GraLMatch: Matching Groups of Entities with Graphs and Language Models

In this paper, we present an end-to-end multi-source Entity Matching problem, which we call entity group matching, where the goal is to assign to the same group, records originating from multiple data sources but representing the same real-world entity. We focus on the effects of transitively matched records, i.e. the records connected by paths in the graph G = (V,E) whose nodes and edges represent the records and whether they are a match or not. We present a real-world instance of this problem, where the challenge is to match records of companies and financial securities originating from different data providers. We also introduce two new multi-source benchmark datasets that present similar matching challenges as real-world records. A distinctive characteristic of these records is that they are regularly updated following real-world events, but updates are not applied uniformly across data sources. This phenomenon makes the matching of certain groups of records only possible through the use of transitive information. In our experiments, we illustrate how considering transitively matched records is challenging since a limited amount of false positive pairwise match predictions can throw off the group assignment of large quantities of records. Thus, we propose GraLMatch, a method that can partially detect and remove false positive pairwise predictions through graph-based properties. Finally, we showcase how fine-tuning a Transformer-based model (DistilBERT) on a reduced number of labeled samples yields a better final entity group matching than training on more samples and/or incorporating fine-tuning optimizations, illustrating how precision becomes the deciding factor in the entity group matching of large volumes of records.

StatBot.Swiss: Bilingual Open Data Exploration in Natural Language

The potential for improvements brought by Large Language Models (LLMs) in Text-to-SQL systems is mostly assessed on monolingual English datasets. However, LLMs' performance for other languages remains vastly unexplored. In this work, we release the StatBot.Swiss dataset, the first bilingual benchmark for evaluating Text-to-SQL systems based on real-world applications. The StatBot.Swiss dataset contains 455 natural language/SQL-pairs over 35 big databases with varying level of complexity for both English and German. We evaluate the performance of state-of-the-art LLMs such as GPT-3.5-Turbo and mixtral-8x7b-instruct for the Text-to-SQL translation task using an in-context learning approach. Our experimental analysis illustrates that current LLMs struggle to generalize well in generating SQL queries on our novel bilingual dataset.

Evaluating the Data Model Robustness of Text-to-SQL Systems Based on Real User Queries

Text-to-SQL systems (also known as NL-to-SQL systems) have become an increasingly popular solution for bridging the gap between user capabilities and SQL-based data access. These systems translate user requests in natural language to valid SQL statements for a specific database. Recent Text-to-SQL systems have benefited from the rapid improvement of transformer-based language models. However, while Text-to-SQL systems that incorporate such models continuously reach new high scores on -- often synthetic -- benchmark datasets, a systematic exploration of their robustness towards different data models in a real-world, realistic scenario is notably missing. This paper provides the first in-depth evaluation of the data model robustness of Text-to-SQL systems in practice based on a multi-year international project focused on Text-to-SQL interfaces. Our evaluation is based on a real-world deployment of FootballDB, a system that was deployed over a 9 month period in the context of the FIFA World Cup 2022, during which about 6K natural language questions were asked and executed. All of our data is based on real user questions that were asked live to the system. We manually labeled and translated a subset of these questions for three different data models. For each data model, we explore the performance of representative Text-to-SQL systems and language models. We further quantify the impact of training data size, pre-, and post-processing steps as well as language model inference time. Our comprehensive evaluation sheds light on the design choices of real-world Text-to-SQL systems and their impact on moving from research prototypes to real deployments. Last, we provide a new benchmark dataset to the community, which is the first to enable the evaluation of different data models for the same dataset and is substantially more challenging than most previous datasets in terms of query complexity.

