions, established performance thresholds, and recommended evaluation protocols; (2) empirical validation of correlation structure preservation showing moderate distortion from downsampling and minimal effects from distribution shifts and sparsification; and (3) an extensible data generation framework enabling structure-first clustering evaluation. A case study demonstrates CSTS's practical utility by identifying an algorithm's previously undocumented sensitivity to non-normal distributions, illustrating how the benchmark enables precise diagnosis of methodological limitations. CSTS advances rigorous evaluation standards for correlation-based time series clustering.

Automatic extraction of chemical structures from scientific literature plays a crucial role in accelerating research across fields ranging from drug discovery to materials science. Patent documents, in particular, contain molecular information in visual form, which is often inaccessible through traditional text-based searches. In this work, we introduce SubGrapher, a method for the visual fingerprinting of chemical structure images. Unlike conventional Optical Chemical Structure Recognition (OCSR) models that attempt to reconstruct full molecular graphs, SubGrapher focuses on extracting molecular fingerprints directly from chemical structure images. Using learning-based instance segmentation, SubGrapher identifies functional groups and carbon backbones, constructing a substructure-based fingerprint that enables chemical structure retrieval. Our approach is evaluated against state-of-the-art OCSR and fingerprinting methods, demonstrating superior retrieval performance and robustness across diverse molecular depictions. The dataset, models, and code are publicly available.

Universal Information Extraction (UIE) is an area of interest due to the challenges posed by varying targets, heterogeneous structures, and demand-specific schemas. However, previous works have only achieved limited success by unifying a few tasks, such as Named Entity Recognition (NER) and Relation Extraction (RE), which fall short of being authentic UIE models particularly when extracting other general schemas such as quadruples and quintuples. Additionally, these models used an implicit structural schema instructor, which could lead to incorrect links between types, hindering the model's generalization and performance in low-resource scenarios. In this paper, we redefine the authentic UIE with a formal formulation that encompasses almost all extraction schemas. To the best of our knowledge, we are the first to introduce UIE for any kind of schemas. In addition, we propose RexUIE, which is a Recursive Method with Explicit Schema Instructor for UIE. To avoid interference between different types, we reset the position ids and attention mask matrices. RexUIE shows strong performance under both full-shot and few-shot settings and achieves State-of-the-Art results on the tasks of extracting complex schemas.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

The difficulty of the information extraction task lies in dealing with the task-specific label schemas and heterogeneous data structures. Recent work has proposed methods based on large language models to uniformly model different information extraction tasks. However, these existing methods are deficient in their information extraction capabilities for Chinese languages other than English. In this paper, we propose an end-to-end chat-enhanced instruction tuning framework for universal information extraction (YAYI-UIE), which supports both Chinese and English. Specifically, we utilize dialogue data and information extraction data to enhance the information extraction performance jointly. Experimental results show that our proposed framework achieves state-of-the-art performance on Chinese datasets while also achieving comparable performance on English datasets under both supervised settings and zero-shot settings.

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular structures with spectral information, is the core step in understanding the experimental results and to close the loop. However, current approaches usually divide the task into either database-dependent retrieval and database-independent generation and neglect the inherent complementarity between them. In this study, we proposed Vib2Mol, a general deep learning model designed to flexibly handle diverse spectrum-to-structure tasks according to the available prior knowledge by bridging the retrieval and generation. It achieves state-of-the-art performance, even for the most demanding Raman spectra, over previous models in predicting reaction products and sequencing peptides as well as analyzing experimental spectra and integrating multi-modal spectral data. Vib2Mol enables vibrational spectroscopy a real-time guide for autonomous scientific discovery workflows.

Pixel-level segmentation of structural cracks across various scenarios remains a considerable challenge. Current methods encounter challenges in effectively modeling crack morphology and texture, facing challenges in balancing segmentation quality with low computational resource usage. To overcome these limitations, we propose a lightweight Structure-Aware Vision Mamba Network (SCSegamba), capable of generating high-quality pixel-level segmentation maps by leveraging both the morphological information and texture cues of crack pixels with minimal computational cost. Specifically, we developed a Structure-Aware Visual State Space module (SAVSS), which incorporates a lightweight Gated Bottleneck Convolution (GBC) and a Structure-Aware Scanning Strategy (SASS). The key insight of GBC lies in its effectiveness in modeling the morphological information of cracks, while the SASS enhances the perception of crack topology and texture by strengthening the continuity of semantic information between crack pixels. Experiments on crack benchmark datasets demonstrate that our method outperforms other state-of-the-art (SOTA) methods, achieving the highest performance with only 2.8M parameters. On the multi-scenario dataset, our method reached 0.8390 in F1 score and 0.8479 in mIoU. The code is available at https://github.com/Karl1109/SCSegamba.

Despite advancements in Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems, their effectiveness is often hindered by a lack of integration with entity relationships and community structures, limiting their ability to provide contextually rich and accurate information retrieval for fact-checking. We introduce CommunityKG-RAG (Community Knowledge Graph-Retrieval Augmented Generation), a novel zero-shot framework that integrates community structures within Knowledge Graphs (KGs) with RAG systems to enhance the fact-checking process. Capable of adapting to new domains and queries without additional training, CommunityKG-RAG utilizes the multi-hop nature of community structures within KGs to significantly improve the accuracy and relevance of information retrieval. Our experimental results demonstrate that CommunityKG-RAG outperforms traditional methods, representing a significant advancement in fact-checking by offering a robust, scalable, and efficient solution.

Unsupervised constituency parsing focuses on identifying word sequences that form a syntactic unit (i.e., constituents) in target sentences. Linguists identify the constituent by evaluating a set of Predicate-Argument Structure (PAS) equivalent sentences where we find the constituent appears more frequently than non-constituents (i.e., the constituent corresponds to a frequent word sequence within the sentence set). However, such frequency information is unavailable in previous parsing methods that identify the constituent by observing sentences with diverse PAS. In this study, we empirically show that constituents correspond to frequent word sequences in the PAS-equivalent sentence set. We propose a frequency-based parser span-overlap that (1) computes the span-overlap score as the word sequence's frequency in the PAS-equivalent sentence set and (2) identifies the constituent structure by finding a constituent tree with the maximum span-overlap score. The parser achieves state-of-the-art level parsing accuracy, outperforming existing unsupervised parsers in eight out of ten languages. Additionally, we discover a multilingual phenomenon: participant-denoting constituents tend to have higher span-overlap scores than equal-length event-denoting constituents, meaning that the former tend to appear more frequently in the PAS-equivalent sentence set than the latter. The phenomenon indicates a statistical difference between the two constituent types, laying the foundation for future labeled unsupervised parsing research.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Self-supervised monocular depth estimation has garnered considerable attention for its applications in autonomous driving and robotics. While recent methods have made strides in leveraging techniques like the Self Query Layer (SQL) to infer depth from motion, they often overlook the potential of strengthening pose information. In this paper, we introduce SPIdepth, a novel approach that prioritizes enhancing the pose network for improved depth estimation. Building upon the foundation laid by SQL, SPIdepth emphasizes the importance of pose information in capturing fine-grained scene structures. By enhancing the pose network's capabilities, SPIdepth achieves remarkable advancements in scene understanding and depth estimation. Experimental results on benchmark datasets such as KITTI, Cityscapes, and Make3D showcase SPIdepth's state-of-the-art performance, surpassing previous methods by significant margins. Specifically, SPIdepth tops the self-supervised KITTI benchmark. Additionally, SPIdepth achieves the lowest AbsRel (0.029), SqRel (0.069), and RMSE (1.394) on KITTI, establishing new state-of-the-art results. On Cityscapes, SPIdepth shows improvements over SQLdepth of 21.7% in AbsRel, 36.8% in SqRel, and 16.5% in RMSE, even without using motion masks. On Make3D, SPIdepth in zero-shot outperforms all other models. Remarkably, SPIdepth achieves these results using only a single image for inference, surpassing even methods that utilize video sequences for inference, thus demonstrating its efficacy and efficiency in real-world applications. Our approach represents a significant leap forward in self-supervised monocular depth estimation, underscoring the importance of strengthening pose information for advancing scene understanding in real-world applications. The code and pre-trained models are publicly available at https://github.com/Lavreniuk/SPIdepth.

Retrieval-augmented generation (RAG) is a key means to effectively enhance large language models (LLMs) in many knowledge-based tasks. However, existing RAG methods struggle with knowledge-intensive reasoning tasks, because useful information required to these tasks are badly scattered. This characteristic makes it difficult for existing RAG methods to accurately identify key information and perform global reasoning with such noisy augmentation. In this paper, motivated by the cognitive theories that humans convert raw information into various structured knowledge when tackling knowledge-intensive reasoning, we proposes a new framework, StructRAG, which can identify the optimal structure type for the task at hand, reconstruct original documents into this structured format, and infer answers based on the resulting structure. Extensive experiments across various knowledge-intensive tasks show that StructRAG achieves state-of-the-art performance, particularly excelling in challenging scenarios, demonstrating its potential as an effective solution for enhancing LLMs in complex real-world applications.

