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Apr 13

Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor

High-quality, "rich" metadata are essential for making research data findable, interoperable, and reusable. The Center for Expanded Data Annotation and Retrieval (CEDAR) has long addressed this need by providing tools to design machine-actionable metadata templates that encode community standards in a computable form. To make these capabilities more accessible within real-world research workflows, we have developed the CEDAR Embeddable Editor (CEE)-a lightweight, interoperable Web Component that brings structured, standards-based metadata authoring directly into third-party platforms. The CEE dynamically renders metadata forms from machine-actionable templates and produces semantically rich metadata in JSON-LD format. It supports ontology-based value selection via the BioPortal ontology repository, and it includes external authority resolution for persistent identifiers such as ORCIDs for individuals and RORs for research organizations. Crucially, the CEE requires no custom user-interface development, allowing deployment across diverse platforms. The CEE has been successfully integrated into generalist scientific data repositories such as Dryad and the Open Science Framework, demonstrating its ability to support discipline-specific metadata creation. By supporting the embedding of metadata authoring within existing research environments, the CEE can facilitate the adoption of community standards and help improve metadata quality across scientific disciplines.

  • 6 authors
·
Jul 16, 2025

New Methods for Metadata Extraction from Scientific Literature

Within the past few decades we have witnessed digital revolution, which moved scholarly communication to electronic media and also resulted in a substantial increase in its volume. Nowadays keeping track with the latest scientific achievements poses a major challenge for the researchers. Scientific information overload is a severe problem that slows down scholarly communication and knowledge propagation across the academia. Modern research infrastructures facilitate studying scientific literature by providing intelligent search tools, proposing similar and related documents, visualizing citation and author networks, assessing the quality and impact of the articles, and so on. In order to provide such high quality services the system requires the access not only to the text content of stored documents, but also to their machine-readable metadata. Since in practice good quality metadata is not always available, there is a strong demand for a reliable automatic method of extracting machine-readable metadata directly from source documents. This research addresses these problems by proposing an automatic, accurate and flexible algorithm for extracting wide range of metadata directly from scientific articles in born-digital form. Extracted information includes basic document metadata, structured full text and bibliography section. Designed as a universal solution, proposed algorithm is able to handle a vast variety of publication layouts with high precision and thus is well-suited for analyzing heterogeneous document collections. This was achieved by employing supervised and unsupervised machine-learning algorithms trained on large, diverse datasets. The evaluation we conducted showed good performance of proposed metadata extraction algorithm. The comparison with other similar solutions also proved our algorithm performs better than competition for most metadata types.

  • 1 authors
·
Oct 27, 2017

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

MetaGen Blended RAG: Higher Accuracy for Domain-Specific Q&A Without Fine-Tuning

Despite the widespread exploration of Retrieval-Augmented Generation (RAG), its deployment in enterprises for domain-specific datasets remains limited due to poor answer accuracy. These corpora, often shielded behind firewalls in private enterprise knowledge bases, having complex, domain-specific terminology, rarely seen by LLMs during pre-training; exhibit significant semantic variability across domains (like networking, military, or legal, etc.), or even within a single domain like medicine, and thus result in poor context precision for RAG systems. Currently, in such situations, fine-tuning or RAG with fine-tuning is attempted, but these approaches are slow, expensive, and lack generalization for accuracy as the new domain-specific data emerges. We propose an approach for Enterprise Search that focuses on enhancing the retriever for a domain-specific corpus through hybrid query indexes and metadata enrichment. This 'MetaGen Blended RAG' method constructs a metadata generation pipeline using key concepts, topics, and acronyms, and then creates a metadata-enriched hybrid index with boosted search queries. This approach avoids overfitting and generalizes effectively across domains. On the PubMedQA benchmark for the biomedical domain, the proposed method achieves 82% retrieval accuracy and 77% RAG accuracy, surpassing all previous RAG accuracy results without fine-tuning and sets a new benchmark for zero-shot results while outperforming much larger models like GPT3.5. The results are even comparable to the best fine-tuned models on this dataset, and we further demonstrate the robustness and scalability of the approach by evaluating it on other Q&A datasets like SQuAD, NQ etc.

  • 3 authors
·
May 23, 2025

A Systematic Framework for Enterprise Knowledge Retrieval: Leveraging LLM-Generated Metadata to Enhance RAG Systems

In enterprise settings, efficiently retrieving relevant information from large and complex knowledge bases is essential for operational productivity and informed decision-making. This research presents a systematic framework for metadata enrichment using large language models (LLMs) to enhance document retrieval in Retrieval-Augmented Generation (RAG) systems. Our approach employs a comprehensive, structured pipeline that dynamically generates meaningful metadata for document segments, substantially improving their semantic representations and retrieval accuracy. Through extensive experiments, we compare three chunking strategies-semantic, recursive, and naive-and evaluate their effectiveness when combined with advanced embedding techniques. The results demonstrate that metadata-enriched approaches consistently outperform content-only baselines, with recursive chunking paired with TF-IDF weighted embeddings yielding an 82.5% precision rate compared to 73.3% for semantic content-only approaches. The naive chunking strategy with prefix-fusion achieved the highest Hit Rate@10 of 0.925. Our evaluation employs cross-encoder reranking for ground truth generation, enabling rigorous assessment via Hit Rate and Metadata Consistency metrics. These findings confirm that metadata enrichment enhances vector clustering quality while reducing retrieval latency, making it a key optimization for RAG systems across knowledge domains. This work offers practical insights for deploying high-performance, scalable document retrieval solutions in enterprise settings, demonstrating that metadata enrichment is a powerful approach for enhancing RAG effectiveness.