Spider4SPARQL: A Complex Benchmark for Evaluating Knowledge Graph Question Answering Systems

With the recent spike in the number and availability of Large Language Models (LLMs), it has become increasingly important to provide large and realistic benchmarks for evaluating Knowledge Graph Question Answering (KBQA) systems. So far the majority of benchmarks rely on pattern-based SPARQL query generation approaches. The subsequent natural language (NL) question generation is conducted through crowdsourcing or other automated methods, such as rule-based paraphrasing or NL question templates. Although some of these datasets are of considerable size, their pitfall lies in their pattern-based generation approaches, which do not always generalize well to the vague and linguistically diverse questions asked by humans in real-world contexts. In this paper, we introduce Spider4SPARQL - a new SPARQL benchmark dataset featuring 9,693 previously existing manually generated NL questions and 4,721 unique, novel, and complex SPARQL queries of varying complexity. In addition to the NL/SPARQL pairs, we also provide their corresponding 166 knowledge graphs and ontologies, which cover 138 different domains. Our complex benchmark enables novel ways of evaluating the strengths and weaknesses of modern KGQA systems. We evaluate the system with state-of-the-art KGQA systems as well as LLMs, which achieve only up to 45\% execution accuracy, demonstrating that Spider4SPARQL is a challenging benchmark for future research.

Data-Driven Information Extraction and Enrichment of Molecular Profiling Data for Cancer Cell Lines

With the proliferation of research means and computational methodologies, published biomedical literature is growing exponentially in numbers and volume. As a consequence, in the fields of biological, medical and clinical research, domain experts have to sift through massive amounts of scientific text to find relevant information. However, this process is extremely tedious and slow to be performed by humans. Hence, novel computational information extraction and correlation mechanisms are required to boost meaningful knowledge extraction. In this work, we present the design, implementation and application of a novel data extraction and exploration system. This system extracts deep semantic relations between textual entities from scientific literature to enrich existing structured clinical data in the domain of cancer cell lines. We introduce a new public data exploration portal, which enables automatic linking of genomic copy number variants plots with ranked, related entities such as affected genes. Each relation is accompanied by literature-derived evidences, allowing for deep, yet rapid, literature search, using existing structured data as a springboard. Our system is publicly available on the web at https://cancercelllines.org

ScienceBenchmark: A Complex Real-World Benchmark for Evaluating Natural Language to SQL Systems

Natural Language to SQL systems (NL-to-SQL) have recently shown a significant increase in accuracy for natural language to SQL query translation. This improvement is due to the emergence of transformer-based language models, and the popularity of the Spider benchmark - the de-facto standard for evaluating NL-to-SQL systems. The top NL-to-SQL systems reach accuracies of up to 85\%. However, Spider mainly contains simple databases with few tables, columns, and entries, which does not reflect a realistic setting. Moreover, complex real-world databases with domain-specific content have little to no training data available in the form of NL/SQL-pairs leading to poor performance of existing NL-to-SQL systems. In this paper, we introduce ScienceBenchmark, a new complex NL-to-SQL benchmark for three real-world, highly domain-specific databases. For this new benchmark, SQL experts and domain experts created high-quality NL/SQL-pairs for each domain. To garner more data, we extended the small amount of human-generated data with synthetic data generated using GPT-3. We show that our benchmark is highly challenging, as the top performing systems on Spider achieve a very low performance on our benchmark. Thus, the challenge is many-fold: creating NL-to-SQL systems for highly complex domains with a small amount of hand-made training data augmented with synthetic data. To our knowledge, ScienceBenchmark is the first NL-to-SQL benchmark designed with complex real-world scientific databases, containing challenging training and test data carefully validated by domain experts.

Multiple Query Optimization using a Hybrid Approach of Classical and Quantum Computing

Quantum computing promises to solve difficult optimization problems in chemistry, physics and mathematics more efficiently than classical computers, but requires fault-tolerant quantum computers with millions of qubits. To overcome errors introduced by today's quantum computers, hybrid algorithms combining classical and quantum computers are used. In this paper we tackle the multiple query optimization problem (MQO) which is an important NP-hard problem in the area of data-intensive problems. We propose a novel hybrid classical-quantum algorithm to solve the MQO on a gate-based quantum computer. We perform a detailed experimental evaluation of our algorithm and compare its performance against a competing approach that employs a quantum annealer -- another type of quantum computer. Our experimental results demonstrate that our algorithm currently can only handle small problem sizes due to the limited number of qubits available on a gate-based quantum computer compared to a quantum computer based on quantum annealing. However, our algorithm shows a qubit efficiency of close to 99% which is almost a factor of 2 higher compared to the state of the art implementation. Finally, we analyze how our algorithm scales with larger problem sizes and conclude that our approach shows promising results for near-term quantum computers.

