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Feb 2

Visual Data-Type Understanding does not emerge from Scaling Vision-Language Models

Recent advances in the development of vision-language models (VLMs) are yielding remarkable success in recognizing visual semantic content, including impressive instances of compositional image understanding. Here, we introduce the novel task of Visual Data-Type Identification, a basic perceptual skill with implications for data curation (e.g., noisy data-removal from large datasets, domain-specific retrieval) and autonomous vision (e.g., distinguishing changing weather conditions from camera lens staining). We develop two datasets consisting of animal images altered across a diverse set of 27 visual data-types, spanning four broad categories. An extensive zero-shot evaluation of 39 VLMs, ranging from 100M to 80B parameters, shows a nuanced performance landscape. While VLMs are reasonably good at identifying certain stylistic data-types, such as cartoons and sketches, they struggle with simpler data-types arising from basic manipulations like image rotations or additive noise. Our findings reveal that (i) model scaling alone yields marginal gains for contrastively-trained models like CLIP, and (ii) there is a pronounced drop in performance for the largest auto-regressively trained VLMs like OpenFlamingo. This finding points to a blind spot in current frontier VLMs: they excel in recognizing semantic content but fail to acquire an understanding of visual data-types through scaling. By analyzing the pre-training distributions of these models and incorporating data-type information into the captions during fine-tuning, we achieve a significant enhancement in performance. By exploring this previously uncharted task, we aim to set the stage for further advancing VLMs to equip them with visual data-type understanding. Code and datasets are released at https://github.com/bethgelab/DataTypeIdentification.

  • 4 authors
·
Oct 12, 2023

MultiModN- Multimodal, Multi-Task, Interpretable Modular Networks

Predicting multiple real-world tasks in a single model often requires a particularly diverse feature space. Multimodal (MM) models aim to extract the synergistic predictive potential of multiple data types to create a shared feature space with aligned semantic meaning across inputs of drastically varying sizes (i.e. images, text, sound). Most current MM architectures fuse these representations in parallel, which not only limits their interpretability but also creates a dependency on modality availability. We present MultiModN, a multimodal, modular network that fuses latent representations in a sequence of any number, combination, or type of modality while providing granular real-time predictive feedback on any number or combination of predictive tasks. MultiModN's composable pipeline is interpretable-by-design, as well as innately multi-task and robust to the fundamental issue of biased missingness. We perform four experiments on several benchmark MM datasets across 10 real-world tasks (predicting medical diagnoses, academic performance, and weather), and show that MultiModN's sequential MM fusion does not compromise performance compared with a baseline of parallel fusion. By simulating the challenging bias of missing not-at-random (MNAR), this work shows that, contrary to MultiModN, parallel fusion baselines erroneously learn MNAR and suffer catastrophic failure when faced with different patterns of MNAR at inference. To the best of our knowledge, this is the first inherently MNAR-resistant approach to MM modeling. In conclusion, MultiModN provides granular insights, robustness, and flexibility without compromising performance.

  • 8 authors
·
Sep 25, 2023

Intra- & Extra-Source Exemplar-Based Style Synthesis for Improved Domain Generalization

The generalization with respect to domain shifts, as they frequently appear in applications such as autonomous driving, is one of the remaining big challenges for deep learning models. Therefore, we propose an exemplar-based style synthesis pipeline to improve domain generalization in semantic segmentation. Our method is based on a novel masked noise encoder for StyleGAN2 inversion. The model learns to faithfully reconstruct the image, preserving its semantic layout through noise prediction. Using the proposed masked noise encoder to randomize style and content combinations in the training set, i.e., intra-source style augmentation (ISSA) effectively increases the diversity of training data and reduces spurious correlation. As a result, we achieve up to 12.4% mIoU improvements on driving-scene semantic segmentation under different types of data shifts, i.e., changing geographic locations, adverse weather conditions, and day to night. ISSA is model-agnostic and straightforwardly applicable with CNNs and Transformers. It is also complementary to other domain generalization techniques, e.g., it improves the recent state-of-the-art solution RobustNet by 3% mIoU in Cityscapes to Dark Z\"urich. In addition, we demonstrate the strong plug-n-play ability of the proposed style synthesis pipeline, which is readily usable for extra-source exemplars e.g., web-crawled images, without any retraining or fine-tuning. Moreover, we study a new use case to indicate neural network's generalization capability by building a stylized proxy validation set. This application has significant practical sense for selecting models to be deployed in the open-world environment. Our code is available at https://github.com/boschresearch/ISSA.