  • 5 authors
·
Dec 4, 2025

Biomed-Enriched: A Biomedical Dataset Enriched with LLMs for Pretraining and Extracting Rare and Hidden Content

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

  • 3 authors
·
Jun 25, 2025 1

Autoregressive Entity Retrieval

Entities are at the center of how we represent and aggregate knowledge. For instance, Encyclopedias such as Wikipedia are structured by entities (e.g., one per Wikipedia article). The ability to retrieve such entities given a query is fundamental for knowledge-intensive tasks such as entity linking and open-domain question answering. Current approaches can be understood as classifiers among atomic labels, one for each entity. Their weight vectors are dense entity representations produced by encoding entity meta information such as their descriptions. This approach has several shortcomings: (i) context and entity affinity is mainly captured through a vector dot product, potentially missing fine-grained interactions; (ii) a large memory footprint is needed to store dense representations when considering large entity sets; (iii) an appropriately hard set of negative data has to be subsampled at training time. In this work, we propose GENRE, the first system that retrieves entities by generating their unique names, left to right, token-by-token in an autoregressive fashion. This mitigates the aforementioned technical issues since: (i) the autoregressive formulation directly captures relations between context and entity name, effectively cross encoding both; (ii) the memory footprint is greatly reduced because the parameters of our encoder-decoder architecture scale with vocabulary size, not entity count; (iii) the softmax loss is computed without subsampling negative data. We experiment with more than 20 datasets on entity disambiguation, end-to-end entity linking and document retrieval tasks, achieving new state-of-the-art or very competitive results while using a tiny fraction of the memory footprint of competing systems. Finally, we demonstrate that new entities can be added by simply specifying their names. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

  • 4 authors
·
Oct 2, 2020

Infini-gram mini: Exact n-gram Search at the Internet Scale with FM-Index

Language models are trained mainly on massive text data from the Internet, and it becomes increasingly important to understand this data source. Exact-match search engines enable searching in large text corpora -- counting string appearances and retrieving the enclosing documents -- yet the high storage overhead hinders their application on Internet-scale data. We present Infini-gram mini, an efficient and scalable system that can make petabyte-level text corpora searchable. Based on the FM-index data structure (Ferragina and Manzini, 2000), which simultaneously indexes and compresses text, our system creates indexes with size only 44% of the corpus. Infini-gram mini greatly improves upon the best existing implementation of FM-index in terms of indexing speed (18times) and memory use during both indexing (3.2times reduction) and querying (down to a negligible amount). We index 46TB of Internet text in 50 days with a single 128-core CPU node (or 19 hours if using 75 such nodes). We show one important use case of Infini-gram mini in a large-scale analysis of benchmark contamination. We find several core LM evaluation benchmarks to be heavily contaminated in Internet crawls (up to 40% in SQuAD), which could lead to overestimating the capabilities of language models if trained on such data. We host a benchmark contamination bulletin to share the contamination rate of many core and community-contributed benchmarks. We also release a web interface and an API endpoint to serve general search queries on Infini-gram mini indexes.

  • 5 authors
·
Jun 13, 2025 3

All that structure matches does not glitter

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

  • 10 authors
·
Sep 15, 2025

BiblioPage: A Dataset of Scanned Title Pages for Bibliographic Metadata Extraction

Manual digitization of bibliographic metadata is time consuming and labor intensive, especially for historical and real-world archives with highly variable formatting across documents. Despite advances in machine learning, the absence of dedicated datasets for metadata extraction hinders automation. To address this gap, we introduce BiblioPage, a dataset of scanned title pages annotated with structured bibliographic metadata. The dataset consists of approximately 2,000 monograph title pages collected from 14 Czech libraries, spanning a wide range of publication periods, typographic styles, and layout structures. Each title page is annotated with 16 bibliographic attributes, including title, contributors, and publication metadata, along with precise positional information in the form of bounding boxes. To extract structured information from this dataset, we valuated object detection models such as YOLO and DETR combined with transformer-based OCR, achieving a maximum mAP of 52 and an F1 score of 59. Additionally, we assess the performance of various visual large language models, including LlamA 3.2-Vision and GPT-4o, with the best model reaching an F1 score of 67. BiblioPage serves as a real-world benchmark for bibliographic metadata extraction, contributing to document understanding, document question answering, and document information extraction. Dataset and evaluation scripts are availible at: https://github.com/DCGM/biblio-dataset

  • 4 authors
·
Mar 25, 2025 2

Fine Tuning LLM for Enterprise: Practical Guidelines and Recommendations

There is a compelling necessity from enterprises for fine tuning LLMs (Large Language Models) o get them trained on proprietary domain knowledge. The challenge is to imbibe the LLMs with domain specific knowledge using the most optimial resource and cost and in the best possible time. Many enterprises rely on RAG (Retrieval Augmented Generation) which does not need LLMs to be ine-tuned but they are limited by the quality of vector databases and their retrieval capabilities rather than the intrinsic capabilities of the LLMs themselves. In our current work we focus on fine tuning LLaMA, an open source LLM using proprietary documents and code from an enterprise repository and use the fine tuned models to evaluate the quality of responses. As part of this work, we aim to guide beginners on how to start with fine tuning an LLM for documentation and code by making educated guesses on size of GPU required and options that are available for formatting the data. We also propose pre processing recipes for both documentation and code to prepare dataset in different formats. The proposed methods of data preparation for document datasets are forming paragraph chunks, forming question and answer pairs and forming keyword and paragraph chunk pairs. For code dataset we propose forming summary and function pairs. Further, we qualitatively evaluate the results of the models for domain specific queries. Finally, we also propose practical guidelines and recommendations for fine tuning LLMs.