INODE: Building an End-to-End Data Exploration System in Practice

A full-fledged data exploration system must combine different access modalities with a powerful concept of guiding the user in the exploration process, by being reactive and anticipative both for data discovery and for data linking. Such systems are a real opportunity for our community to cater to users with different domain and data science expertise. We introduce INODE -- an end-to-end data exploration system -- that leverages, on the one hand, Machine Learning and, on the other hand, semantics for the purpose of Data Management (DM). Our vision is to develop a classic unified, comprehensive platform that provides extensive access to open datasets, and we demonstrate it in three significant use cases in the fields of Cancer Biomarker Reearch, Research and Innovation Policy Making, and Astrophysics. INODE offers sustainable services in (a) data modeling and linking, (b) integrated query processing using natural language, (c) guidance, and (d) data exploration through visualization, thus facilitating the user in discovering new insights. We demonstrate that our system is uniquely accessible to a wide range of users from larger scientific communities to the public. Finally, we briefly illustrate how this work paves the way for new research opportunities in DM.

ValueNet: A Neural Text-to-SQL Architecture Incorporating Values

Building natural language interfaces for databases has been a long-standing challenge for several decades. The major advantage of these so-called text-to-SQL systems is that end-users can query complex databases without the need to know SQL or the underlying database schema. Due to significant advancements in machine learning, the recent focus of research has been on neural networks to tackle this challenge on complex datasets like Spider. Several recent text-to-SQL systems achieve promising results on this dataset. However, none of them extracts and incorporates values from the user questions for generating SQL statements. Thus, the practical use of these systems in a real-world scenario has not been sufficiently demonstrated yet. In this paper we propose ValueNet light and ValueNet -- the first end-to-end text-to-SQL system incorporating values on the challenging Spider dataset. The main idea of our approach is to use not only metadata information about the underlying database but also information on the base data as input for our neural network architecture. In particular, we propose a novel architecture sketch to extract values from a user question and come up with possible value candidates which are not explicitly mentioned in the question. We then use a neural model based on an encoder-decoder architecture to synthesize the SQL query. Finally, we evaluate our model on the Spider challenge using the Execution Accuracy metric, a more difficult metric than used by most participants of the challenge. Our experimental evaluation demonstrates that ValueNet light and ValueNet reach state-of-the-art results of 64% and 60% accuracy, respectively, for translating from text to SQL, even when applying this more difficult metric than used by previous work.

A Methodology for Creating Question Answering Corpora Using Inverse Data Annotation

In this paper, we introduce a novel methodology to efficiently construct a corpus for question answering over structured data. For this, we introduce an intermediate representation that is based on the logical query plan in a database called Operation Trees (OT). This representation allows us to invert the annotation process without losing flexibility in the types of queries that we generate. Furthermore, it allows for fine-grained alignment of query tokens to OT operations. In our method, we randomly generate OTs from a context-free grammar. Afterwards, annotators have to write the appropriate natural language question that is represented by the OT. Finally, the annotators assign the tokens to the OT operations. We apply the method to create a new corpus OTTA (Operation Trees and Token Assignment), a large semantic parsing corpus for evaluating natural language interfaces to databases. We compare OTTA to Spider and LC-QuaD 2.0 and show that our methodology more than triples the annotation speed while maintaining the complexity of the queries. Finally, we train a state-of-the-art semantic parsing model on our data and show that our corpus is a challenging dataset and that the token alignment can be leveraged to increase the performance significantly.