arXiv subjects

Tobias Kuhn

Publications and source records attributed to Tobias Kuhn.

At least 19 recordsLinked to original sources

arXiv2026

Lindblad theory of linear response susceptibility and dispersive readout in minimal Kitaev junctions

The field of hybrid superconductor-semiconductor quantum dots is advancing toward the development of functional devices that leverage the advantages of both types of materials. However, the inherent complexity of these devices demands a comprehensive theoretical framework for a complete understanding of their responses to external probes, readout and the dissipation arising from environmental coupling. We present a Lindblad-based linear response formalism that captures the multi-level nature of these devices, their probe-readout flexibility, and the non-unitary effects of finite-frequency response, including the so-called Sisyphus and Hermes dynamical susceptibilities. These arise from fluctuations in the rates and jump operators, and are hence absent in standard Kubo linear response treatments. We exemplify the framework using quantum dot-based Kitaev chain setups which are promising candidates for topologically protected Majorana-based parity qubits. Our results shed light onto the validity of the standard curvature-based approximation for fermionic parity and qubit readout, show that Hermes terms compensate decoherence in dispersive readout and implement important corrections beyond thermalized states.

cond-mat.mes-hall↗

arXiv2025

Metadata-driven Table Union Search: Leveraging Semantics for Restricted Access Data Integration

Over the past decade, the Table Union Search (TUS) task has aimed to identify unionable tables within data lakes to improve data integration and discovery. While numerous solutions and approaches have been introduced, they primarily rely on open data, making them not applicable to restricted access data, such as medical records or government statistics, due to privacy concerns. Restricted data can still be shared through metadata, which ensures confidentiality while supporting data reuse. This paper explores how TUS can be computed on restricted access data using metadata alone. We propose a method that achieves 81% accuracy in unionability and outperforms existing benchmarks in precision and recall. Our results highlight the potential of metadata-driven approaches for integrating restricted data, facilitating secure data discovery in privacy-sensitive domains. This aligns with the FAIR principles, by ensuring data is Findable, Accessible, Interoperable, and Reusable while preserving confidentiality.

cs.DB↗

arXiv2024

Zero-Shot Topic Classification of Column Headers: Leveraging LLMs for Metadata Enrichment

Traditional dataset retrieval systems rely on metadata for indexing, rather than on the underlying data values. However, high-quality metadata creation and enrichment often require manual annotations, which is a labour-intensive and challenging process to automate. In this study, we propose a method to support metadata enrichment using topic annotations generated by three Large Language Models (LLMs): ChatGPT-3.5, GoogleBard, and GoogleGemini. Our analysis focuses on classifying column headers based on domain-specific topics from the Consortium of European Social Science Data Archives (CESSDA), a Linked Data controlled vocabulary. Our approach operates in a zero-shot setting, integrating the controlled topic vocabulary directly within the input prompt. This integration serves as a Large Context Windows approach, with the aim of improving the results of the topic classification task. We evaluated the performance of the LLMs in terms of internal consistency, inter-machine alignment, and agreement with human classification. Additionally, we investigate the impact of contextual information (i.e., dataset description) on the classification outcomes. Our findings suggest that ChatGPT and GoogleGemini outperform GoogleBard in terms of internal consistency as well as LLM-human-agreement. Interestingly, we found that contextual information had no significant impact on LLM performance. This work proposes a novel approach that leverages LLMs for topic classification of column headers using a controlled vocabulary, presenting a practical application of LLMs and Large Context Windows within the Semantic Web domain. This approach has the potential to facilitate automated metadata enrichment, thereby enhancing dataset retrieval and the Findability, Accessibility, Interoperability, and Reusability (FAIR) of research data on the Web.

cs.DB↗

arXiv2024

Column Vocabulary Association (CVA): semantic interpretation of dataless tables

Traditional Semantic Table Interpretation (STI) methods rely primarily on the underlying table data to create semantic annotations. This year's SemTab challenge introduced the ``Metadata to KG'' track, which focuses on performing STI by using only metadata information, without access to the underlying data. In response to this new challenge, we introduce a new term: Column Vocabulary Association (CVA). This term refers to the task of semantic annotation of column headers solely based on metadata information. In this study, we evaluate the performance of various methods in executing the CVA task, including a Large Language Models (LLMs) and Retrieval Augmented Generation (RAG) approach, as well as a more traditional similarity approach with SemanticBERT. Our methodology uses a zero-shot setting, with no pretraining or examples passed to the Large Language Models (LLMs), as we aim to avoid a domain-specific setting. We investigate a total of 7 different LLMs, of which three commercial GPT models (i.e. gpt-3.5-turbo-0.125, gpt-4o and gpt-4-turbo) and four open source models (i.e. llama3-80b, llama3-7b, gemma-7b and mixtral-8x7b). We integrate this models with RAG systems, and we explore how variations in temperature settings affect performances. Moreover, we continue our investigation by performing the CVA task utilizing SemanticBERT, analyzing how various metadata information influence its performance. Initial findings indicate that LLMs generally perform well at temperatures below 1.0, achieving an accuracy of 100\% in certain cases. Nevertheless, our investigation also reveal that the nature of the data significantly influences CVA task outcomes. In fact, in cases where the input data and glossary are related (for example by being created by the same organizations) traditional methods appear to surpass the performance of LLMs.

