Objective: Healthcare data fragmentation presents a major challenge for linking patient data, necessitating robust record linkage to integrate patient records from diverse sources. This study investigates the feasibility of leveraging language models for automated patient record linkage, focusing on two key tasks: blocking and matching. Materials and Methods: We utilized real-world healthcare data from the Missouri Cancer Registry and Research Center, linking patient records from two independent sources using probabilistic linkage as a baseline. A transformer-based model, RoBERTa, was fine-tuned for blocking using sentence embeddings. For matching, several language models were experimented under fine-tuned and zero-shot settings, assessing their performance against ground truth labels. Results: The fine-tuned blocking model achieved a 92% reduction in the number of candidate pairs while maintaining near-perfect recall. In the matching task, fine-tuned Mistral-7B achieved the best performance with only 6 incorrect predictions. Among zero-shot models, Mistral-Small-24B performed best, with a total of 55 incorrect predictions. Discussion: Fine-tuned language models achieved strong performance in patient record blocking and matching with minimal errors. However, they remain less accurate and efficient than a hybrid rule-based and probabilistic approach for blocking. Additionally, reasoning models like DeepSeek-R1 are impractical for large-scale record linkage due to high computational costs. Conclusion: This study highlights the potential of language models for automating patient record linkage, offering improved efficiency by eliminating the manual efforts required to perform patient record linkage. Overall, language models offer a scalable solution that can enhance data integration, reduce manual effort, and support disease surveillance and research.

Record linkage, also known as entity resolution, aims at identifying different representations of the same real-world entity, such as a person. It is a crucial step in many data integration tasks in order to combine multiple data sources allowing enhanced data analysis. Typically, unique record identifiers are not available which would enable a join-like operation. Therefore, records are compared pairwise based on their identifying attributes, such as first name, last name and date of birth, and classified as match or non-match. However, record linkage may potentially harm the privacy of individuals by combining information that can be used against their interests. As a consequence, the conduction of such a linkage is subject to many legal and organizational constraints [CRS20]. Privacypreserving record linkage (PPRL) methods aim for enabling such linkages without sharing sensitive plaintext information between the data owners or with a third party. To protect the identifying data, the data owners encode it before sending it to an independent linkage unit which performs the matching on the encoded data only. A variety of such perturbation-based encoding techniques have been proposed, but the most popular and a quasi-standard is based on Bloom filters [Gk21].

Record linkage integrates diverse data sources by identifying records that refer to the same entity. In the context of mineral site records, accurate record linkage is crucial for identifying and mapping mineral deposits. Properly linking records that refer to the same mineral deposit helps define the spatial coverage of mineral areas, benefiting resource identification and site data archiving. Mineral site record linkage falls under the spatial record linkage category since the records contain information about the physical locations and non-spatial attributes in a tabular format. The task is particularly challenging due to the heterogeneity and vast scale of the data. While prior research employs pre-trained discriminative language models (PLMs) on spatial entity linkage, they often require substantial amounts of curated ground-truth data for fine-tuning. Gathering and creating ground truth data is both time-consuming and costly. Therefore, such approaches are not always feasible in real-world scenarios where gold-standard data are unavailable. Although large generative language models (LLMs) have shown promising results in various natural language processing tasks, including record linkage, their high inference time and resource demand present challenges. We propose a method that leverages an LLM to generate training data and fine-tune a PLM to address the training data gap while preserving the efficiency of PLMs. Our approach achieves over 45\% improvement in F1 score for record linkage compared to traditional PLM-based methods using ground truth data while reducing the inference time by nearly 18 times compared to relying on LLMs. Additionally, we offer an automated pipeline that eliminates the need for human intervention, highlighting this approach's potential to overcome record linkage challenges.

Record matching, the task of identifying records that correspond to the same real-world entities across databases, is critical for data integration in domains like healthcare, finance, and e-commerce. While traditional record matching models focus on optimizing accuracy, fairness issues, such as demographic disparities in model performance, have attracted increasing attention. Biased outcomes in record matching can result in unequal error rates across demographic groups, raising ethical and legal concerns. Existing research primarily addresses fairness at specific decision thresholds, using bias metrics like Demographic Parity (DP), Equal Opportunity (EO), and Equalized Odds (EOD) differences. However, threshold-specific metrics may overlook cumulative biases across varying thresholds. In this paper, we adapt fairness metrics traditionally applied in regression models to evaluate cumulative bias across all thresholds in record matching. We propose a novel post-processing calibration method, leveraging optimal transport theory and Wasserstein barycenters, to balance matching scores across demographic groups. This approach treats any matching model as a black box, making it applicable to a wide range of models without access to their training data. Our experiments demonstrate the effectiveness of the calibration method in reducing demographic parity difference in matching scores. To address limitations in reducing EOD and EO differences, we introduce a conditional calibration method, which empirically achieves fairness across widely used benchmarks and state-of-the-art matching methods. This work provides a comprehensive framework for fairness-aware record matching, setting the foundation for more equitable data integration processes.