Document Question Answering (QA) presents a challenge in understanding visually-rich documents (VRD), particularly those dominated by lengthy textual content like research journal articles. Existing studies primarily focus on real-world documents with sparse text, while challenges persist in comprehending the hierarchical semantic relations among multiple pages to locate multimodal components. To address this gap, we propose PDF-MVQA, which is tailored for research journal articles, encompassing multiple pages and multimodal information retrieval. Unlike traditional machine reading comprehension (MRC) tasks, our approach aims to retrieve entire paragraphs containing answers or visually rich document entities like tables and figures. Our contributions include the introduction of a comprehensive PDF Document VQA dataset, allowing the examination of semantically hierarchical layout structures in text-dominant documents. We also present new VRD-QA frameworks designed to grasp textual contents and relations among document layouts simultaneously, extending page-level understanding to the entire multi-page document. Through this work, we aim to enhance the capabilities of existing vision-and-language models in handling challenges posed by text-dominant documents in VRD-QA.

Time in relativity theory has a status different from that adopted by standard quantum mechanics, where time is considered as a parameter measured with reference to an external absolute Newtonian frame. This status strongly restricts its role in the dynamics of systems and hinders any formulation to merge quantum mechanics with general relativity, specifically when considering quantum gravity. To overcome those limitations, several authors tried to construct an operator which is conjugate to the Hamiltonian of quantum systems implementing some essential features of the relativistic time. These formulations use the concept of internal or intrinsic time instead of the universal coordinate time used in textbooks. Furthermore, recently it is remarked that the consideration of time with relativistic features could enhance the analysis techniques in quantum information processing and have an impact on its status in causal orders and causal structures of quantum information. The role of clocks, their accuracy and stability has become an important issue in quantum information processing. This article present a substantiative review of recent works which reflect the possibility of utilizing quantum time, measured by quantum clock devised according to Page-Wootters scheme, to stand as a resource for quantum information processing.

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

The rise of misinformation, exacerbated by Large Language Models (LLMs) like GPT and Gemini, demands robust fact-checking solutions, especially for low-resource languages like Vietnamese. Existing methods struggle with semantic ambiguity, homonyms, and complex linguistic structures, often trading accuracy for efficiency. We introduce SemViQA, a novel Vietnamese fact-checking framework integrating Semantic-based Evidence Retrieval (SER) and Two-step Verdict Classification (TVC). Our approach balances precision and speed, achieving state-of-the-art results with 78.97\% strict accuracy on ISE-DSC01 and 80.82\% on ViWikiFC, securing 1st place in the UIT Data Science Challenge. Additionally, SemViQA Faster improves inference speed 7x while maintaining competitive accuracy. SemViQA sets a new benchmark for Vietnamese fact verification, advancing the fight against misinformation. The source code is available at: https://github.com/DAVID-NGUYEN-S16/SemViQA.

Graph neural networks (GNNs) have shown great power in modeling graph structured data. However, similar to other machine learning models, GNNs may make predictions biased on protected sensitive attributes, e.g., skin color and gender. Because machine learning algorithms including GNNs are trained to reflect the distribution of the training data which often contains historical bias towards sensitive attributes. In addition, the discrimination in GNNs can be magnified by graph structures and the message-passing mechanism. As a result, the applications of GNNs in sensitive domains such as crime rate prediction would be largely limited. Though extensive studies of fair classification have been conducted on i.i.d data, methods to address the problem of discrimination on non-i.i.d data are rather limited. Furthermore, the practical scenario of sparse annotations in sensitive attributes is rarely considered in existing works. Therefore, we study the novel and important problem of learning fair GNNs with limited sensitive attribute information. FairGNN is proposed to eliminate the bias of GNNs whilst maintaining high node classification accuracy by leveraging graph structures and limited sensitive information. Our theoretical analysis shows that FairGNN can ensure the fairness of GNNs under mild conditions given limited nodes with known sensitive attributes. Extensive experiments on real-world datasets also demonstrate the effectiveness of FairGNN in debiasing and keeping high accuracy.

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex protein-ligand interactions across multiple scales remains challenging, as current methods often overlook the hierarchical organization and intrinsic asymmetry of these interactions. To address these limitations, we propose MSCoD, a novel Bayesian updating-based generative framework for structure-based drug design. In our MSCoD, Multi-Scale Information Bottleneck (MSIB) was developed, which enables semantic compression at multiple abstraction levels for efficient hierarchical feature extraction. Furthermore, a multi-head cooperative attention (MHCA) mechanism was developed, which employs asymmetric protein-to-ligand attention to capture diverse interaction types while addressing the dimensionality disparity between proteins and ligands. Empirical studies showed that MSCoD outperforms state-of-the-art methods on the benchmark dataset. Case studies on challenging targets such as KRAS G12D further demonstrate its applicability in real-world scenarios. The code and data underlying this article are freely available at https://github.com/xulong0826/MSCoD.

Automatically generating coherent and semantically meaningful text has many applications in machine translation, dialogue systems, image captioning, etc. Recently, by combining with policy gradient, Generative Adversarial Nets (GAN) that use a discriminative model to guide the training of the generative model as a reinforcement learning policy has shown promising results in text generation. However, the scalar guiding signal is only available after the entire text has been generated and lacks intermediate information about text structure during the generative process. As such, it limits its success when the length of the generated text samples is long (more than 20 words). In this paper, we propose a new framework, called LeakGAN, to address the problem for long text generation. We allow the discriminative net to leak its own high-level extracted features to the generative net to further help the guidance. The generator incorporates such informative signals into all generation steps through an additional Manager module, which takes the extracted features of current generated words and outputs a latent vector to guide the Worker module for next-word generation. Our extensive experiments on synthetic data and various real-world tasks with Turing test demonstrate that LeakGAN is highly effective in long text generation and also improves the performance in short text generation scenarios. More importantly, without any supervision, LeakGAN would be able to implicitly learn sentence structures only through the interaction between Manager and Worker.

Converting user interfaces into code (UI2Code) is a crucial step in website development, which is time-consuming and labor-intensive. The automation of UI2Code is essential to streamline this task, beneficial for improving the development efficiency. There exist deep learning-based methods for the task; however, they heavily rely on a large amount of labeled training data and struggle with generalizing to real-world, unseen web page designs. The advent of Multimodal Large Language Models (MLLMs) presents potential for alleviating the issue, but they are difficult to comprehend the complex layouts in UIs and generate the accurate code with layout preserved. To address these issues, we propose LayoutCoder, a novel MLLM-based framework generating UI code from real-world webpage images, which includes three key modules: (1) Element Relation Construction, which aims at capturing UI layout by identifying and grouping components with similar structures; (2) UI Layout Parsing, which aims at generating UI layout trees for guiding the subsequent code generation process; and (3) Layout-Guided Code Fusion, which aims at producing the accurate code with layout preserved. For evaluation, we build a new benchmark dataset which involves 350 real-world websites named Snap2Code, divided into seen and unseen parts for mitigating the data leakage issue, besides the popular dataset Design2Code. Extensive evaluation shows the superior performance of LayoutCoder over the state-of-the-art approaches. Compared with the best-performing baseline, LayoutCoder improves 10.14% in the BLEU score and 3.95% in the CLIP score on average across all datasets.

Localizing user-queried events through natural language is crucial for video understanding models. Recent methods predominantly adapt Video LLMs to generate event boundary timestamps to handle temporal localization tasks, which struggle to leverage LLMs' powerful semantic understanding. In this work, we introduce MeCo, a novel timestamp-free framework that enables video LLMs to fully harness their intrinsic semantic capabilities for temporal localization tasks. Rather than outputting boundary timestamps, MeCo partitions videos into holistic event and transition segments based on the proposed structural token generation and grounding pipeline, derived from video LLMs' temporal structure understanding capability. We further propose a query-focused captioning task that compels the LLM to extract fine-grained, event-specific details, bridging the gap between localization and higher-level semantics and enhancing localization performance. Extensive experiments on diverse temporal localization tasks show that MeCo consistently outperforms boundary-centric methods, underscoring the benefits of a semantic-driven approach for temporal localization with video LLMs.