  • 4 authors
·
Mar 23, 2024

Dense Text Retrieval based on Pretrained Language Models: A Survey

Text retrieval is a long-standing research topic on information seeking, where a system is required to return relevant information resources to user's queries in natural language. From classic retrieval methods to learning-based ranking functions, the underlying retrieval models have been continually evolved with the ever-lasting technical innovation. To design effective retrieval models, a key point lies in how to learn the text representation and model the relevance matching. The recent success of pretrained language models (PLMs) sheds light on developing more capable text retrieval approaches by leveraging the excellent modeling capacity of PLMs. With powerful PLMs, we can effectively learn the representations of queries and texts in the latent representation space, and further construct the semantic matching function between the dense vectors for relevance modeling. Such a retrieval approach is referred to as dense retrieval, since it employs dense vectors (a.k.a., embeddings) to represent the texts. Considering the rapid progress on dense retrieval, in this survey, we systematically review the recent advances on PLM-based dense retrieval. Different from previous surveys on dense retrieval, we take a new perspective to organize the related work by four major aspects, including architecture, training, indexing and integration, and summarize the mainstream techniques for each aspect. We thoroughly survey the literature, and include 300+ related reference papers on dense retrieval. To support our survey, we create a website for providing useful resources, and release a code repertory and toolkit for implementing dense retrieval models. This survey aims to provide a comprehensive, practical reference focused on the major progress for dense text retrieval.

  • 4 authors
·
Nov 27, 2022

The Science Data Lake: A Unified Open Infrastructure Integrating 293 Million Papers Across Eight Scholarly Sources with Embedding-Based Ontology Alignment

Scholarly data are largely fragmented across siloed databases with divergent metadata and missing linkages among them. We present the Science Data Lake, a locally-deployable infrastructure built on DuckDB and simple Parquet files that unifies eight open sources - Semantic Scholar, OpenAlex, SciSciNet, Papers with Code, Retraction Watch, Reliance on Science, a preprint-to-published mapping, and Crossref - via DOI normalization while preserving source-level schemas. The resource comprises approximately 960GB of Parquet files spanning ~293 million uniquely identifiable papers across ~22 schemas and ~153 SQL views. An embedding-based ontology alignment using BGE-large sentence embeddings maps 4,516 OpenAlex topics to 13 scientific ontologies (~1.3 million terms), yielding 16,150 mappings covering 99.8% of topics (geq 0.65 threshold) with F1 = 0.77 at the recommended geq 0.85 operating point, outperforming TF-IDF, BM25, and Jaro-Winkler baselines on a 300-pair gold-standard evaluation. We validate through 10 automated checks, cross-source citation agreement analysis (pairwise Pearson r = 0.76 - 0.87), and stratified manual annotation. Four vignettes demonstrate cross-source analyses infeasible with any single database. The resource is open source, deployable on a single drive or queryable remotely via HuggingFace, and includes structured documentation suitable for large language model (LLM) based research agents.

  • 1 authors
·
Mar 3

An Automatic Approach for Generating Rich, Linked Geo-Metadata from Historical Map Images

Historical maps contain detailed geographic information difficult to find elsewhere covering long-periods of time (e.g., 125 years for the historical topographic maps in the US). However, these maps typically exist as scanned images without searchable metadata. Existing approaches making historical maps searchable rely on tedious manual work (including crowd-sourcing) to generate the metadata (e.g., geolocations and keywords). Optical character recognition (OCR) software could alleviate the required manual work, but the recognition results are individual words instead of location phrases (e.g., "Black" and "Mountain" vs. "Black Mountain"). This paper presents an end-to-end approach to address the real-world problem of finding and indexing historical map images. This approach automatically processes historical map images to extract their text content and generates a set of metadata that is linked to large external geospatial knowledge bases. The linked metadata in the RDF (Resource Description Framework) format support complex queries for finding and indexing historical maps, such as retrieving all historical maps covering mountain peaks higher than 1,000 meters in California. We have implemented the approach in a system called mapKurator. We have evaluated mapKurator using historical maps from several sources with various map styles, scales, and coverage. Our results show significant improvement over the state-of-the-art methods. The code has been made publicly available as modules of the Kartta Labs project at https://github.com/kartta-labs/Project.