  • 4 authors
·
Jul 2, 2023

Semantic2D: Enabling Semantic Scene Understanding with 2D Lidar Alone

This article presents a complete semantic scene understanding workflow using only a single 2D lidar. This fills the gap in 2D lidar semantic segmentation, thereby enabling the rethinking and enhancement of existing 2D lidar-based algorithms for application in various mobile robot tasks. It introduces the first publicly available 2D lidar semantic segmentation dataset and the first fine-grained semantic segmentation algorithm specifically designed for 2D lidar sensors on autonomous mobile robots. To annotate this dataset, we propose a novel semi-automatic semantic labeling framework that requires minimal human effort and provides point-level semantic annotations. The data was collected by three different types of 2D lidar sensors across twelve indoor environments, featuring a range of common indoor objects. Furthermore, the proposed semantic segmentation algorithm fully exploits raw lidar information -- position, range, intensity, and incident angle -- to deliver stochastic, point-wise semantic segmentation. We present a series of semantic occupancy grid mapping experiments and demonstrate two semantically-aware navigation control policies based on 2D lidar. These results demonstrate that the proposed semantic 2D lidar dataset, semi-automatic labeling framework, and segmentation algorithm are effective and can enhance different components of the robotic navigation pipeline. Multimedia resources are available at: https://youtu.be/P1Hsvj6WUSY.

  • 5 authors
·
Sep 15, 2024

Autoregressive Semantic Visual Reconstruction Helps VLMs Understand Better

Typical large vision-language models (LVLMs) apply autoregressive supervision solely to textual sequences, without fully incorporating the visual modality into the learning process. This results in three key limitations: (1) an inability to utilize images without accompanying captions, (2) the risk that captions omit critical visual details, and (3) the challenge that certain vision-centric content cannot be adequately conveyed through text. As a result, current LVLMs often prioritize vision-to-language alignment while potentially overlooking fine-grained visual information. While some prior works have explored autoregressive image generation, effectively leveraging autoregressive visual supervision to enhance image understanding remains an open challenge. In this paper, we introduce Autoregressive Semantic Visual Reconstruction (ASVR), which enables joint learning of visual and textual modalities within a unified autoregressive framework. We show that autoregressively reconstructing the raw visual appearance of images does not enhance and may even impair multimodal understanding. In contrast, autoregressively reconstructing the semantic representation of images consistently improves comprehension. Notably, we find that even when models are given continuous image features as input, they can effectively reconstruct discrete semantic tokens, resulting in stable and consistent improvements across a wide range of multimodal understanding benchmarks. Our approach delivers significant performance gains across varying data scales (556k-2M) and types of LLM bacbones. Specifically, ASVR improves LLaVA-1.5 by 5% in average scores across 14 multimodal benchmarks. The code is available at https://github.com/AlenjandroWang/ASVR.

  • 7 authors
·
Jun 10, 2025 2

Enhancing Paraphrase Type Generation: The Impact of DPO and RLHF Evaluated with Human-Ranked Data

Paraphrasing re-expresses meaning to enhance applications like text simplification, machine translation, and question-answering. Specific paraphrase types facilitate accurate semantic analysis and robust language models. However, existing paraphrase-type generation methods often misalign with human preferences due to reliance on automated metrics and limited human-annotated training data, obscuring crucial aspects of semantic fidelity and linguistic transformations. This study addresses this gap by leveraging a human-ranked paraphrase-type dataset and integrating Direct Preference Optimization (DPO) to align model outputs directly with human judgments. DPO-based training increases paraphrase-type generation accuracy by 3 percentage points over a supervised baseline and raises human preference ratings by 7 percentage points. A newly created human-annotated dataset supports more rigorous future evaluations. Additionally, a paraphrase-type detection model achieves F1 scores of 0.91 for addition/deletion, 0.78 for same polarity substitution, and 0.70 for punctuation changes. These findings demonstrate that preference data and DPO training produce more reliable, semantically accurate paraphrases, enabling downstream applications such as improved summarization and more robust question-answering. The PTD model surpasses automated metrics and provides a more reliable framework for evaluating paraphrase quality, advancing paraphrase-type research toward richer, user-aligned language generation and establishing a stronger foundation for future evaluations grounded in human-centric criteria.

  • 1 authors
·
May 28, 2025

VDC: Versatile Data Cleanser for Detecting Dirty Samples via Visual-Linguistic Inconsistency

The role of data in building AI systems has recently been emphasized by the emerging concept of data-centric AI. Unfortunately, in the real-world, datasets may contain dirty samples, such as poisoned samples from backdoor attack, noisy labels in crowdsourcing, and even hybrids of them. The presence of such dirty samples makes the DNNs vunerable and unreliable.Hence, it is critical to detect dirty samples to improve the quality and realiability of dataset. Existing detectors only focus on detecting poisoned samples or noisy labels, that are often prone to weak generalization when dealing with dirty samples from other domains.In this paper, we find a commonality of various dirty samples is visual-linguistic inconsistency between images and associated labels. To capture the semantic inconsistency between modalities, we propose versatile data cleanser (VDC) leveraging the surpassing capabilities of multimodal large language models (MLLM) in cross-modal alignment and reasoning.It consists of three consecutive modules: the visual question generation module to generate insightful questions about the image; the visual question answering module to acquire the semantics of the visual content by answering the questions with MLLM; followed by the visual answer evaluation module to evaluate the inconsistency.Extensive experiments demonstrate its superior performance and generalization to various categories and types of dirty samples.