Idiopathic pulmonary fibrosis (IPF) is a progressive disease that irreversibly transforms lung tissue into rigid fibrotic structures, leading to debilitating symptoms such as shortness of breath and chronic fatigue. The heterogeneity and complexity of this disease, particularly regarding its severity and progression rate, have made predicting its future course a complex and challenging task. Besides, traditional diagnostic methods based on clinical evaluations and imaging have limitations in capturing the disease's complexity. Using the Kaggle Pulmonary Fibrosis Progression dataset, which includes computed tomography images, and clinical information, the model predicts changes in forced vital capacity (FVC), a key progression indicator. Our method uses a proposed context-aware sequential-parallel hybrid transformer model and clinical information enrichment for its prediction. The proposed method achieved a Laplace Log-Likelihood score of -6.508, outperforming prior methods and demonstrating superior predictive capabilities. These results highlight the potential of advanced deep learning techniques to provide more accurate and timely predictions, offering a transformative approach to the diagnosis and management of IPF, with implications for improved patient outcomes and therapeutic advancements.

Both graph structures and textual information play a critical role in Knowledge Graph Completion (KGC). With the success of Pre-trained Language Models (PLMs) such as BERT, they have been applied for text encoding for KGC. However, the current methods mostly prefer to fine-tune PLMs, leading to huge training costs and limited scalability to larger PLMs. In contrast, we propose to utilize prompts and perform KGC on a frozen PLM with only the prompts trained. Accordingly, we propose a new KGC method named PDKGC with two prompts -- a hard task prompt which is to adapt the KGC task to the PLM pre-training task of token prediction, and a disentangled structure prompt which learns disentangled graph representation so as to enable the PLM to combine more relevant structure knowledge with the text information. With the two prompts, PDKGC builds a textual predictor and a structural predictor, respectively, and their combination leads to more comprehensive entity prediction. Solid evaluation on two widely used KGC datasets has shown that PDKGC often outperforms the baselines including the state-of-the-art, and its components are all effective. Our codes and data are available at https://github.com/genggengcss/PDKGC.

We develop information geometric techniques to understand the representations learned by deep networks when they are trained on different tasks using supervised, meta-, semi-supervised and contrastive learning. We shed light on the following phenomena that relate to the structure of the space of tasks: (1) the manifold of probabilistic models trained on different tasks using different representation learning methods is effectively low-dimensional; (2) supervised learning on one task results in a surprising amount of progress even on seemingly dissimilar tasks; progress on other tasks is larger if the training task has diverse classes; (3) the structure of the space of tasks indicated by our analysis is consistent with parts of the Wordnet phylogenetic tree; (4) episodic meta-learning algorithms and supervised learning traverse different trajectories during training but they fit similar models eventually; (5) contrastive and semi-supervised learning methods traverse trajectories similar to those of supervised learning. We use classification tasks constructed from the CIFAR-10 and Imagenet datasets to study these phenomena.

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that incorporating the knowledge of the directed acyclic graph (DAG) can be beneficial if suitable source encoders are employed. As a possible source encoder in this context, we derive a variational inference based conditional variational autoencoder for causal structured survival prediction, which we refer to as DAGSurv. We illustrate the performance of DAGSurv on low and high-dimensional synthetic datasets, and real-world datasets such as METABRIC and GBSG. We demonstrate that the proposed method outperforms other survival analysis baselines such as Cox Proportional Hazards, DeepSurv and Deephit, which are oblivious to the underlying causal relationship between data entities.

Documents are visually rich structures that convey information through text, as well as tables, figures, page layouts, or fonts. While modern document retrieval systems exhibit strong performance on query-to-text matching, they struggle to exploit visual cues efficiently, hindering their performance on practical document retrieval applications such as Retrieval Augmented Generation. To benchmark current systems on visually rich document retrieval, we introduce the Visual Document Retrieval Benchmark ViDoRe, composed of various page-level retrieving tasks spanning multiple domains, languages, and settings. The inherent shortcomings of modern systems motivate the introduction of a new retrieval model architecture, ColPali, which leverages the document understanding capabilities of recent Vision Language Models to produce high-quality contextualized embeddings solely from images of document pages. Combined with a late interaction matching mechanism, ColPali largely outperforms modern document retrieval pipelines while being drastically faster and end-to-end trainable.

Rendering moving human bodies at free viewpoints only from a monocular video is quite a challenging problem. The information is too sparse to model complicated human body structures and motions from both view and pose dimensions. Neural radiance fields (NeRF) have shown great power in novel view synthesis and have been applied to human body rendering. However, most current NeRF-based methods bear huge costs for both training and rendering, which impedes the wide applications in real-life scenarios. In this paper, we propose a rendering framework that can learn moving human body structures extremely quickly from a monocular video. The framework is built by integrating both neural fields and neural voxels. Especially, a set of generalizable neural voxels are constructed. With pretrained on various human bodies, these general voxels represent a basic skeleton and can provide strong geometric priors. For the fine-tuning process, individual voxels are constructed for learning differential textures, complementary to general voxels. Thus learning a novel body can be further accelerated, taking only a few minutes. Our method shows significantly higher training efficiency compared with previous methods, while maintaining similar rendering quality. The project page is at https://taoranyi.com/gneuvox .

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

We apply category theory to extract multimodal document structure which leads us to develop information theoretic measures, content summarization and extension, and self-supervised improvement of large pretrained models. We first develop a mathematical representation of a document as a category of question-answer pairs. Second, we develop an orthogonalization procedure to divide the information contained in one or more documents into non-overlapping pieces. The structures extracted in the first and second steps lead us to develop methods to measure and enumerate the information contained in a document. We also build on those steps to develop new summarization techniques, as well as to develop a solution to a new problem viz. exegesis resulting in an extension of the original document. Our question-answer pair methodology enables a novel rate distortion analysis of summarization techniques. We implement our techniques using large pretrained models, and we propose a multimodal extension of our overall mathematical framework. Finally, we develop a novel self-supervised method using RLVR to improve large pretrained models using consistency constraints such as composability and closure under certain operations that stem naturally from our category theoretic framework.

Animal vocalizations contain sequential structures that carry important communicative information, yet most computational bioacoustics studies average the extracted frame-level features across the temporal axis, discarding the order of the sub-units within a vocalization. This paper investigates whether discrete acoustic token sequences, derived through vector quantization and gumbel-softmax vector quantization of extracted self-supervised speech model representations can effectively capture and leverage temporal information. To that end, pairwise distance analysis of token sequences generated from HuBERT embeddings shows that they can discriminate call-types and callers across four bioacoustics datasets. Sequence classification experiments using k-Nearest Neighbour with Levenshtein distance show that the vector-quantized token sequences yield reasonable call-type and caller classification performances, and hold promise as alternative feature representations towards leveraging sequential information in animal vocalizations.

In this paper, we propose a unified pre-training approach called UniSpeech to learn speech representations with both unlabeled and labeled data, in which supervised phonetic CTC learning and phonetically-aware contrastive self-supervised learning are conducted in a multi-task learning manner. The resultant representations can capture information more correlated with phonetic structures and improve the generalization across languages and domains. We evaluate the effectiveness of UniSpeech for cross-lingual representation learning on public CommonVoice corpus. The results show that UniSpeech outperforms self-supervised pretraining and supervised transfer learning for speech recognition by a maximum of 13.4% and 17.8% relative phone error rate reductions respectively (averaged over all testing languages). The transferability of UniSpeech is also demonstrated on a domain-shift speech recognition task, i.e., a relative word error rate reduction of 6% against the previous approach.

Stabilizer states are extensively studied in quantum information theory for their structures based on the Pauli group. Calderbank-Shor-Steane (CSS) stabilizer states are of particular importance in their application to fault-tolerant quantum computation (FTQC). However, how to fault-tolerantly prepare arbitrary CSS stabilizer states for general CSS stabilizer codes is still unknown, and their preparation can be highly costly in computational resources. In this paper, we show how to prepare a large class of CSS stabilizer states useful for FTQC. We propose distillation protocols using syndrome encoding by classical codes or quantum CSS codes. Along the same lines, we show that classical coding techniques can reduce the ancilla consumption in Steane syndrome extraction by using additional transversal controlled-NOT gates and classical computing power. In the scenario of a fixed ancilla consumption rate, we can increase the frequency of quantum error correction and effectively lower the error rate.

Retrieval-Augmented Generation (RAG) systems enhance large language models (LLMs) by integrating external knowledge sources, enabling more accurate and contextually relevant responses tailored to user needs. However, existing RAG systems have significant limitations, including reliance on flat data representations and inadequate contextual awareness, which can lead to fragmented answers that fail to capture complex inter-dependencies. To address these challenges, we propose LightRAG, which incorporates graph structures into text indexing and retrieval processes. This innovative framework employs a dual-level retrieval system that enhances comprehensive information retrieval from both low-level and high-level knowledge discovery. Additionally, the integration of graph structures with vector representations facilitates efficient retrieval of related entities and their relationships, significantly improving response times while maintaining contextual relevance. This capability is further enhanced by an incremental update algorithm that ensures the timely integration of new data, allowing the system to remain effective and responsive in rapidly changing data environments. Extensive experimental validation demonstrates considerable improvements in retrieval accuracy and efficiency compared to existing approaches. We have made our LightRAG open-source and available at the link: https://github.com/HKUDS/LightRAG.