  • 7 authors
·
Dec 2, 2021

Meta-Chunking: Learning Efficient Text Segmentation via Logical Perception

Retrieval-Augmented Generation (RAG), while serving as a viable complement to large language models (LLMs), often overlooks the crucial aspect of text chunking within its pipeline, which impacts the quality of knowledge-intensive tasks. This paper introduces the concept of Meta-Chunking, which refers to a granularity between sentences and paragraphs, consisting of a collection of sentences within a paragraph that have deep linguistic logical connections. To implement Meta-Chunking, we designed two strategies based on LLMs: Margin Sampling Chunking and Perplexity Chunking. The former employs LLMs to perform binary classification on whether consecutive sentences need to be segmented, making decisions based on the probability difference obtained from margin sampling. The latter precisely identifies text chunk boundaries by analyzing the characteristics of perplexity distribution. Additionally, considering the inherent complexity of different texts, we propose a strategy that combines Meta-Chunking with dynamic merging to achieve a balance between fine-grained and coarse-grained text chunking. Experiments conducted on eleven datasets demonstrate that Meta-Chunking can more efficiently improve the performance of single-hop and multi-hop question answering based on RAG. For instance, on the 2WikiMultihopQA dataset, it outperforms similarity chunking by 1.32 while only consuming 45.8% of the time. Our code is available at https://github.com/IAAR-Shanghai/Meta-Chunking.

  • 7 authors
·
Oct 16, 2024 4

DOM-LM: Learning Generalizable Representations for HTML Documents

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.

  • 5 authors
·
Jan 25, 2022

Retrieval Augmented Generation with Collaborative Filtering for Personalized Text Generation

Recently, the personalization of Large Language Models (LLMs) to generate content that aligns with individual user preferences has garnered widespread attention. Personalized Retrieval-Augmented Generation (RAG), which retrieves relevant documents from the user's history to reflect their preferences and enhance LLM generation, is one commonly used approach for personalization. However, existing personalized RAG methods do not consider that the histories of similar users can also assist in personalized generation for the current user, meaning that collaborative information between users can also benefit personalized generation. Inspired by the application of collaborative filtering in recommender systems, we propose a method called CFRAG, which adapts Collaborative Filtering to RAG for personalized text generation. However, this presents two challenges: (1)~how to incorporate collaborative information without explicit user similarity labels? (2)~how to retrieve documents that support personalized LLM generation? For Challenge 1, we use contrastive learning to train user embeddings to retrieve similar users and introduce collaborative information. For Challenge 2, we design a personalized retriever and reranker to retrieve the top-k documents from these users' histories. We take into account the user's preference during retrieval and reranking. Then we leverage feedback from the LLM to fine-tune the personalized retriever and reranker, enabling them to retrieve documents that meet the personalized generation needs of the LLM. Experimental results on the Language Model Personalization (LaMP) benchmark validate the effectiveness of CFRAG. Further analysis confirms the importance of incorporating collaborative information.

  • 7 authors
·
Apr 8, 2025

Metadata Conditioning Accelerates Language Model Pre-training

The vast diversity of styles, domains, and quality levels present in language model pre-training corpora is essential in developing general model capabilities, but efficiently learning and deploying the correct behaviors exemplified in each of these heterogeneous data sources is challenging. To address this, we propose a new method, termed Metadata Conditioning then Cooldown (MeCo), to incorporate additional learning cues during pre-training. MeCo first provides metadata (e.g., URLs like en.wikipedia.org) alongside the text during training and later uses a cooldown phase with only the standard text, thereby enabling the model to function normally even without metadata. MeCo significantly accelerates pre-training across different model scales (600M to 8B parameters) and training sources (C4, RefinedWeb, and DCLM). For instance, a 1.6B language model trained with MeCo matches the downstream task performance of standard pre-training while using 33% less data. Additionally, MeCo enables us to steer language models by conditioning the inference prompt on either real or fabricated metadata that encodes the desired properties of the output: for example, prepending wikipedia.org to reduce harmful generations or factquizmaster.com (fabricated) to improve common knowledge task performance. We also demonstrate that MeCo is compatible with different types of metadata, such as model-generated topics. MeCo is remarkably simple, adds no computational overhead, and demonstrates promise in producing more capable and steerable language models.

  • 6 authors
·
Jan 3, 2025

CoIR: A Comprehensive Benchmark for Code Information Retrieval Models

Despite the substantial success of Information Retrieval (IR) in various NLP tasks, most IR systems predominantly handle queries and corpora in natural language, neglecting the domain of code retrieval. Code retrieval is critically important yet remains under-explored, with existing methods and benchmarks inadequately representing the diversity of code in various domains and tasks. Addressing this gap, we present \name (Code Information Retrieval Benchmark), a robust and comprehensive benchmark specifically designed to assess code retrieval capabilities. \name comprises ten meticulously curated code datasets, spanning eight distinctive retrieval tasks across seven diverse domains. We first discuss the construction of \name and its diverse dataset composition. Further, we evaluate nine widely used retrieval models using \name, uncovering significant difficulties in performing code retrieval tasks even with state-of-the-art systems. To facilitate easy adoption and integration within existing research workflows, \name has been developed as a user-friendly Python framework, readily installable via pip. It shares same data schema as other popular benchmarks like MTEB and BEIR, enabling seamless cross-benchmark evaluations. Through \name, we aim to invigorate research in the code retrieval domain, providing a versatile benchmarking tool that encourages further development and exploration of code retrieval systems\url{ https://github.com/CoIR-team/coir}.