  • 5 authors
·
Sep 28, 2023

ColorMAE: Exploring data-independent masking strategies in Masked AutoEncoders

Masked AutoEncoders (MAE) have emerged as a robust self-supervised framework, offering remarkable performance across a wide range of downstream tasks. To increase the difficulty of the pretext task and learn richer visual representations, existing works have focused on replacing standard random masking with more sophisticated strategies, such as adversarial-guided and teacher-guided masking. However, these strategies depend on the input data thus commonly increasing the model complexity and requiring additional calculations to generate the mask patterns. This raises the question: Can we enhance MAE performance beyond random masking without relying on input data or incurring additional computational costs? In this work, we introduce a simple yet effective data-independent method, termed ColorMAE, which generates different binary mask patterns by filtering random noise. Drawing inspiration from color noise in image processing, we explore four types of filters to yield mask patterns with different spatial and semantic priors. ColorMAE requires no additional learnable parameters or computational overhead in the network, yet it significantly enhances the learned representations. We provide a comprehensive empirical evaluation, demonstrating our strategy's superiority in downstream tasks compared to random masking. Notably, we report an improvement of 2.72 in mIoU in semantic segmentation tasks relative to baseline MAE implementations.

  • 3 authors
·
Jul 17, 2024 2

ValUES: A Framework for Systematic Validation of Uncertainty Estimation in Semantic Segmentation

Uncertainty estimation is an essential and heavily-studied component for the reliable application of semantic segmentation methods. While various studies exist claiming methodological advances on the one hand, and successful application on the other hand, the field is currently hampered by a gap between theory and practice leaving fundamental questions unanswered: Can data-related and model-related uncertainty really be separated in practice? Which components of an uncertainty method are essential for real-world performance? Which uncertainty method works well for which application? In this work, we link this research gap to a lack of systematic and comprehensive evaluation of uncertainty methods. Specifically, we identify three key pitfalls in current literature and present an evaluation framework that bridges the research gap by providing 1) a controlled environment for studying data ambiguities as well as distribution shifts, 2) systematic ablations of relevant method components, and 3) test-beds for the five predominant uncertainty applications: OoD-detection, active learning, failure detection, calibration, and ambiguity modeling. Empirical results on simulated as well as real-world data demonstrate how the proposed framework is able to answer the predominant questions in the field revealing for instance that 1) separation of uncertainty types works on simulated data but does not necessarily translate to real-world data, 2) aggregation of scores is a crucial but currently neglected component of uncertainty methods, 3) While ensembles are performing most robustly across the different downstream tasks and settings, test-time augmentation often constitutes a light-weight alternative. Code is at: https://github.com/IML-DKFZ/values

  • 5 authors
·
Jan 16, 2024

Familiarity: Better Evaluation of Zero-Shot Named Entity Recognition by Quantifying Label Shifts in Synthetic Training Data

Zero-shot named entity recognition (NER) is the task of detecting named entities of specific types (such as 'Person' or 'Medicine') without any training examples. Current research increasingly relies on large synthetic datasets, automatically generated to cover tens of thousands of distinct entity types, to train zero-shot NER models. However, in this paper, we find that these synthetic datasets often contain entity types that are semantically highly similar to (or even the same as) those in standard evaluation benchmarks. Because of this overlap, we argue that reported F1 scores for zero-shot NER overestimate the true capabilities of these approaches. Further, we argue that current evaluation setups provide an incomplete picture of zero-shot abilities since they do not quantify the label shift (i.e., the similarity of labels) between training and evaluation datasets. To address these issues, we propose Familiarity, a novel metric that captures both the semantic similarity between entity types in training and evaluation, as well as their frequency in the training data, to provide an estimate of label shift. It allows researchers to contextualize reported zero-shot NER scores when using custom synthetic training datasets. Further, it enables researchers to generate evaluation setups of various transfer difficulties for fine-grained analysis of zero-shot NER.

  • 6 authors
·
Dec 13, 2024

Heterogeneous Directed Hypergraph Neural Network over abstract syntax tree (AST) for Code Classification

Code classification is a difficult issue in program understanding and automatic coding. Due to the elusive syntax and complicated semantics in programs, most existing studies use techniques based on abstract syntax tree (AST) and graph neural network (GNN) to create code representations for code classification. These techniques utilize the structure and semantic information of the code, but they only take into account pairwise associations and neglect the high-order correlations that already exist between nodes in the AST, which may result in the loss of code structural information. On the other hand, while a general hypergraph can encode high-order data correlations, it is homogeneous and undirected which will result in a lack of semantic and structural information such as node types, edge types, and directions between child nodes and parent nodes when modeling AST. In this study, we propose to represent AST as a heterogeneous directed hypergraph (HDHG) and process the graph by heterogeneous directed hypergraph neural network (HDHGN) for code classification. Our method improves code understanding and can represent high-order data correlations beyond paired interactions. We assess heterogeneous directed hypergraph neural network (HDHGN) on public datasets of Python and Java programs. Our method outperforms previous AST-based and GNN-based methods, which demonstrates the capability of our model.