Document parsing is essential for analyzing complex document structures and extracting fine-grained information, supporting numerous downstream applications. However, existing methods often require integrating multiple independent models to handle various parsing tasks, leading to high complexity and maintenance overhead. To address this, we propose DocFusion, a lightweight generative model with only 0.28B parameters. It unifies task representations and achieves collaborative training through an improved objective function. Experiments reveal and leverage the mutually beneficial interaction among recognition tasks, and integrating recognition data significantly enhances detection performance. The final results demonstrate that DocFusion achieves state-of-the-art (SOTA) performance across four key tasks.

While multi-agent systems have been shown to significantly enhance the performance of Large Language Models (LLMs) across various tasks and applications, the dense interaction between scaling agents potentially hampers their efficiency and diversity. To address these challenges, we draw inspiration from the sparse mixture-of-agents (SMoE) and propose a sparse mixture-of-agents (SMoA) framework to improve the efficiency and diversity of multi-agent LLMs. Unlike completely connected structures, SMoA introduces novel Response Selection and Early Stopping mechanisms to sparsify information flows among individual LLM agents, striking a balance between performance and efficiency. Additionally, inspired by the expert diversity principle in SMoE frameworks for workload balance between experts, we assign distinct role descriptions to each LLM agent, fostering diverse and divergent thinking. Extensive experiments on reasoning, alignment, and fairness benchmarks demonstrate that SMoA achieves performance comparable to traditional mixture-of-agents approaches but with significantly lower computational costs. Further analysis reveals that SMoA is more stable, has a greater capacity to scale, and offers considerable potential through hyper-parameter optimization. Code and data will be available at: https://github.com/David-Li0406/SMoA.

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

Structured output representation is a generative task explored in computer vision that often times requires the mapping of low dimensional features to high dimensional structured outputs. Losses in complex spatial information in deterministic approaches such as Convolutional Neural Networks (CNN) lead to uncertainties and ambiguous structures within a single output representation. A probabilistic approach through deep Conditional Generative Models (CGM) is presented by Sohn et al. in which a particular model known as the Conditional Variational Auto-encoder (CVAE) is introduced and explored. While the original paper focuses on the task of image segmentation, this paper adopts the CVAE framework for the task of controlled output representation through attributes. This approach allows us to learn a disentangled multimodal prior distribution, resulting in more controlled and robust approach to sample generation. In this work we recreate the CVAE architecture and train it on images conditioned on various attributes obtained from two image datasets; the Large-scale CelebFaces Attributes (CelebA) dataset and the Caltech-UCSD Birds (CUB-200-2011) dataset. We attempt to generate new faces with distinct attributes such as hair color and glasses, as well as different bird species samples with various attributes. We further introduce strategies for improving generalized sample generation by applying a weighted term to the variational lower bound.

Physics-aware driving world model is essential for drive planning, out-of-distribution data synthesis, and closed-loop evaluation. However, existing methods often rely on a single diffusion model to directly map driving actions to videos, which makes learning difficult and leads to physically inconsistent outputs. To overcome these challenges, we propose GenieDrive, a novel framework designed for physics-aware driving video generation. Our approach starts by generating 4D occupancy, which serves as a physics-informed foundation for subsequent video generation. 4D occupancy contains rich physical information, including high-resolution 3D structures and dynamics. To facilitate effective compression of such high-resolution occupancy, we propose a VAE that encodes occupancy into a latent tri-plane representation, reducing the latent size to only 58% of that used in previous methods. We further introduce Mutual Control Attention (MCA) to accurately model the influence of control on occupancy evolution, and we jointly train the VAE and the subsequent prediction module in an end-to-end manner to maximize forecasting accuracy. Together, these designs yield a 7.2% improvement in forecasting mIoU at an inference speed of 41 FPS, while using only 3.47 M parameters. Additionally, a Normalized Multi-View Attention is introduced in the video generation model to generate multi-view driving videos with guidance from our 4D occupancy, significantly improving video quality with a 20.7% reduction in FVD. Experiments demonstrate that GenieDrive enables highly controllable, multi-view consistent, and physics-aware driving video generation.

The topic of stitching images with globally natural structures holds paramount significance. Current methodologies exhibit the ability to preserve local geometric structures, yet fall short in maintaining relationships between these geometric structures. In this paper, we endeavor to safeguard the overall, OBJect-level structures within images based on Global Similarity Prior, while concurrently mitigating distortion and ghosting artifacts with OBJ-GSP. Our approach leverages the Segment Anything Model to extract geometric structures with semantic information, enhancing the algorithm's ability to preserve objects in a manner that aligns more intuitively with human perception. We seek to identify spatial constraints that govern the relationships between various geometric boundaries. Recognizing that multiple geometric boundaries collectively define complete objects, we employ triangular meshes to safeguard not only individual geometric structures but also the overall shapes of objects within the images. Empirical evaluations across multiple image stitching datasets demonstrate that our method establishes a new state-of-the-art benchmark in image stitching. Our implementation and dataset is publicly available at https://github.com/RussRobin/OBJ-GSP .

Automated brain structure segmentation is important to many clinical quantitative analysis and diagnoses. In this work, we introduce MixNet, a 2D semantic-wise deep convolutional neural network to segment brain structure in multi-modality MRI images. The network is composed of our modified deep residual learning units. In the unit, we replace the traditional convolution layer with the dilated convolutional layer, which avoids the use of pooling layers and deconvolutional layers, reducing the number of network parameters. Final predictions are made by aggregating information from multiple scales and modalities. A pyramid pooling module is used to capture spatial information of the anatomical structures at the output end. In addition, we test three architectures (MixNetv1, MixNetv2 and MixNetv3) which fuse the modalities differently to see the effect on the results. Our network achieves the state-of-the-art performance. MixNetv2 was submitted to the MRBrainS challenge at MICCAI 2018 and won the 3rd place in the 3-label task. On the MRBrainS2018 dataset, which includes subjects with a variety of pathologies, the overall DSC (Dice Coefficient) of 84.7% (gray matter), 87.3% (white matter) and 83.4% (cerebrospinal fluid) were obtained with only 7 subjects as training data.

Large language models with retrieval-augmented generation encounter a pivotal challenge in intricate retrieval tasks, e.g., multi-hop question answering, which requires the model to navigate across multiple documents and generate comprehensive responses based on fragmented information. To tackle this challenge, we introduce a novel Knowledge Graph-based RAG framework with a hierarchical knowledge retriever, termed KG-Retriever. The retrieval indexing in KG-Retriever is constructed on a hierarchical index graph that consists of a knowledge graph layer and a collaborative document layer. The associative nature of graph structures is fully utilized to strengthen intra-document and inter-document connectivity, thereby fundamentally alleviating the information fragmentation problem and meanwhile improving the retrieval efficiency in cross-document retrieval of LLMs. With the coarse-grained collaborative information from neighboring documents and concise information from the knowledge graph, KG-Retriever achieves marked improvements on five public QA datasets, showing the effectiveness and efficiency of our proposed RAG framework.

Vector data is one of the two core data structures in geographic information science (GIS), essential for accurately storing and representing geospatial information. Shapefile, the most widely used vector data format, has become the industry standard supported by all major geographic information systems. However, processing this data typically requires specialized GIS knowledge and skills, creating a barrier for researchers from other fields and impeding interdisciplinary research in spatial data analysis. Moreover, while large language models (LLMs) have made significant advancements in natural language processing and task automation, they still face challenges in handling the complex spatial and topological relationships inherent in GIS vector data. To address these challenges, we propose ShapefileGPT, an innovative framework powered by LLMs, specifically designed to automate Shapefile tasks. ShapefileGPT utilizes a multi-agent architecture, in which the planner agent is responsible for task decomposition and supervision, while the worker agent executes the tasks. We developed a specialized function library for handling Shapefiles and provided comprehensive API documentation, enabling the worker agent to operate Shapefiles efficiently through function calling. For evaluation, we developed a benchmark dataset based on authoritative textbooks, encompassing tasks in categories such as geometric operations and spatial queries. ShapefileGPT achieved a task success rate of 95.24%, outperforming the GPT series models. In comparison to traditional LLMs, ShapefileGPT effectively handles complex vector data analysis tasks, overcoming the limitations of traditional LLMs in spatial analysis. This breakthrough opens new pathways for advancing automation and intelligence in the GIS field, with significant potential in interdisciplinary data analysis and application contexts.