  • 9 authors
·
Jul 3, 2024

M2TRec: Metadata-aware Multi-task Transformer for Large-scale and Cold-start free Session-based Recommendations

Session-based recommender systems (SBRSs) have shown superior performance over conventional methods. However, they show limited scalability on large-scale industrial datasets since most models learn one embedding per item. This leads to a large memory requirement (of storing one vector per item) and poor performance on sparse sessions with cold-start or unpopular items. Using one public and one large industrial dataset, we experimentally show that state-of-the-art SBRSs have low performance on sparse sessions with sparse items. We propose M2TRec, a Metadata-aware Multi-task Transformer model for session-based recommendations. Our proposed method learns a transformation function from item metadata to embeddings, and is thus, item-ID free (i.e., does not need to learn one embedding per item). It integrates item metadata to learn shared representations of diverse item attributes. During inference, new or unpopular items will be assigned identical representations for the attributes they share with items previously observed during training, and thus will have similar representations with those items, enabling recommendations of even cold-start and sparse items. Additionally, M2TRec is trained in a multi-task setting to predict the next item in the session along with its primary category and subcategories. Our multi-task strategy makes the model converge faster and significantly improves the overall performance. Experimental results show significant performance gains using our proposed approach on sparse items on the two datasets.

  • 5 authors
·
Sep 23, 2022

DAPFAM: A Domain-Aware Family-level Dataset to benchmark cross domain patent retrieval

Patent prior-art retrieval becomes especially challenging when relevant disclosures cross technological boundaries. Existing benchmarks lack explicit domain partitions, making it difficult to assess how retrieval systems cope with such shifts. We introduce DAPFAM, a family-level benchmark with explicit IN-domain and OUT-domain partitions defined by a new IPC3 overlap scheme. The dataset contains 1,247 query families and 45,336 target families aggregated at the family level to reduce international redundancy, with citation based relevance judgments. We conduct 249 controlled experiments spanning lexical (BM25) and dense (transformer) backends, document and passage level retrieval, multiple query and document representations, aggregation strategies, and hybrid fusion via Reciprocal Rank Fusion (RRF). Results reveal a pronounced domain gap: OUT-domain performance remains roughly five times lower than IN-domain across all configurations. Passage-level retrieval consistently outperforms document-level, and dense methods provide modest gains over BM25, but none close the OUT-domain gap. Document-level RRF yields strong effectiveness efficiency trade-offs with minimal overhead. By exposing the persistent challenge of cross-domain retrieval, DAPFAM provides a reproducible, compute-aware testbed for developing more robust patent IR systems. The dataset is publicly available on huggingface at https://huggingface.co/datasets/datalyes/DAPFAM_patent.

  • 3 authors
·
Jun 27, 2025

Automated Extraction of Material Properties using LLM-based AI Agents

The rapid discovery of materials is constrained by the lack of large, machine-readable datasets that couple performance metrics with structural context. Existing databases are either small, manually curated, or biased toward first principles results, leaving experimental literature underexploited. We present an agentic, large language model (LLM)-driven workflow that autonomously extracts thermoelectric and structural-properties from about 10,000 full-text scientific articles. The pipeline integrates dynamic token allocation, zeroshot multi-agent extraction, and conditional table parsing to balance accuracy against computational cost. Benchmarking on 50 curated papers shows that GPT-4.1 achieves the highest accuracy (F1 = 0.91 for thermoelectric properties and 0.82 for structural fields), while GPT-4.1 Mini delivers nearly comparable performance (F1 = 0.89 and 0.81) at a fraction of the cost, enabling practical large scale deployment. Applying this workflow, we curated 27,822 temperature resolved property records with normalized units, spanning figure of merit (ZT), Seebeck coefficient, conductivity, resistivity, power factor, and thermal conductivity, together with structural attributes such as crystal class, space group, and doping strategy. Dataset analysis reproduces known thermoelectric trends, such as the superior performance of alloys over oxides and the advantage of p-type doping, while also surfacing broader structure-property correlations. To facilitate community access, we release an interactive web explorer with semantic filters, numeric queries, and CSV export. This study delivers the largest LLM-curated thermoelectric dataset to date, provides a reproducible and cost-profiled extraction pipeline, and establishes a foundation for scalable, data-driven materials discovery beyond thermoelectrics.

  • 2 authors
·
Sep 23, 2025

ChemTEB: Chemical Text Embedding Benchmark, an Overview of Embedding Models Performance & Efficiency on a Specific Domain

Recent advancements in language models have started a new era of superior information retrieval and content generation, with embedding models playing an important role in optimizing data representation efficiency and performance. While benchmarks like the Massive Text Embedding Benchmark (MTEB) have standardized the evaluation of general domain embedding models, a gap remains in specialized fields such as chemistry, which require tailored approaches due to domain-specific challenges. This paper introduces a novel benchmark, the Chemical Text Embedding Benchmark (ChemTEB), designed specifically for the chemical sciences. ChemTEB addresses the unique linguistic and semantic complexities of chemical literature and data, offering a comprehensive suite of tasks on chemical domain data. Through the evaluation of 34 open-source and proprietary models using this benchmark, we illuminate the strengths and weaknesses of current methodologies in processing and understanding chemical information. Our work aims to equip the research community with a standardized, domain-specific evaluation framework, promoting the development of more precise and efficient NLP models for chemistry-related applications. Furthermore, it provides insights into the performance of generic models in a domain-specific context. ChemTEB comes with open-source code and data, contributing further to its accessibility and utility.