  • 3 authors
·
May 7, 2023

Infusing clinical knowledge into tokenisers for language models

This study introduces a novel knowledge enhanced tokenisation mechanism, K-Tokeniser, for clinical text processing. Technically, at initialisation stage, K-Tokeniser populates global representations of tokens based on semantic types of domain concepts (such as drugs or diseases) from either a domain ontology like Unified Medical Language System or the training data of the task related corpus. At training or inference stage, sentence level localised context will be utilised for choosing the optimal global token representation to realise the semantic-based tokenisation. To avoid pretraining using the new tokeniser, an embedding initialisation approach is proposed to generate representations for new tokens. Using three transformer-based language models, a comprehensive set of experiments are conducted on four real-world datasets for evaluating K-Tokeniser in a wide range of clinical text analytics tasks including clinical concept and relation extraction, automated clinical coding, clinical phenotype identification, and clinical research article classification. Overall, our models demonstrate consistent improvements over their counterparts in all tasks. In particular, substantial improvements are observed in the automated clinical coding task with 13\% increase on Micro F_1 score. Furthermore, K-Tokeniser also shows significant capacities in facilitating quicker converge of language models. Specifically, using K-Tokeniser, the language models would only require 50\% of the training data to achieve the best performance of the baseline tokeniser using all training data in the concept extraction task and less than 20\% of the data for the automated coding task. It is worth mentioning that all these improvements require no pre-training process, making the approach generalisable.

  • 10 authors
·
Jun 20, 2024

OCR Hinders RAG: Evaluating the Cascading Impact of OCR on Retrieval-Augmented Generation

Retrieval-augmented Generation (RAG) enhances Large Language Models (LLMs) by integrating external knowledge to reduce hallucinations and incorporate up-to-date information without retraining. As an essential part of RAG, external knowledge bases are commonly built by extracting structured data from unstructured PDF documents using Optical Character Recognition (OCR). However, given the imperfect prediction of OCR and the inherent non-uniform representation of structured data, knowledge bases inevitably contain various OCR noises. In this paper, we introduce OHRBench, the first benchmark for understanding the cascading impact of OCR on RAG systems. OHRBench includes 350 carefully selected unstructured PDF documents from six real-world RAG application domains, along with Q&As derived from multimodal elements in documents, challenging existing OCR solutions used for RAG To better understand OCR's impact on RAG systems, we identify two primary types of OCR noise: Semantic Noise and Formatting Noise and apply perturbation to generate a set of structured data with varying degrees of each OCR noise. Using OHRBench, we first conduct a comprehensive evaluation of current OCR solutions and reveal that none is competent for constructing high-quality knowledge bases for RAG systems. We then systematically evaluate the impact of these two noise types and demonstrate the vulnerability of RAG systems. Furthermore, we discuss the potential of employing Vision-Language Models (VLMs) without OCR in RAG systems. Code: https://github.com/opendatalab/OHR-Bench

  • 9 authors
·
Dec 3, 2024 2

JanusVLN: Decoupling Semantics and Spatiality with Dual Implicit Memory for Vision-Language Navigation

Vision-and-Language Navigation requires an embodied agent to navigate through unseen environments, guided by natural language instructions and a continuous video stream. Recent advances in VLN have been driven by the powerful semantic understanding of Multimodal Large Language Models. However, these methods typically rely on explicit semantic memory, such as building textual cognitive maps or storing historical visual frames. This type of method suffers from spatial information loss, computational redundancy, and memory bloat, which impede efficient navigation. Inspired by the implicit scene representation in human navigation, analogous to the left brain's semantic understanding and the right brain's spatial cognition, we propose JanusVLN, a novel VLN framework featuring a dual implicit neural memory that models spatial-geometric and visual-semantic memory as separate, compact, and fixed-size neural representations. This framework first extends the MLLM to incorporate 3D prior knowledge from the spatial-geometric encoder, thereby enhancing the spatial reasoning capabilities of models based solely on RGB input. Then, the historical key-value caches from the spatial-geometric and visual-semantic encoders are constructed into a dual implicit memory. By retaining only the KVs of tokens in the initial and sliding window, redundant computation is avoided, enabling efficient incremental updates. Extensive experiments demonstrate that JanusVLN outperforms over 20 recent methods to achieve SOTA performance. For example, the success rate improves by 10.5-35.5 compared to methods using multiple data types as input and by 3.6-10.8 compared to methods using more RGB training data. This indicates that the proposed dual implicit neural memory, as a novel paradigm, explores promising new directions for future VLN research. Ours project page: https://miv-xjtu.github.io/JanusVLN.github.io/.

  • 9 authors
·
Sep 26, 2025 1

CodeSearchNet Challenge: Evaluating the State of Semantic Code Search

Semantic code search is the task of retrieving relevant code given a natural language query. While related to other information retrieval tasks, it requires bridging the gap between the language used in code (often abbreviated and highly technical) and natural language more suitable to describe vague concepts and ideas. To enable evaluation of progress on code search, we are releasing the CodeSearchNet Corpus and are presenting the CodeSearchNet Challenge, which consists of 99 natural language queries with about 4k expert relevance annotations of likely results from CodeSearchNet Corpus. The corpus contains about 6 million functions from open-source code spanning six programming languages (Go, Java, JavaScript, PHP, Python, and Ruby). The CodeSearchNet Corpus also contains automatically generated query-like natural language for 2 million functions, obtained from mechanically scraping and preprocessing associated function documentation. In this article, we describe the methodology used to obtain the corpus and expert labels, as well as a number of simple baseline solutions for the task. We hope that CodeSearchNet Challenge encourages researchers and practitioners to study this interesting task further and will host a competition and leaderboard to track the progress on the challenge. We are also keen on extending CodeSearchNet Challenge to more queries and programming languages in the future.