Long document question answering (DocQA) aims to answer questions from long documents over 10k words. They usually contain content structures such as sections, sub-sections, and paragraph demarcations. However, the indexing methods of long documents remain under-explored, while existing systems generally employ fixed-length chunking. As they do not consider content structures, the resultant chunks can exclude vital information or include irrelevant content. Motivated by this, we propose the Multi-view Content-aware indexing (MC-indexing) for more effective long DocQA via (i) segment structured document into content chunks, and (ii) represent each content chunk in raw-text, keywords, and summary views. We highlight that MC-indexing requires neither training nor fine-tuning. Having plug-and-play capability, it can be seamlessly integrated with any retrievers to boost their performance. Besides, we propose a long DocQA dataset that includes not only question-answer pair, but also document structure and answer scope. When compared to state-of-art chunking schemes, MC-indexing has significantly increased the recall by 42.8%, 30.0%, 23.9%, and 16.3% via top k= 1.5, 3, 5, and 10 respectively. These improved scores are the average of 8 widely used retrievers (2 sparse and 6 dense) via extensive experiments.

Music is characterized by complex hierarchical structures. Developing a comprehensive model to capture these structures has been a significant challenge in the field of Music Information Retrieval (MIR). Prior research has mainly focused on addressing individual tasks for specific hierarchical levels, rather than providing a unified approach. In this paper, we introduce a versatile, all-in-one model that jointly performs beat and downbeat tracking as well as functional structure segmentation and labeling. The model leverages source-separated spectrograms as inputs and employs dilated neighborhood attentions to capture temporal long-term dependencies, along with non-dilated attentions for local instrumental dependencies. Consequently, the proposed model achieves state-of-the-art performance in all four tasks on the Harmonix Set while maintaining a relatively lower number of parameters compared to recent state-of-the-art models. Furthermore, our ablation study demonstrates that the concurrent learning of beats, downbeats, and segments can lead to enhanced performance, with each task mutually benefiting from the others.

In this paper, we propose a novel network, SVDFormer, to tackle two specific challenges in point cloud completion: understanding faithful global shapes from incomplete point clouds and generating high-accuracy local structures. Current methods either perceive shape patterns using only 3D coordinates or import extra images with well-calibrated intrinsic parameters to guide the geometry estimation of the missing parts. However, these approaches do not always fully leverage the cross-modal self-structures available for accurate and high-quality point cloud completion. To this end, we first design a Self-view Fusion Network that leverages multiple-view depth image information to observe incomplete self-shape and generate a compact global shape. To reveal highly detailed structures, we then introduce a refinement module, called Self-structure Dual-generator, in which we incorporate learned shape priors and geometric self-similarities for producing new points. By perceiving the incompleteness of each point, the dual-path design disentangles refinement strategies conditioned on the structural type of each point. SVDFormer absorbs the wisdom of self-structures, avoiding any additional paired information such as color images with precisely calibrated camera intrinsic parameters. Comprehensive experiments indicate that our method achieves state-of-the-art performance on widely-used benchmarks. Code will be available at https://github.com/czvvd/SVDFormer.

Markov categories are a novel framework to describe and treat problems in probability and information theory. In this work we combine the categorical formalism with the traditional quantitative notions of entropy, mutual information, and data processing inequalities. We show that several quantitative aspects of information theory can be captured by an enriched version of Markov categories, where the spaces of morphisms are equipped with a divergence or even a metric. As it is customary in information theory, mutual information can be defined as a measure of how far a joint source is from displaying independence of its components. More strikingly, Markov categories give a notion of determinism for sources and channels, and we can define entropy exactly by measuring how far a source or channel is from being deterministic. This recovers Shannon and R\'enyi entropies, as well as the Gini-Simpson index used in ecology to quantify diversity, and it can be used to give a conceptual definition of generalized entropy.

Most music source separation systems require large collections of isolated sources for training, which can be difficult to obtain. In this work, we use musical scores, which are comparatively easy to obtain, as a weak label for training a source separation system. In contrast with previous score-informed separation approaches, our system does not require isolated sources, and score is used only as a training target, not required for inference. Our model consists of a separator that outputs a time-frequency mask for each instrument, and a transcriptor that acts as a critic, providing both temporal and frequency supervision to guide the learning of the separator. A harmonic mask constraint is introduced as another way of leveraging score information during training, and we propose two novel adversarial losses for additional fine-tuning of both the transcriptor and the separator. Results demonstrate that using score information outperforms temporal weak-labels, and adversarial structures lead to further improvements in both separation and transcription performance.

To learn intrinsic low-dimensional structures from high-dimensional data that most discriminate between classes, we propose the principle of Maximal Coding Rate Reduction (MCR^2), an information-theoretic measure that maximizes the coding rate difference between the whole dataset and the sum of each individual class. We clarify its relationships with most existing frameworks such as cross-entropy, information bottleneck, information gain, contractive and contrastive learning, and provide theoretical guarantees for learning diverse and discriminative features. The coding rate can be accurately computed from finite samples of degenerate subspace-like distributions and can learn intrinsic representations in supervised, self-supervised, and unsupervised settings in a unified manner. Empirically, the representations learned using this principle alone are significantly more robust to label corruptions in classification than those using cross-entropy, and can lead to state-of-the-art results in clustering mixed data from self-learned invariant features.

Most existing zero-shot learning approaches exploit transfer learning via an intermediate-level semantic representation shared between an annotated auxiliary dataset and a target dataset with different classes and no annotation. A projection from a low-level feature space to the semantic representation space is learned from the auxiliary dataset and is applied without adaptation to the target dataset. In this paper we identify two inherent limitations with these approaches. First, due to having disjoint and potentially unrelated classes, the projection functions learned from the auxiliary dataset/domain are biased when applied directly to the target dataset/domain. We call this problem the projection domain shift problem and propose a novel framework, transductive multi-view embedding, to solve it. The second limitation is the prototype sparsity problem which refers to the fact that for each target class, only a single prototype is available for zero-shot learning given a semantic representation. To overcome this problem, a novel heterogeneous multi-view hypergraph label propagation method is formulated for zero-shot learning in the transductive embedding space. It effectively exploits the complementary information offered by different semantic representations and takes advantage of the manifold structures of multiple representation spaces in a coherent manner. We demonstrate through extensive experiments that the proposed approach (1) rectifies the projection shift between the auxiliary and target domains, (2) exploits the complementarity of multiple semantic representations, (3) significantly outperforms existing methods for both zero-shot and N-shot recognition on three image and video benchmark datasets, and (4) enables novel cross-view annotation tasks.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Methods to evaluate Large Language Model (LLM) responses and detect inconsistencies, also known as hallucinations, with respect to the provided knowledge, are becoming increasingly important for LLM applications. Current metrics fall short in their ability to provide explainable decisions, systematically check all pieces of information in the response, and are often too computationally expensive to be used in practice. We present GraphEval: a hallucination evaluation framework based on representing information in Knowledge Graph (KG) structures. Our method identifies the specific triples in the KG that are prone to hallucinations and hence provides more insight into where in the response a hallucination has occurred, if at all, than previous methods. Furthermore, using our approach in conjunction with state-of-the-art natural language inference (NLI) models leads to an improvement in balanced accuracy on various hallucination benchmarks, compared to using the raw NLI models. Lastly, we explore the use of GraphEval for hallucination correction by leveraging the structure of the KG, a method we name GraphCorrect, and demonstrate that the majority of hallucinations can indeed be rectified.

Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein engineering. Existing methods either construct a supervised learning scheme on small-scale datasets with manually processed physicochemical properties, or blindly apply pre-trained protein language models to extract amino acid interaction information. The scale and quality of available training datasets leave significant room for improvement in terms of accuracy and generalization. To address these research gaps, we propose \sol, a novel deep learning method that combines pre-training and fine-tuning schemes for protein solubility prediction. ProtSolM integrates information from multiple dimensions, including physicochemical properties, amino acid sequences, and protein backbone structures. Our model is trained using \data, the largest solubility dataset that we have constructed. PDBSol includes over 60,000 protein sequences and structures. We provide a comprehensive leaderboard of existing statistical learning and deep learning methods on independent datasets with computational and experimental labels. ProtSolM achieved state-of-the-art performance across various evaluation metrics, demonstrating its potential to significantly advance the accuracy of protein solubility prediction.

Retrieval-Augmented Generation (RAG) systems have revolutionized information retrieval and question answering, but traditional text-based chunking methods struggle with complex document structures, multi-page tables, embedded figures, and contextual dependencies across page boundaries. We present a novel multimodal document chunking approach that leverages Large Multimodal Models (LMMs) to process PDF documents in batches while maintaining semantic coherence and structural integrity. Our method processes documents in configurable page batches with cross-batch context preservation, enabling accurate handling of tables spanning multiple pages, embedded visual elements, and procedural content. We evaluate our approach on a curated dataset of PDF documents with manually crafted queries, demonstrating improvements in chunk quality and downstream RAG performance. Our vision-guided approach achieves better accuracy compared to traditional vanilla RAG systems, with qualitative analysis showing superior preservation of document structure and semantic coherence.