  • 7 authors
·
Nov 30, 2024

MMDocIR: Benchmarking Multi-Modal Retrieval for Long Documents

Multi-modal document retrieval is designed to identify and retrieve various forms of multi-modal content, such as figures, tables, charts, and layout information from extensive documents. Despite its significance, there is a notable lack of a robust benchmark to effectively evaluate the performance of systems in multi-modal document retrieval. To address this gap, this work introduces a new benchmark, named as MMDocIR, encompassing two distinct tasks: page-level and layout-level retrieval. The former focuses on localizing the most relevant pages within a long document, while the latter targets the detection of specific layouts, offering a more fine-grained granularity than whole-page analysis. A layout can refer to a variety of elements such as textual paragraphs, equations, figures, tables, or charts. The MMDocIR benchmark comprises a rich dataset featuring expertly annotated labels for 1,685 questions and bootstrapped labels for 173,843 questions, making it a pivotal resource for advancing multi-modal document retrieval for both training and evaluation. Through rigorous experiments, we reveal that (i) visual retrievers significantly outperform their text counterparts, (ii) MMDocIR train set can effectively benefit the training process of multi-modal document retrieval and (iii) text retrievers leveraging on VLM-text perform much better than those using OCR-text. These findings underscores the potential advantages of integrating visual elements for multi-modal document retrieval.

  • 6 authors
·
Jan 15, 2025 2

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.

Contrastive Learning and Mixture of Experts Enables Precise Vector Embeddings

The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, particularly in creating effective vector representations of natural language inputs. However, these models face notable challenges in domain-specific contexts, especially in highly specialized scientific sub-fields. Traditional methods often struggle in this regime, either overgeneralizing similarities within a niche or being overly sensitive to minor differences, resulting in inaccurate text classification and subpar vector representation. In an era where retrieval augmentation and search are increasingly crucial, precise and concise numerical representations are essential. In this paper, we target this issue by assembling niche datasets using co-citations as a similarity metric, focusing on biomedical domains. We employ two key strategies for fine-tuning state-of-the-art models: 1. Domain-specific Fine-Tuning, which tailors pretrained models to a single domain, and 2. Universal Applicability with Mixture of Experts (MoE), adapting pretrained models with enforced routing for multiple domains simultaneously. Our training approach emphasizes the use of abstracts for faster training, incorporating Multiple Negative Rankings loss for efficient contrastive learning. Notably, our MoE variants, equipped with N experts, achieve the efficacy of N individual models, heralding a new era of versatile, One-Size-Fits-All transformer networks for various tasks. This methodology marks significant advancements in scientific text classification metrics and holds promise for enhancing vector database search and compilation.

  • 4 authors
·
Jan 28, 2024

MatText: Do Language Models Need More than Text & Scale for Materials Modeling?

Effectively representing materials as text has the potential to leverage the vast advancements of large language models (LLMs) for discovering new materials. While LLMs have shown remarkable success in various domains, their application to materials science remains underexplored. A fundamental challenge is the lack of understanding of how to best utilize text-based representations for materials modeling. This challenge is further compounded by the absence of a comprehensive benchmark to rigorously evaluate the capabilities and limitations of these text representations in capturing the complexity of material systems. To address this gap, we propose MatText, a suite of benchmarking tools and datasets designed to systematically evaluate the performance of language models in modeling materials. MatText encompasses nine distinct text-based representations for material systems, including several novel representations. Each representation incorporates unique inductive biases that capture relevant information and integrate prior physical knowledge about materials. Additionally, MatText provides essential tools for training and benchmarking the performance of language models in the context of materials science. These tools include standardized dataset splits for each representation, probes for evaluating sensitivity to geometric factors, and tools for seamlessly converting crystal structures into text. Using MatText, we conduct an extensive analysis of the capabilities of language models in modeling materials. Our findings reveal that current language models consistently struggle to capture the geometric information crucial for materials modeling across all representations. Instead, these models tend to leverage local information, which is emphasized in some of our novel representations. Our analysis underscores MatText's ability to reveal shortcomings of text-based methods for materials design.

  • 3 authors
·
Jun 25, 2024

Structural Text Segmentation of Legal Documents

The growing complexity of legal cases has lead to an increasing interest in legal information retrieval systems that can effectively satisfy user-specific information needs. However, such downstream systems typically require documents to be properly formatted and segmented, which is often done with relatively simple pre-processing steps, disregarding topical coherence of segments. Systems generally rely on representations of individual sentences or paragraphs, which may lack crucial context, or document-level representations, which are too long for meaningful search results. To address this issue, we propose a segmentation system that can predict topical coherence of sequential text segments spanning several paragraphs, effectively segmenting a document and providing a more balanced representation for downstream applications. We build our model on top of popular transformer networks and formulate structural text segmentation as topical change detection, by performing a series of independent classifications that allow for efficient fine-tuning on task-specific data. We crawl a novel dataset consisting of roughly 74,000 online Terms-of-Service documents, including hierarchical topic annotations, which we use for training. Results show that our proposed system significantly outperforms baselines, and adapts well to structural peculiarities of legal documents. We release both data and trained models to the research community for future work.https://github.com/dennlinger/TopicalChange