cs.CL↗

arXiv2024

Floquet engineering Higgs dynamics in time-periodic superconductors

Higgs modes emerge in superconductors as collective excitations of the order parameter amplitude when periodically driven by electromagnetic radiation. In this work, we develop a Floquet approach to study Higgs modes in superconductors under time-periodic driving, where the dynamics of the order parameter is captured by anomalous Floquet Green's functions. We show that the Floquet description is particularly powerful as it allows one to exploit the time-periodic nature of the driving, thus considerably reducing the complexity of the time-dependent problem. Interestingly, the Floquet approach is also enlightening because it naturally offers a physical explanation for the renormalized steady-state order parameter as a result of photon processes between Floquet sidebands. We demonstrate the usefulness of Floquet engineering Higgs modes in time-periodic $s$-wave superconductors.

cond-mat.supr-con↗

arXiv2023

Semantic Units: Organizing knowledge graphs into semantically meaningful units of representation

Knowledge graphs and ontologies are becoming increasingly important as technical solutions for Findable, Accessible, Interoperable, and Reusable data and metadata (FAIR Guiding Principles). We discuss four challenges that impede the use of FAIR knowledge graphs and propose semantic units as their potential solution. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs. Each unit is represented by its own resource, instantiates a corresponding semantic unit class, and can be implemented as a FAIR Digital Object and a nanopublication in RDF/OWL and property graphs. We distinguish statement and compound units as basic categories of semantic units. Statement units represent smallest, independent propositions that are semantically meaningful for a human reader. They consist of one or more triples and mathematically partition a knowledge graph. We distinguish assertional, contingent (prototypical), and universal statement units as basic types of statement units and propose representational schemes and formal semantics for them (including for absence statements, negations, and cardinality restrictions) that do not involve blank nodes and that translate back to OWL. Compound units, on the other hand, represent semantically meaningful collections of semantic units and we distinguish various types of compound units, representing different levels of representational granularity, different types of granularity trees, and different frames of reference. Semantic units support making statements about statements, can be used for graph-alignment, subgraph-matching, knowledge graph profiling, and for managing access restrictions to sensitive data. Organizing the graph into semantic units supports the separation of ontological, diagnostic (i.e., referential), and discursive information, and it also supports the differentiation of multiple frames of reference.

cs.DB↗

arXiv2022

Nanopublication-Based Semantic Publishing and Reviewing: A Field Study with Formalization Papers

With the rapidly increasing amount of scientific literature,it is getting continuously more difficult for researchers in different disciplines to be updated with the recent findings in their field of study.Processing scientific articles in an automated fashion has been proposed as a solution to this problem,but the accuracy of such processing remains very poor for extraction tasks beyond the basic ones.Few approaches have tried to change how we publish scientific results in the first place,by making articles machine-interpretable by expressing them with formal semantics from the start.In the work presented here,we set out to demonstrate that we can formally publish high-level scientific claims in formal logic,and publish the results in a special issue of an existing journal.We use the concept and technology of nanopublications for this endeavor,and represent not just the submissions and final papers in this RDF-based format,but also the whole process in between,including reviews,responses,and decisions.We do this by performing a field study with what we call formalization papers,which contribute a novel formalization of a previously published claim.We received 15 submissions from 18 authors,who then went through the whole publication process leading to the publication of their contributions in the special issue.Our evaluation shows the technical and practical feasibility of our approach.The participating authors mostly showed high levels of interest and confidence,and mostly experienced the process as not very difficult,despite the technical nature of the current user interfaces.We believe that these results indicate that it is possible to publish scientific results from different fields with machine-interpretable semantics from the start,which in turn opens countless possibilities to radically improve in the future the effectiveness and efficiency of the scientific endeavor as a whole.