  • 5 authors
·
Sep 20, 2019

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

  • 17 authors
·
Oct 8, 2024

Towards Contextual Sensitive Data Detection

The emergence of open data portals necessitates more attention to protecting sensitive data before datasets get published and exchanged. While an abundance of methods for suppressing sensitive data exist, the conceptualization of sensitive data and methods to detect it, focus particularly on personal data that, if disclosed, may be harmful or violate privacy. We observe the need for refining and broadening our definitions of sensitive data, and argue that the sensitivity of data depends on its context. Based on this definition, we introduce two mechanisms for contextual sensitive data detection that consider the broader context of a dataset at hand. First, we introduce type contextualization, which first detects the semantic type of particular data values, then considers the overall context of the data values within the dataset or document. Second, we introduce domain contextualization which determines sensitivity of a given dataset in the broader context based on the retrieval of relevant rules from documents that specify data sensitivity (e.g., data topic and geographic origin). Experiments with these mechanisms, assisted by large language models (LLMs), confirm that: 1) type-contextualization significantly reduces the number of false positives for type-based sensitive data detection and reaches a recall of 94% compared to 63% with commercial tools, and 2) domain-contextualization leveraging sensitivity rule retrieval is effective for context-grounded sensitive data detection in non-standard data domains such as humanitarian datasets. Evaluation with humanitarian data experts also reveals that context-grounded LLM explanations provide useful guidance in manual data auditing processes, improving consistency. We open-source mechanisms and annotated datasets for contextual sensitive data detection at https://github.com/trl-lab/sensitive-data-detection.

  • 2 authors
·
Dec 2, 2025

Demo of the Linguistic Field Data Management and Analysis System -- LiFE

In the proposed demo, we will present a new software - Linguistic Field Data Management and Analysis System - LiFE (https://github.com/kmi-linguistics/life) - an open-source, web-based linguistic data management and analysis application that allows for systematic storage, management, sharing and usage of linguistic data collected from the field. The application allows users to store lexical items, sentences, paragraphs, audio-visual content with rich glossing / annotation; generate interactive and print dictionaries; and also train and use natural language processing tools and models for various purposes using this data. Since its a web-based application, it also allows for seamless collaboration among multiple persons and sharing the data, models, etc with each other. The system uses the Python-based Flask framework and MongoDB in the backend and HTML, CSS and Javascript at the frontend. The interface allows creation of multiple projects that could be shared with the other users. At the backend, the application stores the data in RDF format so as to allow its release as Linked Data over the web using semantic web technologies - as of now it makes use of the OntoLex-Lemon for storing the lexical data and Ligt for storing the interlinear glossed text and then internally linking it to the other linked lexicons and databases such as DBpedia and WordNet. Furthermore it provides support for training the NLP systems using scikit-learn and HuggingFace Transformers libraries as well as make use of any model trained using these libraries - while the user interface itself provides limited options for tuning the system, an externally-trained model could be easily incorporated within the application; similarly the dataset itself could be easily exported into a standard machine-readable format like JSON or CSV that could be consumed by other programs and pipelines.

  • 4 authors
·
Mar 21, 2022

Matching Table Metadata with Business Glossaries Using Large Language Models

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

  • 6 authors
·
Sep 7, 2023 2

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

  • 2 authors
·
Apr 19, 2024

ModelTables: A Corpus of Tables about Models

We present ModelTables, a benchmark of tables in Model Lakes that captures the structured semantics of performance and configuration tables often overlooked by text only retrieval. The corpus is built from Hugging Face model cards, GitHub READMEs, and referenced papers, linking each table to its surrounding model and publication context. Compared with open data lake tables, model tables are smaller yet exhibit denser inter table relationships, reflecting tightly coupled model and benchmark evolution. The current release covers over 60K models and 90K tables. To evaluate model and table relatedness, we construct a multi source ground truth using three complementary signals: (1) paper citation links, (2) explicit model card links and inheritance, and (3) shared training datasets. We present one extensive empirical use case for the benchmark which is table search. We compare canonical Data Lake search operators (unionable, joinable, keyword) and Information Retrieval baselines (dense, sparse, hybrid retrieval) on this benchmark. Union based semantic table retrieval attains 54.8 % P@1 overall (54.6 % on citation, 31.3 % on inheritance, 30.6 % on shared dataset signals); table based dense retrieval reaches 66.5 % P@1, and metadata hybrid retrieval achieves 54.1 %. This evaluation indicates clear room for developing better table search methods. By releasing ModelTables and its creation protocol, we provide the first large scale benchmark of structured data describing AI model. Our use case of table discovery in Model Lakes, provides intuition and evidence for developing more accurate semantic retrieval, structured comparison, and principled organization of structured model knowledge. Source code, data, and other artifacts have been made available at https://github.com/RJMillerLab/ModelTables.