  • 4 authors
·
Dec 7, 2020

PODTILE: Facilitating Podcast Episode Browsing with Auto-generated Chapters

Listeners of long-form talk-audio content, such as podcast episodes, often find it challenging to understand the overall structure and locate relevant sections. A practical solution is to divide episodes into chapters--semantically coherent segments labeled with titles and timestamps. Since most episodes on our platform at Spotify currently lack creator-provided chapters, automating the creation of chapters is essential. Scaling the chapterization of podcast episodes presents unique challenges. First, episodes tend to be less structured than written texts, featuring spontaneous discussions with nuanced transitions. Second, the transcripts are usually lengthy, averaging about 16,000 tokens, which necessitates efficient processing that can preserve context. To address these challenges, we introduce PODTILE, a fine-tuned encoder-decoder transformer to segment conversational data. The model simultaneously generates chapter transitions and titles for the input transcript. To preserve context, each input text is augmented with global context, including the episode's title, description, and previous chapter titles. In our intrinsic evaluation, PODTILE achieved an 11% improvement in ROUGE score over the strongest baseline. Additionally, we provide insights into the practical benefits of auto-generated chapters for listeners navigating episode content. Our findings indicate that auto-generated chapters serve as a useful tool for engaging with less popular podcasts. Finally, we present empirical evidence that using chapter titles can enhance effectiveness of sparse retrieval in search tasks.

  • 17 authors
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Oct 21, 2024

ULMRec: User-centric Large Language Model for Sequential Recommendation

Recent advances in Large Language Models (LLMs) have demonstrated promising performance in sequential recommendation tasks, leveraging their superior language understanding capabilities. However, existing LLM-based recommendation approaches predominantly focus on modeling item-level co-occurrence patterns while failing to adequately capture user-level personalized preferences. This is problematic since even users who display similar behavioral patterns (e.g., clicking or purchasing similar items) may have fundamentally different underlying interests. To alleviate this problem, in this paper, we propose ULMRec, a framework that effectively integrates user personalized preferences into LLMs for sequential recommendation. Considering there has the semantic gap between item IDs and LLMs, we replace item IDs with their corresponding titles in user historical behaviors, enabling the model to capture the item semantics. For integrating the user personalized preference, we design two key components: (1) user indexing: a personalized user indexing mechanism that leverages vector quantization on user reviews and user IDs to generate meaningful and unique user representations, and (2) alignment tuning: an alignment-based tuning stage that employs comprehensive preference alignment tasks to enhance the model's capability in capturing personalized information. Through this design, ULMRec achieves deep integration of language semantics with user personalized preferences, facilitating effective adaptation to recommendation. Extensive experiments on two public datasets demonstrate that ULMRec significantly outperforms existing methods, validating the effectiveness of our approach.

  • 4 authors
·
Dec 7, 2024

Meta-training with Demonstration Retrieval for Efficient Few-shot Learning

Large language models show impressive results on few-shot NLP tasks. However, these models are memory and computation-intensive. Meta-training allows one to leverage smaller models for few-shot generalization in a domain-general and task-agnostic manner; however, these methods alone results in models that may not have sufficient parameterization or knowledge to adapt quickly to a large variety of tasks. To overcome this issue, we propose meta-training with demonstration retrieval, where we use a dense passage retriever to retrieve semantically similar labeled demonstrations to each example for more varied supervision. By separating external knowledge from model parameters, we can use meta-training to train parameter-efficient models that generalize well on a larger variety of tasks. We construct a meta-training set from UnifiedQA and CrossFit, and propose a demonstration bank based on UnifiedQA tasks. To our knowledge, our work is the first to combine retrieval with meta-training, to use DPR models to retrieve demonstrations, and to leverage demonstrations from many tasks simultaneously, rather than randomly sampling demonstrations from the training set of the target task. Our approach outperforms a variety of targeted parameter-efficient and retrieval-augmented few-shot methods on QA, NLI, and text classification tasks (including SQuAD, QNLI, and TREC). Our approach can be meta-trained and fine-tuned quickly on a single GPU.

  • 5 authors
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Jun 30, 2023

Mining experimental data from Materials Science literature with Large Language Models: an evaluation study

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

  • 4 authors
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Jan 19, 2024 1

HoneyBee: Progressive Instruction Finetuning of Large Language Models for Materials Science

We propose an instruction-based process for trustworthy data curation in materials science (MatSci-Instruct), which we then apply to finetune a LLaMa-based language model targeted for materials science (HoneyBee). MatSci-Instruct helps alleviate the scarcity of relevant, high-quality materials science textual data available in the open literature, and HoneyBee is the first billion-parameter language model specialized to materials science. In MatSci-Instruct we improve the trustworthiness of generated data by prompting multiple commercially available large language models for generation with an Instructor module (e.g. Chat-GPT) and verification from an independent Verifier module (e.g. Claude). Using MatSci-Instruct, we construct a dataset of multiple tasks and measure the quality of our dataset along multiple dimensions, including accuracy against known facts, relevance to materials science, as well as completeness and reasonableness of the data. Moreover, we iteratively generate more targeted instructions and instruction-data in a finetuning-evaluation-feedback loop leading to progressively better performance for our finetuned HoneyBee models. Our evaluation on the MatSci-NLP benchmark shows HoneyBee's outperformance of existing language models on materials science tasks and iterative improvement in successive stages of instruction-data refinement. We study the quality of HoneyBee's language modeling through automatic evaluation and analyze case studies to further understand the model's capabilities and limitations. Our code and relevant datasets are publicly available at https://github.com/BangLab-UdeM-Mila/NLP4MatSci-HoneyBee.