Graph Retrieval Augmented Generation (GraphRAG) effectively enhances external knowledge integration capabilities by explicitly modeling knowledge relationships, thereby improving the factual accuracy and generation quality of Large Language Models (LLMs) in specialized domains. However, existing methods suffer from two inherent limitations: 1) Inefficient Information Aggregation: They rely on a single agent and fixed iterative patterns, making it difficult to adaptively capture multi-level textual, structural, and degree information within graph data. 2) Rigid Reasoning Mechanism: They employ preset reasoning schemes, which cannot dynamically adjust reasoning depth nor achieve precise semantic correction. To overcome these limitations, we propose Graph Counselor, an GraphRAG method based on multi-agent collaboration. This method uses the Adaptive Graph Information Extraction Module (AGIEM), where Planning, Thought, and Execution Agents work together to precisely model complex graph structures and dynamically adjust information extraction strategies, addressing the challenges of multi-level dependency modeling and adaptive reasoning depth. Additionally, the Self-Reflection with Multiple Perspectives (SR) module improves the accuracy and semantic consistency of reasoning results through self-reflection and backward reasoning mechanisms. Experiments demonstrate that Graph Counselor outperforms existing methods in multiple graph reasoning tasks, exhibiting higher reasoning accuracy and generalization ability. Our code is available at https://github.com/gjq100/Graph-Counselor.git.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Large Language Models (LLMs) (e.g., ChatGPT) have shown impressive performance in code generation. LLMs take prompts as inputs, and Chain-of-Thought (CoT) prompting is the state-of-the-art prompting technique. CoT prompting asks LLMs first to generate CoTs (i.e., intermediate natural language reasoning steps) and then output the code. However, CoT prompting is designed for natural language generation and has low accuracy in code generation. In this paper, we propose Structured CoTs (SCoTs) and present a novel prompting technique for code generation, named SCoT prompting. Our motivation is source code contains rich structural information and any code can be composed of three program structures (i.e., sequence, branch, and loop structures). Intuitively, structured intermediate reasoning steps make for structured source code. Thus, we ask LLMs to use program structures to build CoTs, obtaining SCoTs. Then, LLMs generate the final code based on SCoTs. Compared to CoT prompting, SCoT prompting explicitly constrains LLMs to think about how to solve requirements from the view of source code and further the performance of LLMs in code generation. We apply SCoT prompting to two LLMs (i.e., ChatGPT and Codex) and evaluate it on three benchmarks (i.e., HumanEval, MBPP, and MBCPP). (1) SCoT prompting outperforms the state-of-the-art baseline - CoT prompting by up to 13.79% in Pass@1. (2) Human evaluation shows human developers prefer programs from SCoT prompting. (3) SCoT prompting is robust to examples and achieves substantial improvements.

Medical vision-language pre-training shows great potential in learning representative features from massive paired radiographs and reports. However, in computed tomography (CT) scans, the distribution of lesions which contain intricate structures is characterized by spatial sparsity. Besides, the complex and implicit relationships between different pathological descriptions in each sentence of the report and their corresponding sub-regions in radiographs pose additional challenges. In this paper, we propose a Similarity-Driven Cross-Granularity Pre-training (SimCroP) framework on chest CTs, which combines similarity-driven alignment and cross-granularity fusion to improve radiograph interpretation. We first leverage multi-modal masked modeling to optimize the encoder for understanding precise low-level semantics from radiographs. Then, similarity-driven alignment is designed to pre-train the encoder to adaptively select and align the correct patches corresponding to each sentence in reports. The cross-granularity fusion module integrates multimodal information across instance level and word-patch level, which helps the model better capture key pathology structures in sparse radiographs, resulting in improved performance for multi-scale downstream tasks. SimCroP is pre-trained on a large-scale paired CT-reports dataset and validated on image classification and segmentation tasks across five public datasets. Experimental results demonstrate that SimCroP outperforms both cutting-edge medical self-supervised learning methods and medical vision-language pre-training methods. Codes and models are available at https://github.com/ToniChopp/SimCroP.

Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical organization inherent in protein structures. We introduce Topotein, a comprehensive framework that applies topological deep learning to PRL through the novel Protein Combinatorial Complex (PCC) and Topology-Complete Perceptron Network (TCPNet). Our PCC represents proteins at multiple hierarchical levels -- from residues to secondary structures to complete proteins -- while preserving geometric information at each level. TCPNet employs SE(3)-equivariant message passing across these hierarchical structures, enabling more effective capture of multi-scale structural patterns. Through extensive experiments on four PRL tasks, TCPNet consistently outperforms state-of-the-art geometric graph neural networks. Our approach demonstrates particular strength in tasks such as fold classification which require understanding of secondary structure arrangements, validating the importance of hierarchical topological features for protein analysis.

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making them well-suited for modeling complex molecular systems. In this work, we introduce EquiHGNN, an Equivariant HyperGraph Neural Network framework that integrates symmetry-aware representations to improve molecular modeling. By enforcing the equivariance under relevant transformation groups, our approach preserves geometric and topological properties, leading to more robust and physically meaningful representations. We examine a range of equivariant architectures and demonstrate that integrating symmetry constraints leads to notable performance gains on large-scale molecular datasets. Experiments on both small and large molecules show that high-order interactions offer limited benefits for small molecules but consistently outperform 2D graphs on larger ones. Adding geometric features to these high-order structures further improves the performance, emphasizing the value of spatial information in molecular learning. Our source code is available at https://github.com/HySonLab/EquiHGNN/

The convolutional neural network-based methods have become more and more popular for medical image segmentation due to their outstanding performance. However, they struggle with capturing long-range dependencies, which are essential for accurately modeling global contextual correlations. Thanks to the ability to model long-range dependencies by expanding the receptive field, the transformer-based methods have gained prominence. Inspired by this, we propose an advanced 2D feature extraction method by combining the convolutional neural network and Transformer architectures. More specifically, we introduce a parallelized encoder structure, where one branch uses ResNet to extract local information from images, while the other branch uses Transformer to extract global information. Furthermore, we integrate pyramid structures into the Transformer to extract global information at varying resolutions, especially in intensive prediction tasks. To efficiently utilize the different information in the parallelized encoder at the decoder stage, we use a channel attention module to merge the features of the encoder and propagate them through skip connections and bottlenecks. Intensive numerical experiments are performed on both aortic vessel tree, cardiac, and multi-organ datasets. By comparing with state-of-the-art medical image segmentation methods, our method is shown with better segmentation accuracy, especially on small organs. The code is publicly available on https://github.com/HongkunSun/ParaTransCNN.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

Different medical imaging modalities capture diagnostic information at varying spatial resolutions, from coarse global patterns to fine-grained localized structures. However, most existing vision-language frameworks in the medical domain apply a uniform strategy for local feature extraction, overlooking the modality-specific demands. In this work, we present MedMoE, a modular and extensible vision-language processing framework that dynamically adapts visual representation based on the diagnostic context. MedMoE incorporates a Mixture-of-Experts (MoE) module conditioned on the report type, which routes multi-scale image features through specialized expert branches trained to capture modality-specific visual semantics. These experts operate over feature pyramids derived from a Swin Transformer backbone, enabling spatially adaptive attention to clinically relevant regions. This framework produces localized visual representations aligned with textual descriptions, without requiring modality-specific supervision at inference. Empirical results on diverse medical benchmarks demonstrate that MedMoE improves alignment and retrieval performance across imaging modalities, underscoring the value of modality-specialized visual representations in clinical vision-language systems.

Due to the presence of the natural gap between Knowledge Graph (KG) structures and the natural language, the effective integration of holistic structural information of KGs with Large Language Models (LLMs) has emerged as a significant question. To this end, we propose a two-stage framework to learn and apply quantized codes for each entity, aiming for the seamless integration of KGs with LLMs. Firstly, a self-supervised quantized representation (SSQR) method is proposed to compress both KG structural and semantic knowledge into discrete codes (\ie, tokens) that align the format of language sentences. We further design KG instruction-following data by viewing these learned codes as features to directly input to LLMs, thereby achieving seamless integration. The experiment results demonstrate that SSQR outperforms existing unsupervised quantized methods, producing more distinguishable codes. Further, the fine-tuned LLaMA2 and LLaMA3.1 also have superior performance on KG link prediction and triple classification tasks, utilizing only 16 tokens per entity instead of thousands in conventional prompting methods.