From Commands to Prompts: LLM-based Semantic File System for AIOS

Large language models (LLMs) have demonstrated significant potential in the development of intelligent applications and systems such as LLM-based agents and agent operating systems (AIOS). However, when these applications and systems interact with the underlying file system, the file system still remains the traditional paradigm: reliant on manual navigation through precise commands. This paradigm poses a bottleneck to the usability of these systems as users are required to navigate complex folder hierarchies and remember cryptic file names. To address this limitation, we propose an LLM-based semantic file system ( LSFS ) for prompt-driven file management. Unlike conventional approaches, LSFS incorporates LLMs to enable users or agents to interact with files through natural language prompts, facilitating semantic file management. At the macro-level, we develop a comprehensive API set to achieve semantic file management functionalities, such as semantic file retrieval, file update monitoring and summarization, and semantic file rollback). At the micro-level, we store files by constructing semantic indexes for them, design and implement syscalls of different semantic operations (e.g., CRUD, group by, join) powered by vector database. Our experiments show that LSFS offers significant improvements over traditional file systems in terms of user convenience, the diversity of supported functions, and the accuracy and efficiency of file operations. Additionally, with the integration of LLM, our system enables more intelligent file management tasks, such as content summarization and version comparison, further enhancing its capabilities.

  • 12 authors
·
Sep 23, 2024 1

Can LLMs Clean Up Your Mess? A Survey of Application-Ready Data Preparation with LLMs

Data preparation aims to denoise raw datasets, uncover cross-dataset relationships, and extract valuable insights from them, which is essential for a wide range of data-centric applications. Driven by (i) rising demands for application-ready data (e.g., for analytics, visualization, decision-making), (ii) increasingly powerful LLM techniques, and (iii) the emergence of infrastructures that facilitate flexible agent construction (e.g., using Databricks Unity Catalog), LLM-enhanced methods are rapidly becoming a transformative and potentially dominant paradigm for data preparation. By investigating hundreds of recent literature works, this paper presents a systematic review of this evolving landscape, focusing on the use of LLM techniques to prepare data for diverse downstream tasks. First, we characterize the fundamental paradigm shift, from rule-based, model-specific pipelines to prompt-driven, context-aware, and agentic preparation workflows. Next, we introduce a task-centric taxonomy that organizes the field into three major tasks: data cleaning (e.g., standardization, error processing, imputation), data integration (e.g., entity matching, schema matching), and data enrichment (e.g., data annotation, profiling). For each task, we survey representative techniques, and highlight their respective strengths (e.g., improved generalization, semantic understanding) and limitations (e.g., the prohibitive cost of scaling LLMs, persistent hallucinations even in advanced agents, the mismatch between advanced methods and weak evaluation). Moreover, we analyze commonly used datasets and evaluation metrics (the empirical part). Finally, we discuss open research challenges and outline a forward-looking roadmap that emphasizes scalable LLM-data systems, principled designs for reliable agentic workflows, and robust evaluation protocols.

Semantic Operators: A Declarative Model for Rich, AI-based Data Processing

The semantic capabilities of large language models (LLMs) have the potential to enable rich analytics and reasoning over vast knowledge corpora. Unfortunately, existing systems either empirically optimize expensive LLM-powered operations with no performance guarantees, or serve a limited set of row-wise LLM operations, providing limited robustness, expressiveness and usability. We introduce semantic operators, the first formalism for declarative and general-purpose AI-based transformations based on natural language specifications (e.g., filtering, sorting, joining or aggregating records using natural language criteria). Each operator opens a rich space for execution plans, similar to relational operators. Our model specifies the expected behavior of each operator with a high-quality gold algorithm, and we develop an optimization framework that reduces cost, while providing accuracy guarantees with respect to a gold algorithm. Using this approach, we propose several novel optimizations to accelerate semantic filtering, joining, group-by and top-k operations by up to 1,000times. We implement semantic operators in the LOTUS system and demonstrate LOTUS' effectiveness on real, bulk-semantic processing applications, including fact-checking, biomedical multi-label classification, search, and topic analysis. We show that the semantic operator model is expressive, capturing state-of-the-art AI pipelines in a few operator calls, and making it easy to express new pipelines that match or exceed quality of recent LLM-based analytic systems by up to 170%, while offering accuracy guarantees. Overall, LOTUS programs match or exceed the accuracy of state-of-the-art AI pipelines for each task while running up to 3.6times faster than the highest-quality baselines. LOTUS is publicly available at https://github.com/lotus-data/lotus.