Entity matching (EM) is the problem of determining whether two records refer to same real-world entity, which is crucial in data integration, e.g., for product catalogs or address databases. A major drawback of many EM approaches is their dependence on labelled examples. We thus focus on the challenging setting of zero-shot entity matching where no labelled examples are available for an unseen target dataset. Recently, large language models (LLMs) have shown promising results for zero-shot EM, but their low throughput and high deployment cost limit their applicability and scalability. We revisit the zero-shot EM problem with AnyMatch, a small language model fine-tuned in a transfer learning setup. We propose several novel data selection techniques to generate fine-tuning data for our model, e.g., by selecting difficult pairs to match via an AutoML filter, by generating additional attribute-level examples, and by controlling label imbalance in the data. We conduct an extensive evaluation of the prediction quality and deployment cost of our model, in a comparison to thirteen baselines on nine benchmark datasets. We find that AnyMatch provides competitive prediction quality despite its small parameter size: it achieves the second-highest F1 score overall, and outperforms several other approaches that employ models with hundreds of billions of parameters. Furthermore, our approach exhibits major cost benefits: the average prediction quality of AnyMatch is within 4.4% of the state-of-the-art method MatchGPT with the proprietary trillion-parameter model GPT-4, yet AnyMatch requires four orders of magnitude less parameters and incurs a 3,899 times lower inference cost (in dollars per 1,000 tokens).

The goal of entity resolution is to identify records in multiple datasets that represent the same real-world entity. However, comparing all records across datasets can be computationally intensive, leading to long runtimes. To reduce these runtimes, entity resolution pipelines are constructed of two parts: a blocker that applies a computationally cheap method to select candidate record pairs, and a matcher that afterwards identifies matching pairs from this set using more expensive methods. This paper presents SC-Block, a blocking method that utilizes supervised contrastive learning for positioning records in the embedding space, and nearest neighbour search for candidate set building. We benchmark SC-Block against eight state-of-the-art blocking methods. In order to relate the training time of SC-Block to the reduction of the overall runtime of the entity resolution pipeline, we combine SC-Block with four matching methods into complete pipelines. For measuring the overall runtime, we determine candidate sets with 99.5% pair completeness and pass them to the matcher. The results show that SC-Block is able to create smaller candidate sets and pipelines with SC-Block execute 1.5 to 2 times faster compared to pipelines with other blockers, without sacrificing F1 score. Blockers are often evaluated using relatively small datasets which might lead to runtime effects resulting from a large vocabulary size being overlooked. In order to measure runtimes in a more challenging setting, we introduce a new benchmark dataset that requires large numbers of product offers to be blocked. On this large-scale benchmark dataset, pipelines utilizing SC-Block and the best-performing matcher execute 8 times faster than pipelines utilizing another blocker with the same matcher reducing the runtime from 2.5 hours to 18 minutes, clearly compensating for the 5 minutes required for training SC-Block.

This paper introduces a novel evaluation methodology for entity resolution algorithms. It is motivated by PatentsView.org, a U.S. Patents and Trademarks Office patent data exploration tool that disambiguates patent inventors using an entity resolution algorithm. We provide a data collection methodology and tailored performance estimators that account for sampling biases. Our approach is simple, practical and principled -- key characteristics that allow us to paint the first representative picture of PatentsView's disambiguation performance. This approach is used to inform PatentsView's users of the reliability of the data and to allow the comparison of competing disambiguation algorithms.

Deep learning-based linkage of records across different databases is becoming increasingly useful in data integration and mining applications to discover new insights from multiple sources of data. However, due to privacy and confidentiality concerns, organisations often are not willing or allowed to share their sensitive data with any external parties, thus making it challenging to build/train deep learning models for record linkage across different organizations' databases. To overcome this limitation, we propose the first deep learning-based multi-party privacy-preserving record linkage (PPRL) protocol that can be used to link sensitive databases held by multiple different organisations. In our approach, each database owner first trains a local deep learning model, which is then uploaded to a secure environment and securely aggregated to create a global model. The global model is then used by a linkage unit to distinguish unlabelled record pairs as matches and non-matches. We utilise differential privacy to achieve provable privacy protection against re-identification attacks. We evaluate the linkage quality and scalability of our approach using several large real-world databases, showing that it can achieve high linkage quality while providing sufficient privacy protection against existing attacks.

The goal of entity matching is to find the corresponding records representing the same real-world entity from different data sources. At present, in the mainstream methods, rule-based entity matching methods need tremendous domain knowledge. The machine-learning based or deep-learning based entity matching methods need a large number of labeled samples to build the model, which is difficult to achieve in some applications. In addition, learning-based methods are easy to over-fitting, so the quality requirements of training samples are very high. In this paper, we present an active learning method ALMatcher for the entity matching tasks. This method needs to manually label only a small number of valuable samples, and use these samples to build a model with high quality. This paper proposes a hybrid uncertainty as query strategy to find those valuable samples for labeling, which can minimize the number of labeled training samples meanwhile meet the task requirements. The proposed method has been validated on seven data sets in different fields. The experiment shows that ALMatcher uses only a small number of labeled samples and achieves better results compared to existing approaches.

Entity resolution, a longstanding problem of data cleaning and integration, aims at identifying data records that represent the same real-world entity. Existing approaches treat entity resolution as a universal task, assuming the existence of a single interpretation of a real-world entity and focusing only on finding matched records, separating corresponding from non-corresponding ones, with respect to this single interpretation. However, in real-world scenarios, where entity resolution is part of a more general data project, downstream applications may have varying interpretations of real-world entities relating, for example, to various user needs. In what follows, we introduce the problem of multiple intents entity resolution (MIER), an extension to the universal (single intent) entity resolution task. As a solution, we propose FlexER, utilizing contemporary solutions to universal entity resolution tasks to solve multiple intents entity resolution. FlexER addresses the problem as a multi-label classification problem. It combines intent-based representations of tuple pairs using a multiplex graph representation that serves as an input to a graph neural network (GNN). FlexER learns intent representations and improves the outcome to multiple resolution problems. A large-scale empirical evaluation introduces a new benchmark and, using also two well-known benchmarks, shows that FlexER effectively solves the MIER problem and outperforms the state-of-the-art for a universal entity resolution.