  • 4 authors
·
Oct 12, 2023

Synthetic Data Generation with Large Language Models for Personalized Community Question Answering

Personalization in Information Retrieval (IR) is a topic studied by the research community since a long time. However, there is still a lack of datasets to conduct large-scale evaluations of personalized IR; this is mainly due to the fact that collecting and curating high-quality user-related information requires significant costs and time investment. Furthermore, the creation of datasets for Personalized IR (PIR) tasks is affected by both privacy concerns and the need for accurate user-related data, which are often not publicly available. Recently, researchers have started to explore the use of Large Language Models (LLMs) to generate synthetic datasets, which is a possible solution to generate data for low-resource tasks. In this paper, we investigate the potential of Large Language Models (LLMs) for generating synthetic documents to train an IR system for a Personalized Community Question Answering task. To study the effectiveness of IR models fine-tuned on LLM-generated data, we introduce a new dataset, named Sy-SE-PQA. We build Sy-SE-PQA based on an existing dataset, SE-PQA, which consists of questions and answers posted on the popular StackExchange communities. Starting from questions in SE-PQA, we generate synthetic answers using different prompt techniques and LLMs. Our findings suggest that LLMs have high potential in generating data tailored to users' needs. The synthetic data can replace human-written training data, even if the generated data may contain incorrect information.

  • 4 authors
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Oct 29, 2024

MoDora: Tree-Based Semi-Structured Document Analysis System

Semi-structured documents integrate diverse interleaved data elements (e.g., tables, charts, hierarchical paragraphs) arranged in various and often irregular layouts. These documents are widely observed across domains and account for a large portion of real-world data. However, existing methods struggle to support natural language question answering over these documents due to three main technical challenges: (1) The elements extracted by techniques like OCR are often fragmented and stripped of their original semantic context, making them inadequate for analysis. (2) Existing approaches lack effective representations to capture hierarchical structures within documents (e.g., associating tables with nested chapter titles) and to preserve layout-specific distinctions (e.g., differentiating sidebars from main content). (3) Answering questions often requires retrieving and aligning relevant information scattered across multiple regions or pages, such as linking a descriptive paragraph to table cells located elsewhere in the document. To address these issues, we propose MoDora, an LLM-powered system for semi-structured document analysis. First, we adopt a local-alignment aggregation strategy to convert OCR-parsed elements into layout-aware components, and conduct type-specific information extraction for components with hierarchical titles or non-text elements. Second, we design the Component-Correlation Tree (CCTree) to hierarchically organize components, explicitly modeling inter-component relations and layout distinctions through a bottom-up cascade summarization process. Finally, we propose a question-type-aware retrieval strategy that supports (1) layout-based grid partitioning for location-based retrieval and (2) LLM-guided pruning for semantic-based retrieval. Experiments show MoDora outperforms baselines by 5.97%-61.07% in accuracy. The code is at https://github.com/weAIDB/MoDora.

  • 11 authors
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Feb 26 1

MR.Rec: Synergizing Memory and Reasoning for Personalized Recommendation Assistant with LLMs

The application of Large Language Models (LLMs) in recommender systems faces key challenges in delivering deep personalization and intelligent reasoning, especially for interactive scenarios. Current methods are often constrained by limited context windows and single-turn reasoning, hindering their ability to capture dynamic user preferences and proactively reason over recommendation contexts. To address these limitations, we propose MR.Rec, a novel framework that synergizes memory and reasoning for LLM-based recommendations. To achieve personalization, we develop a comprehensive Retrieval-Augmented Generation (RAG) system that efficiently indexes and retrieves relevant external memory to enhance LLM personalization capabilities. Furthermore, to enable the synergy between memory and reasoning, our RAG system goes beyond conventional query-based retrieval by integrating reasoning enhanced memory retrieval. Finally, we design a reinforcement learning framework that trains the LLM to autonomously learn effective strategies for both memory utilization and reasoning refinement. By combining dynamic memory retrieval with adaptive reasoning, this approach ensures more accurate, context-aware, and highly personalized recommendations. Extensive experiments demonstrate that MR.Rec significantly outperforms state-of-the-art baselines across multiple metrics, validating its efficacy in delivering intelligent and personalized recommendations. We will release code and data upon paper notification.

  • 4 authors
·
Oct 16, 2025

Better Generalization with Semantic IDs: A Case Study in Ranking for Recommendations

Randomly-hashed item ids are used ubiquitously in recommendation models. However, the learned representations from random hashing prevents generalization across similar items, causing problems of learning unseen and long-tail items, especially when item corpus is large, power-law distributed, and evolving dynamically. In this paper, we propose using content-derived features as a replacement for random ids. We show that simply replacing ID features with content-based embeddings can cause a drop in quality due to reduced memorization capability. To strike a good balance of memorization and generalization, we propose to use Semantic IDs -- a compact discrete item representation learned from frozen content embeddings using RQ-VAE that captures the hierarchy of concepts in items -- as a replacement for random item ids. Similar to content embeddings, the compactness of Semantic IDs poses a problem of easy adaption in recommendation models. We propose novel methods for adapting Semantic IDs in industry-scale ranking models, through hashing sub-pieces of of the Semantic-ID sequences. In particular, we find that the SentencePiece model that is commonly used in LLM tokenization outperforms manually crafted pieces such as N-grams. To the end, we evaluate our approaches in a real-world ranking model for YouTube recommendations. Our experiments demonstrate that Semantic IDs can replace the direct use of video IDs by improving the generalization ability on new and long-tail item slices without sacrificing overall model quality.

  • 12 authors
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Jun 13, 2023