  • 7 authors
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Jul 16, 2024

Leveraging Large Language Models for Generating Research Topic Ontologies: A Multi-Disciplinary Study

Ontologies and taxonomies of research fields are critical for managing and organising scientific knowledge, as they facilitate efficient classification, dissemination and retrieval of information. However, the creation and maintenance of such ontologies are expensive and time-consuming tasks, usually requiring the coordinated effort of multiple domain experts. Consequently, ontologies in this space often exhibit uneven coverage across different disciplines, limited inter-domain connectivity, and infrequent updating cycles. In this study, we investigate the capability of several large language models to identify semantic relationships among research topics within three academic domains: biomedicine, physics, and engineering. The models were evaluated under three distinct conditions: zero-shot prompting, chain-of-thought prompting, and fine-tuning on existing ontologies. Additionally, we assessed the cross-domain transferability of fine-tuned models by measuring their performance when trained in one domain and subsequently applied to a different one. To support this analysis, we introduce PEM-Rel-8K, a novel dataset consisting of over 8,000 relationships extracted from the most widely adopted taxonomies in the three disciplines considered in this study: MeSH, PhySH, and IEEE. Our experiments demonstrate that fine-tuning LLMs on PEM-Rel-8K yields excellent performance across all disciplines.

  • 4 authors
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Aug 28, 2025

Table Foundation Models: on knowledge pre-training for tabular learning

Table foundation models bring high hopes to data science: pre-trained on tabular data to embark knowledge or priors, they should facilitate downstream tasks on tables. One specific challenge is that of data semantics: numerical entries take their meaning from context, e.g., column name. Pre-trained neural networks that jointly model column names and table entries have recently boosted prediction accuracy. While these models outline the promises of world knowledge to interpret table values, they lack the convenience of popular foundation models in text or vision. Indeed, they must be fine-tuned to bring benefits, come with sizeable computation costs, and cannot easily be reused or combined with other architectures. Here we introduce TARTE, a foundation model that transforms tables to knowledge-enhanced vector representations using the string to capture semantics. Pre-trained on large relational data, TARTE yields representations that facilitate subsequent learning with little additional cost. These representations can be fine-tuned or combined with other learners, giving models that push the state-of-the-art prediction performance and improve the prediction/computation performance trade-off. Specialized to a task or a domain, TARTE gives domain-specific representations that facilitate further learning. Our study demonstrates an effective approach to knowledge pre-training for tabular learning.

  • 5 authors
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May 20, 2025

Deep Learning Driven Natural Languages Text to SQL Query Conversion: A Survey

With the future striving toward data-centric decision-making, seamless access to databases is of utmost importance. There is extensive research on creating an efficient text-to-sql (TEXT2SQL) model to access data from the database. Using a Natural language is one of the best interfaces that can bridge the gap between the data and results by accessing the database efficiently, especially for non-technical users. It will open the doors and create tremendous interest among users who are well versed in technical skills or not very skilled in query languages. Even if numerous deep learning-based algorithms are proposed or studied, there still is very challenging to have a generic model to solve the data query issues using natural language in a real-work scenario. The reason is the use of different datasets in different studies, which comes with its limitations and assumptions. At the same time, we do lack a thorough understanding of these proposed models and their limitations with the specific dataset it is trained on. In this paper, we try to present a holistic overview of 24 recent neural network models studied in the last couple of years, including their architectures involving convolutional neural networks, recurrent neural networks, pointer networks, reinforcement learning, generative models, etc. We also give an overview of the 11 datasets that are widely used to train the models for TEXT2SQL technologies. We also discuss the future application possibilities of TEXT2SQL technologies for seamless data queries.

  • 4 authors
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Aug 8, 2022

Beyond Nearest Neighbors: Semantic Compression and Graph-Augmented Retrieval for Enhanced Vector Search

Vector databases typically rely on approximate nearest neighbor (ANN) search to retrieve the top-k closest vectors to a query in embedding space. While effective, this approach often yields semantically redundant results, missing the diversity and contextual richness required by applications such as retrieval-augmented generation (RAG), multi-hop QA, and memory-augmented agents. We introduce a new retrieval paradigm: semantic compression, which aims to select a compact, representative set of vectors that captures the broader semantic structure around a query. We formalize this objective using principles from submodular optimization and information geometry, and show that it generalizes traditional top-k retrieval by prioritizing coverage and diversity. To operationalize this idea, we propose graph-augmented vector retrieval, which overlays semantic graphs (e.g., kNN or knowledge-based links) atop vector spaces to enable multi-hop, context-aware search. We theoretically analyze the limitations of proximity-based retrieval under high-dimensional concentration and highlight how graph structures can improve semantic coverage. Our work outlines a foundation for meaning-centric vector search systems, emphasizing hybrid indexing, diversity-aware querying, and structured semantic retrieval. We make our implementation publicly available to foster future research in this area.