Large Language Models (LLMs) equipped with web search capabilities have demonstrated impressive potential for deep research tasks. However, current approaches predominantly rely on either manually engineered prompts (prompt engineering-based) with brittle performance or reinforcement learning within controlled Retrieval-Augmented Generation (RAG) environments (RAG-based) that fail to capture the complexities of real-world interaction. In this paper, we introduce DeepResearcher, the first comprehensive framework for end-to-end training of LLM-based deep research agents through scaling reinforcement learning (RL) in real-world environments with authentic web search interactions. Unlike RAG-based approaches that assume all necessary information exists within a fixed corpus, our method trains agents to navigate the noisy, unstructured, and dynamic nature of the open web. We implement a specialized multi-agent architecture where browsing agents extract relevant information from various webpage structures and overcoming significant technical challenges. Extensive experiments on open-domain research tasks demonstrate that DeepResearcher achieves substantial improvements of up to 28.9 points over prompt engineering-based baselines and up to 7.2 points over RAG-based RL agents. Our qualitative analysis reveals emergent cognitive behaviors from end-to-end RL training, including the ability to formulate plans, cross-validate information from multiple sources, engage in self-reflection to redirect research, and maintain honesty when unable to find definitive answers. Our results highlight that end-to-end training in real-world web environments is not merely an implementation detail but a fundamental requirement for developing robust research capabilities aligned with real-world applications. We release DeepResearcher at https://github.com/GAIR-NLP/DeepResearcher.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

Significant advancements have been made in developing parametric models for digital humans, with various approaches concentrating on parts such as the human body, hand, or face. Nevertheless, connectors such as the neck have been overlooked in these models, with rich anatomical priors often unutilized. In this paper, we introduce HACK (Head-And-neCK), a novel parametric model for constructing the head and cervical region of digital humans. Our model seeks to disentangle the full spectrum of neck and larynx motions, facial expressions, and appearance variations, providing personalized and anatomically consistent controls, particularly for the neck regions. To build our HACK model, we acquire a comprehensive multi-modal dataset of the head and neck under various facial expressions. We employ a 3D ultrasound imaging scheme to extract the inner biomechanical structures, namely the precise 3D rotation information of the seven vertebrae of the cervical spine. We then adopt a multi-view photometric approach to capture the geometry and physically-based textures of diverse subjects, who exhibit a diverse range of static expressions as well as sequential head-and-neck movements. Using the multi-modal dataset, we train the parametric HACK model by separating the 3D head and neck depiction into various shape, pose, expression, and larynx blendshapes from the neutral expression and the rest skeletal pose. We adopt an anatomically-consistent skeletal design for the cervical region, and the expression is linked to facial action units for artist-friendly controls. HACK addresses the head and neck as a unified entity, offering more accurate and expressive controls, with a new level of realism, particularly for the neck regions. This approach has significant benefits for numerous applications and enables inter-correlation analysis between head and neck for fine-grained motion synthesis and transfer.

In most cases, word embeddings are learned only from raw tokens or in some cases, lemmas. This includes pre-trained language models like BERT. To investigate on the potential of capturing deeper relations between lexical items and structures and to filter out redundant information, we propose to preserve the morphological, syntactic and other types of linguistic information by combining them with the raw tokens or lemmas. This means, for example, including parts-of-speech or dependency information within the used lexical features. The word embeddings can then be trained on the combinations instead of just raw tokens. It is also possible to later apply this method to the pre-training of huge language models and possibly enhance their performance. This would aid in tackling problems which are more sophisticated from the point of view of linguistic representation, such as detection of cyberbullying.

Relational reasoning lies at the core of many NLP tasks, drawing on complementary signals from text and graphs. While prior research has investigated how to leverage this dual complementarity, a detailed and systematic understanding of text-graph interplay and its effect on hybrid models remains underexplored. We take an analysis-driven approach to investigate text-graph representation complementarity via a unified architecture that supports knowledge co-distillation (CoD). We explore five tasks involving relational reasoning that differ in how text and graph structures encode the information needed to solve that task. By tracking how these dual representations evolve during training, we uncover interpretable patterns of alignment and divergence, and provide insights into when and why their integration is beneficial.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Recently, end-to-end models have been widely used in automatic speech recognition (ASR) systems. Two of the most representative approaches are connectionist temporal classification (CTC) and attention-based encoder-decoder (AED) models. Autoregressive transformers, variants of AED, adopt an autoregressive mechanism for token generation and thus are relatively slow during inference. In this paper, we present a comprehensive study of a CTC Alignment-based Single-Step Non-Autoregressive Transformer (CASS-NAT) for end-to-end ASR. In CASS-NAT, word embeddings in the autoregressive transformer (AT) are substituted with token-level acoustic embeddings (TAE) that are extracted from encoder outputs with the acoustical boundary information offered by the CTC alignment. TAE can be obtained in parallel, resulting in a parallel generation of output tokens. During training, Viterbi-alignment is used for TAE generation, and multiple training strategies are further explored to improve the word error rate (WER) performance. During inference, an error-based alignment sampling method is investigated in depth to reduce the alignment mismatch in the training and testing processes. Experimental results show that the CASS-NAT has a WER that is close to AT on various ASR tasks, while providing a ~24x inference speedup. With and without self-supervised learning, we achieve new state-of-the-art results for non-autoregressive models on several datasets. We also analyze the behavior of the CASS-NAT decoder to explain why it can perform similarly to AT. We find that TAEs have similar functionality to word embeddings for grammatical structures, which might indicate the possibility of learning some semantic information from TAEs without a language model.

As lung cancer evolves, the presence of enlarged and potentially malignant lymph nodes must be assessed to properly estimate disease progression and select the best treatment strategy. Following the clinical guidelines, estimation of short-axis diameter and mediastinum station are paramount for correct diagnosis. A method for accurate and automatic segmentation is hence decisive for quantitatively describing lymph nodes. In this study, the use of 3D convolutional neural networks, either through slab-wise schemes or the leveraging of downsampled entire volumes, is investigated. Furthermore, the potential impact from simple ensemble strategies is considered. As lymph nodes have similar attenuation values to nearby anatomical structures, we suggest using the knowledge of other organs as prior information to guide the segmentation task. To assess the segmentation and instance detection performances, a 5-fold cross-validation strategy was followed over a dataset of 120 contrast-enhanced CT volumes. For the 1178 lymph nodes with a short-axis diameter geq10 mm, our best performing approach reached a patient-wise recall of 92%, a false positive per patient ratio of 5, and a segmentation overlap of 80.5%. The method performs similarly well across all stations. Fusing a slab-wise and a full volume approach within an ensemble scheme generated the best performances. The anatomical priors guiding strategy is promising, yet a larger set than four organs appears needed to generate an optimal benefit. A larger dataset is also mandatory, given the wide range of expressions a lymph node can exhibit (i.e., shape, location, and attenuation), and contrast uptake variations.

Entity relationship classification remains a challenging task in information extraction, especially in scenarios with limited labeled data and complex relational structures. In this study, we conduct a comparative analysis of three distinct AI agent architectures designed to perform relation classification using large language models (LLMs). The agentic architectures explored include (1) reflective self-evaluation, (2) hierarchical task decomposition, and (3) a novel multi-agent dynamic example generation mechanism, each leveraging different modes of reasoning and prompt adaptation. In particular, our dynamic example generation approach introduces real-time cooperative and adversarial prompting. We systematically compare their performance across multiple domains and model backends. Our experiments demonstrate that multi-agent coordination consistently outperforms standard few-shot prompting and approaches the performance of fine-tuned models. These findings offer practical guidance for the design of modular, generalizable LLM-based systems for structured relation extraction. The source codes and dataset are available at https://github.com/maryambrj/ALIEN.git.

Post-merger gravitational wave echoes provide a unique opportunity to probe the near-horizon structure of astrophysical black holes, that may be modified due to non-perturbative quantum gravity phenomena. However, since the waveform is subject to large theoretical uncertainties, it is necessary to develop model-agnostic search methods for detecting echoes from observational data. A promising strategy is to identify the characteristic quasinormal modes (QNMs) associated with echoes, {\it in frequency space}, which complements existing searches of quasiperiodic pulses in time. In this study, we build upon our previous work targeting these modes by incorporating relative phase information to optimize the Bayesian search algorithm. Using a new phase-marginalized likelihood, the performance can be significantly improved for well-resolved QNMs. This enables an efficient model-agnostic search for QNMs of different shapes by using a simple search template. To demonstrate the robustness of the search algorithm, we construct four complementary benchmarks for the echo waveform that span a diverse range of different theoretical possibilities for the near-horizon structure. We then validate our Bayesian search algorithms by injecting the benchmark models into different realizations of Gaussian noise. Using two types of phase-marginalized likelihoods, we find that the search algorithm can efficiently detect the corresponding QNMs. Therefore, our search strategy provides a concrete Bayesian and model-agnostic approach to "quantum black hole seismology".