cs.DL↗

arXiv2021

User-friendly Composition of FAIR Workflows in a Notebook Environment

There has been a large focus in recent years on making assets in scientific research findable, accessible, interoperable and reusable, collectively known as the FAIR principles. A particular area of focus lies in applying these principles to scientific computational workflows. Jupyter notebooks are a very popular medium by which to program and communicate computational scientific analyses. However, they present unique challenges when it comes to reuse of only particular steps of an analysis without disrupting the usual flow and benefits of the notebook approach, making it difficult to fully comply with the FAIR principles. Here we present an approach and toolset for adding the power of semantic technologies to Python-encoded scientific workflows in a simple, automated and minimally intrusive manner. The semantic descriptions are published as a series of nanopublications that can be searched and used in other notebooks by means of a Jupyter Lab plugin. We describe the implementation of the proposed approach and toolset, and provide the results of a user study with 15 participants, designed around image processing workflows, to evaluate the usability of the system and its perceived effect on FAIRness. Our results show that our approach is feasible and perceived as user-friendly. Our system received an overall score of 78.75 on the System Usability Scale, which is above the average score reported in the literature.

cs.HC↗

arXiv2021

Living Literature Reviews

Literature reviews have long played a fundamental role in synthesizing the current state of a research field. However, in recent years, certain fields have evolved at such a rapid rate that literature reviews quickly lose their relevance as new work is published that renders them outdated. We should therefore rethink how to structure and publish such literature reviews with their highly valuable synthesized content. Here, we aim to determine if existing Linked Data technologies can be harnessed to prolong the relevance of literature reviews and whether researchers are comfortable with working with such a solution. We present here our approach of ``living literature reviews'' where the core information is represented as Linked Data which can be amended with new findings after the publication of the literature review. We present a prototype implementation, which we use for a case study where we expose potential users to a concrete literature review modeled with our approach. We observe that our model is technically feasible and is received well by researchers, with our ``living'' versions scoring higher than their traditional counterparts in our user study. In conclusion, we find that there are strong benefits to using a Linked Data solution to extend the effective lifetime of a literature review.

cs.DL↗

arXiv2021

Expressing High-Level Scientific Claims with Formal Semantics

The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the Life Sciences, Computer Science, and the Social Sciences. Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the 'super-pattern'. We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door for expressing high-level scientific findings in a manner they can be automatically interpreted, which on the longer run can allow us to do automated consistency checking, and much more.

cs.DL↗

arXiv2020

Provenance for Linguistic Corpora Through Nanopublications

Research in Computational Linguistics is dependent on text corpora for training and testing new tools and methodologies. While there exists a plethora of annotated linguistic information, these corpora are often not interoperable without significant manual work. Moreover, these annotations might have evolved into different versions, making it challenging for researchers to know the data's provenance. This paper addresses this issue with a case study on event annotated corpora and by creating a new, more interoperable representation of this data in the form of nanopublications. We demonstrate how linguistic annotations from separate corpora can be reliably linked from the start, and thereby be accessed and queried as if they were a single dataset. We describe how such nanopublications can be created and demonstrate how SPARQL queries can be performed to extract interesting content from the new representations. The queries show that information of multiple corpora can be retrieved more easily and effectively because the information of different corpora is represented in a uniform data format.

cs.CL↗

arXiv2020

A Unified Nanopublication Model for Effective and User-Friendly Access to the Elements of Scientific Publishing

Scientific publishing is the means by which we communicate and share scientific knowledge, but this process currently often lacks transparency and machine-interpretable representations. Scientific articles are published in long coarse-grained text with complicated structures, and they are optimized for human readers and not for automated means of organization and access. Peer reviewing is the main method of quality assessment, but these peer reviews are nowadays rarely published and their own complicated structure and linking to the respective articles is not accessible. In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent in a semantic way the elements of publications, their assessments, as well as the involved processes, actors, and provenance in general. To evaluate our approach, we present a dataset of 627 nanopublications representing an interlinked network of the elements of articles (such as individual paragraphs) and their reviews (such as individual review comments). Focusing on the specific scenario of editors performing a meta-review, we introduce seven competency questions and show how they can be executed as SPARQL queries. We then present a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful to answer their competency questions. In summary, we demonstrate that a unified and semantic publication model based on nanopublications can make scientific communication more effective and user-friendly.

cs.DL↗

arXiv2019

Towards FAIR protocols and workflows: The OpenPREDICT case study

It is essential for the advancement of science that scientists and researchers share, reuse and reproduce workflows and protocols used by others. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize a number of important points regarding the means by which digital objects are found and reused by others. The question of how to apply these principles not just to the static input and output data but also to the dynamic workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe our inclusive and overarching approach to apply the FAIR principles to workflows and protocols and demonstrate its benefits. We apply and evaluate our approach on a case study that consists of making the PREDICT workflow, a highly cited drug repurposing workflow, open and FAIR. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces. A semantic model was proposed to better address these specific requirements and were evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.