  • 2 authors
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Jul 25, 2025

Semantic search for 100M+ galaxy images using AI-generated captions

Finding scientifically interesting phenomena through slow, manual labeling campaigns severely limits our ability to explore the billions of galaxy images produced by telescopes. In this work, we develop a pipeline to create a semantic search engine from completely unlabeled image data. Our method leverages Vision-Language Models (VLMs) to generate descriptions for galaxy images, then contrastively aligns a pre-trained multimodal astronomy foundation model with these embedded descriptions to produce searchable embeddings at scale. We find that current VLMs provide descriptions that are sufficiently informative to train a semantic search model that outperforms direct image similarity search. Our model, AION-Search, achieves state-of-the-art zero-shot performance on finding rare phenomena despite training on randomly selected images with no deliberate curation for rare cases. Furthermore, we introduce a VLM-based re-ranking method that nearly doubles the recall for our most challenging targets in the top-100 results. For the first time, AION-Search enables flexible semantic search scalable to 140 million galaxy images, enabling discovery from previously infeasible searches. More broadly, our work provides an approach for making large, unlabeled scientific image archives semantically searchable, expanding data exploration capabilities in fields from Earth observation to microscopy. The code, data, and app are publicly available at https://github.com/NolanKoblischke/AION-Search

  • 6 authors
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Dec 12, 2025

Heterogeneous LLM Methods for Ontology Learning (Few-Shot Prompting, Ensemble Typing, and Attention-Based Taxonomies)

We present a comprehensive system for addressing Tasks A, B, and C of the LLMs4OL 2025 challenge, which together span the full ontology construction pipeline: term extraction, typing, and taxonomy discovery. Our approach combines retrieval-augmented prompting, zero-shot classification, and attention-based graph modeling -- each tailored to the demands of the respective task. For Task A, we jointly extract domain-specific terms and their ontological types using a retrieval-augmented generation (RAG) pipeline. Training data was reformulated into a document to terms and types correspondence, while test-time inference leverages semantically similar training examples. This single-pass method requires no model finetuning and improves overall performance through lexical augmentation Task B, which involves assigning types to given terms, is handled via a dual strategy. In the few-shot setting (for domains with labeled training data), we reuse the RAG scheme with few-shot prompting. In the zero-shot setting (for previously unseen domains), we use a zero-shot classifier that combines cosine similarity scores from multiple embedding models using confidence-based weighting. In Task C, we model taxonomy discovery as graph inference. Using embeddings of type labels, we train a lightweight cross-attention layer to predict is-a relations by approximating a soft adjacency matrix. These modular, task-specific solutions enabled us to achieve top-ranking results in the official leaderboard across all three tasks. Taken together these strategies showcase the scalability, adaptability, and robustness of LLM-based architectures for ontology learning across heterogeneous domains. Code is available at: https://github.com/BelyaevaAlex/LLMs4OL-Challenge-Alexbek

  • 2 authors
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Aug 26, 2025

Under the Surface: Tracking the Artifactuality of LLM-Generated Data

This work delves into the expanding role of large language models (LLMs) in generating artificial data. LLMs are increasingly employed to create a variety of outputs, including annotations, preferences, instruction prompts, simulated dialogues, and free text. As these forms of LLM-generated data often intersect in their application, they exert mutual influence on each other and raise significant concerns about the quality and diversity of the artificial data incorporated into training cycles, leading to an artificial data ecosystem. To the best of our knowledge, this is the first study to aggregate various types of LLM-generated text data, from more tightly constrained data like "task labels" to more lightly constrained "free-form text". We then stress test the quality and implications of LLM-generated artificial data, comparing it with human data across various existing benchmarks. Despite artificial data's capability to match human performance, this paper reveals significant hidden disparities, especially in complex tasks where LLMs often miss the nuanced understanding of intrinsic human-generated content. This study critically examines diverse LLM-generated data and emphasizes the need for ethical practices in data creation and when using LLMs. It highlights the LLMs' shortcomings in replicating human traits and behaviors, underscoring the importance of addressing biases and artifacts produced in LLM-generated content for future research and development. All data and code are available on our project page.

  • 17 authors
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Jan 26, 2024

MLCPD: A Unified Multi-Language Code Parsing Dataset with Universal AST Schema

We introduce the MultiLang Code Parser Dataset (MLCPD), a large-scale, language-agnostic dataset unifying syntactic and structural representations of code across ten major programming languages. MLCPD contains over seven million parsed source files normalized under our proposed universal Abstract Syntax Tree (AST) schema, enabling consistent cross-language reasoning, structural learning, and multilingual software analysis. Unlike existing corpora that focus purely on token-level code or isolated parsers, MLCPD provides both hierarchical tree representations and rich metadata for every file, ensuring lossless syntactic coverage and structural uniformity. Each entry includes a normalized schema, language-level metadata, and abstracted node semantics stored in Parquet format for scalable retrieval. Empirical analyses reveal strong cross-language structural regularities-demonstrating that syntactic graphs from languages as diverse as Python, Java, and Go can be aligned under a shared schema. We release the dataset publicly on Hugging Face and the accompanying codebase on GitHub, which includes complete pipelines for dataset reproduction, grammar compilation, and a visualization tool for exploring the unified AST across languages. Together, these resources establish MLCPD as an open, reproducible foundation for future research in cross-language representation learning and program analysis.

  • 2 authors
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Oct 18, 2025

Valentine: Evaluating Matching Techniques for Dataset Discovery

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

  • 9 authors
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Oct 14, 2020