Digital Surface Models (DSM) offer a wealth of height information for understanding the Earth's surface as well as monitoring the existence or change in natural and man-made structures. Classical height estimation requires multi-view geospatial imagery or LiDAR point clouds which can be expensive to acquire. Single-view height estimation using neural network based models shows promise however it can struggle with reconstructing high resolution features. The latest advancements in diffusion models for high resolution image synthesis and editing have yet to be utilized for remote sensing imagery, particularly height estimation. Our approach involves training a generative diffusion model to learn the joint distribution of optical and DSM images across both domains as a Markov chain. This is accomplished by minimizing a denoising score matching objective while being conditioned on the source image to generate realistic high resolution 3D surfaces. In this paper we experiment with conditional denoising diffusion probabilistic models (DDPM) for height estimation from a single remotely sensed image and show promising results on the Vaihingen benchmark dataset.

In this paper we propose a new approach to detect clusters in undirected graphs with attributed vertices. We incorporate structural and attribute similarities between the vertices in an augmented graph by creating additional vertices and edges as proposed in [1, 2]. The augmented graph is then embedded in a Euclidean space associated to its Laplacian and we cluster vertices via a modified K-means algorithm, using a new vector-valued distance in the embedding space. Main novelty of our method, which can be classified as an early fusion method, i.e., a method in which additional information on vertices are fused to the structure information before applying clustering, is the interpretation of attributes as new realizations of graph vertices, which can be dealt with as coordinate vectors in a related Euclidean space. This allows us to extend a scalable generalized spectral clustering procedure which substitutes graph Laplacian eigenvectors with some vectors, named algebraically smooth vectors, obtained by a linear-time complexity Algebraic MultiGrid (AMG) method. We discuss the performance of our proposed clustering method by comparison with recent literature approaches and public available results. Extensive experiments on different types of synthetic datasets and real-world attributed graphs show that our new algorithm, embedding attributes information in the clustering, outperforms structure-only-based methods, when the attributed network has an ambiguous structure. Furthermore, our new method largely outperforms the method which originally proposed the graph augmentation, showing that our embedding strategy and vector-valued distance are very effective in taking advantages from the augmented-graph representation.

Semantic parsing of large-scale 3D point clouds is an important research topic in computer vision and remote sensing fields. Most existing approaches utilize hand-crafted features for each modality independently and combine them in a heuristic manner. They often fail to consider the consistency and complementary information among features adequately, which makes them difficult to capture high-level semantic structures. The features learned by most of the current deep learning methods can obtain high-quality image classification results. However, these methods are hard to be applied to recognize 3D point clouds due to unorganized distribution and various point density of data. In this paper, we propose a 3DCNN-DQN-RNN method which fuses the 3D convolutional neural network (CNN), Deep Q-Network (DQN) and Residual recurrent neural network (RNN) for an efficient semantic parsing of large-scale 3D point clouds. In our method, an eye window under control of the 3D CNN and DQN can localize and segment the points of the object class efficiently. The 3D CNN and Residual RNN further extract robust and discriminative features of the points in the eye window, and thus greatly enhance the parsing accuracy of large-scale point clouds. Our method provides an automatic process that maps the raw data to the classification results. It also integrates object localization, segmentation and classification into one framework. Experimental results demonstrate that the proposed method outperforms the state-of-the-art point cloud classification methods.

Retrieval-Augmented Generation (RAG) has been shown to improve knowledge capabilities and alleviate the hallucination problem of LLMs. The Web is a major source of external knowledge used in RAG systems, and many commercial systems such as ChatGPT and Perplexity have used Web search engines as their major retrieval systems. Typically, such RAG systems retrieve search results, download HTML sources of the results, and then extract plain texts from the HTML sources. Plain text documents or chunks are fed into the LLMs to augment the generation. However, much of the structural and semantic information inherent in HTML, such as headings and table structures, is lost during this plain-text-based RAG process. To alleviate this problem, we propose HtmlRAG, which uses HTML instead of plain text as the format of retrieved knowledge in RAG. We believe HTML is better than plain text in modeling knowledge in external documents, and most LLMs possess robust capacities to understand HTML. However, utilizing HTML presents new challenges. HTML contains additional content such as tags, JavaScript, and CSS specifications, which bring extra input tokens and noise to the RAG system. To address this issue, we propose HTML cleaning, compression, and pruning strategies, to shorten the HTML while minimizing the loss of information. Specifically, we design a two-step block-tree-based pruning method that prunes useless HTML blocks and keeps only the relevant part of the HTML. Experiments on six QA datasets confirm the superiority of using HTML in RAG systems.

In Unsupervised Domain Adaptive Semantic Segmentation (UDA-SS), a model is trained on labeled source domain data (e.g., synthetic images) and adapted to an unlabeled target domain (e.g., real-world images) without access to target annotations. Existing UDA-SS methods often struggle to balance fine-grained local details with global contextual information, leading to segmentation errors in complex regions. To address this, we introduce the Adaptive Feature Refinement (AFR) module, which enhances segmentation accuracy by refining highresolution features using semantic priors from low-resolution logits. AFR also integrates high-frequency components, which capture fine-grained structures and provide crucial boundary information, improving object delineation. Additionally, AFR adaptively balances local and global information through uncertaintydriven attention, reducing misclassifications. Its lightweight design allows seamless integration into HRDA-based UDA methods, leading to state-of-the-art segmentation performance. Our approach improves existing UDA-SS methods by 1.05% mIoU on GTA V --> Cityscapes and 1.04% mIoU on Synthia-->Cityscapes. The implementation of our framework is available at: https://github.com/Masrur02/AFRDA

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

The goal of decompilation is to convert compiled low-level code (e.g., assembly code) back into high-level programming languages, enabling analysis in scenarios where source code is unavailable. This task supports various reverse engineering applications, such as vulnerability identification, malware analysis, and legacy software migration. The end-to-end decompile method based on large langauge models (LLMs) reduces reliance on additional tools and minimizes manual intervention due to its inherent properties. However, previous end-to-end methods often lose critical information necessary for reconstructing control flow structures and variables when processing binary files, making it challenging to accurately recover the program's logic. To address these issues, we propose the ReF Decompile method, which incorporates the following innovations: (1) The Relabelling strategy replaces jump target addresses with labels, preserving control flow clarity. (2) The Function Call strategy infers variable types and retrieves missing variable information from binary files. Experimental results on the Humaneval-Decompile Benchmark demonstrate that ReF Decompile surpasses comparable baselines and achieves state-of-the-art (SOTA) performance of 61.43%.

Monocular depth estimation aims to infer a dense depth map from a single image, which is a fundamental and prevalent task in computer vision. Many previous works have shown impressive depth estimation results through carefully designed network structures, but they usually ignore the planar information and therefore perform poorly in low-texture areas of indoor scenes. In this paper, we propose Plane2Depth, which adaptively utilizes plane information to improve depth prediction within a hierarchical framework. Specifically, in the proposed plane guided depth generator (PGDG), we design a set of plane queries as prototypes to softly model planes in the scene and predict per-pixel plane coefficients. Then the predicted plane coefficients can be converted into metric depth values with the pinhole camera model. In the proposed adaptive plane query aggregation (APGA) module, we introduce a novel feature interaction approach to improve the aggregation of multi-scale plane features in a top-down manner. Extensive experiments show that our method can achieve outstanding performance, especially in low-texture or repetitive areas. Furthermore, under the same backbone network, our method outperforms the state-of-the-art methods on the NYU-Depth-v2 dataset, achieves competitive results with state-of-the-art methods KITTI dataset and can be generalized to unseen scenes effectively.

Transformer-based methods have exhibited remarkable potential in single image super-resolution (SISR) by effectively extracting long-range dependencies. However, most of the current research in this area has prioritized the design of transformer blocks to capture global information, while overlooking the importance of incorporating high-frequency priors, which we believe could be beneficial. In our study, we conducted a series of experiments and found that transformer structures are more adept at capturing low-frequency information, but have limited capacity in constructing high-frequency representations when compared to their convolutional counterparts. Our proposed solution, the cross-refinement adaptive feature modulation transformer (CRAFT), integrates the strengths of both convolutional and transformer structures. It comprises three key components: the high-frequency enhancement residual block (HFERB) for extracting high-frequency information, the shift rectangle window attention block (SRWAB) for capturing global information, and the hybrid fusion block (HFB) for refining the global representation. Our experiments on multiple datasets demonstrate that CRAFT outperforms state-of-the-art methods by up to 0.29dB while using fewer parameters. The source code will be made available at: https://github.com/AVC2-UESTC/CRAFT-SR.git.