cs.LG↗

arXiv2019

Peer Reviewing Revisited: Assessing Research with Interlinked Semantic Comments

Scientific publishing seems to be at a turning point. Its paradigm has stayed basically the same for 300 years but is now challenged by the increasing volume of articles that makes it very hard for scientists to stay up to date in their respective fields. In fact, many have pointed out serious flaws of current scientific publishing practices, including the lack of accuracy and efficiency of the reviewing process. To address some of these problems, we apply here the general principles of the Web and the Semantic Web to scientific publishing, focusing on the reviewing process. We want to determine if a fine-grained model of the scientific publishing workflow can help us make the reviewing processes better organized and more accurate, by ensuring that review comments are created with formal links and semantics from the start. Our contributions include a novel model called Linkflows that allows for such detailed and semantically rich representations of reviews and the reviewing processes. We evaluate our approach on a manually curated dataset from several recent Computer Science journals and conferences that come with open peer reviews. We gathered ground-truth data by contacting the original reviewers and asking them to categorize their own review comments according to our model. Comparing this ground truth to answers provided by model experts, peers, and automated techniques confirms that our approach of formally capturing the reviewers' intentions from the start prevents substantial discrepancies compared to when this information is later extracted from the plain-text comments. In general, our analysis shows that our model is well understood and easy to apply, and it revealed the semantic properties of such review comments.

cs.DL↗

arXiv2019

Supporting stylists by recommending fashion style

Outfittery is an online personalized styling service targeted at men. We have hundreds of stylists who create thousands of bespoke outfits for our customers every day. A critical challenge faced by our stylists when creating these outfits is selecting an appropriate item of clothing that makes sense in the context of the outfit being created, otherwise known as style fit. Another significant challenge is knowing if the item is relevant to the customer based on their tastes, physical attributes and price sensitivity. At Outfittery we leverage machine learning extensively and combine it with human domain expertise to tackle these challenges. We do this by surfacing relevant items of clothing during the outfit building process based on what our stylist is doing and what the preferences of our customer are. In this paper we describe one way in which we help our stylists to tackle style fit for a particular item of clothing and its relevance to an outfit. A thorough qualitative and quantitative evaluation highlights the method's ability to recommend fashion items by style fit.

cs.LG↗

arXiv2018

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Nanopublications are a Linked Data format for scholarly data publishing that has received considerable uptake in the last few years. In contrast to the common Linked Data publishing practice, nanopublications work at the granular level of atomic information snippets and provide a consistent container format to attach provenance and metadata at this atomic level. While the nanopublications format is domain-independent, the datasets that have become available in this format are mostly from Life Science domains, including data about diseases, genes, proteins, drugs, biological pathways, and biotic interactions. More than 10 million such nanopublications have been published, which now form a valuable resource for studies on the domain level of the given Life Science domains as well as on the more technical levels of provenance modeling and heterogeneous Linked Data. We provide here an overview of this combined nanopublication dataset, show the results of some overarching analyses, and describe how it can be accessed and queried.

cs.DL↗

arXiv2018

Using the AIDA Language to Formally Organize Scientific Claims

Scientific communication still mainly relies on natural language written in scientific papers, which makes the described knowledge very difficult to access with automatic means. We can therefore only make limited use of formal knowledge organization methods to support researchers and other interested parties with features such as automatic aggregations, fact checking, consistency checking, question answering, and powerful semantic search. Existing approaches to solve this problem by improving the scientific communication methods have either very restricted coverage, require formal logic skills on the side of the researchers, or depend on unreliable machine learning for the formalization of knowledge. Here, I propose an approach to this problem that is general, intuitive, and flexible. It is based on a unique kind of controlled natural language, called AIDA, consisting of English sentences that are atomic, independent, declarative, and absolute. Such sentences can then serve as nodes in a network of scientific claims linked to publications, researchers, and domain elements. I present here some small studies on preliminary applications of this language. The results indicate that it is well accepted by users and provides a good basis for the creation of a knowledge graph of scientific findings.

cs.DL↗

arXiv2017

Computational Controversy

Climate change, vaccination, abortion, Trump: Many topics are surrounded by fierce controversies. The nature of such heated debates and their elements have been studied extensively in the social science literature. More recently, various computational approaches to controversy analysis have appeared, using new data sources such as Wikipedia, which help us now better understand these phenomena. However, compared to what social sciences have discovered about such debates, the existing computational approaches mostly focus on just a few of the many important aspects around the concept of controversies. In order to link the two strands, we provide and evaluate here a controversy model that is both, rooted in the findings of the social science literature and at the same time strongly linked to computational methods. We show how this model can lead to computational controversy analytics that have full coverage over all the crucial aspects that make up a controversy.

cs.CY↗