Piotr Wieczorek

University of Wrocław

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Co-Authors

Sławek Staworko

Université de Lille

Jakub Michaliszyn

University of Wrocław

Jan Otop

University of Wrocław

Benoît Groz

Laboratoire Interdisciplinaire des Sciences du Numérique

Aurélien Lemay

Université de Lille

Paolo Guagliardo

University of Edinburgh

Katarzyna Dziarkowska

University of Opole

Anca Muscholl

Institut Polytechnique de Bordeaux

Waldemar Balcerzak

Wroclaw Medical University

Paweł Dżygiel

Roche (Switzerland)

Cooperative Institutions

Centre National de la Recherche Scientifique

University of Wrocław

Institut national de recherche en informatique et en automatique

Centre de recherche Inria Lille - Nord Europe

Université de Lille

Wroclaw Medical University

Jadavpur University

Université Paris Cité

Laboratoire d'Informatique Algorithmique: Fondements et Applications

General Department of Preventive Medicine

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Querying Best Paths in Graph Databases

arXiv (Cornell University) (2017)

Jakub Michaliszyn Jan Otop Piotr Wieczorek

Querying graph databases has recently received much attention. We propose a new approach to this problem, which balances competing goals of expressive power, language clarity and computational complexity. A distinctive feature of our approach is the ability to express properties of minimal (e.g. shortest) and maximal (e.g. most valuable) paths satisfying given criteria. To express complex properties in a modular way, we introduce labelling-generating ontologies. The resulting formalism is computationally attractive -- queries can be answered in non-deterministic logarithmic space in the size of the database.

Expressive power

CLARITY

Formalism (music)

10.48550/arxiv.1710.04419

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Nowotwory tarczycy — klasyczne techniki diagnostyczne i markery nowotworowe

Kosmos (2006)

Katarzyna Dziarkowska Piotr Wieczorek

Thyroid tumors are a very common disorder and can occur in six percent of human population. Despite this fact, there are still no effective and reliable techniques that would allow to pose a reliable differential diagnosis between malignant and benign thyroid tumor. The prevailing diagnostic techniques are: ultrasonography, scinthigraphy and fine needle aspiration cytology. In many cases they can not distinguish carcinomas from benign neoplasms. Such diagnosis is essential, because the patient with malignancy undergoes a very rigorous treatment that is unnecessary and inadvisable for patient with benign lesions. Therefore, the thyroid tumor markers are searched for. Generally tumor markers are substances, which presence or absence is related to malignancy. They can be used for population screening and for detection, diagnosis, staging, prognosis or follow up of malignant diseases. The thyroid tumor markers currently used have very restricted applications. The first one ? calcitonine is produced only by one kind of cancer (medullary carcinoma) and the second ? thyroglobulin is useful only in detection of recurrent follicular and papillary thyroid carcinoma. Therefore, there is a need to search for new tumor marker that could enable to differentiate benign lesions in thyroid from malignancies. This review article presents some information about thyroid neoplasms and methods of their diagnosis, highlighting current and possible usage of tumor markers.

Thyroglobulin

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Learning XML Twig Queries

arXiv (Cornell University) (2011)

Sławek Staworko Piotr Wieczorek

We investigate the problem of learning XML queries, path queries and tree pattern queries, from examples given by the user. A learning algorithm takes on the input a set of XML documents with nodes annotated by the user and returns a query that selects the nodes in a manner consistent with the annotation. We study two learning settings that differ with the types of annotations. In the first setting the user may only indicate required nodes that the query must return. In the second, more general, setting, the user may also indicate forbidden nodes that the query must not return. The query may or may not return any node with no annotation. We formalize what it means for a class of queries to be \emph{learnable}. One requirement is the existence of a learning algorithm that is sound i.e., always returns a query consistent with the examples given by the user. Furthermore, the learning algorithm should be complete i.e., able to produce every query with a sufficiently rich example. Other requirements involve tractability of learning and its robustness to nonessential examples. We show that the classes of simple path queries and path-subsumption-free tree queries are learnable from positive examples. The learnability of the full class of tree pattern queries (and the full class of path queries) remains an open question. We show also that adding negative examples to the picture renders the learning unfeasible. Published in ICDT 2012, Berlin.

Learnability

Tree (set theory)

Robustness

10.48550/arxiv.1106.3725

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Inference of Shape Graphs for Graph Databases

HAL (Le Centre pour la Communication Scientifique Directe) (2022)

Benoît Groz Aurélien Lemay Sławek Staworko Piotr Wieczorek

10.4230/lipics.icdt.2022.7

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Query Answering in Data Integration

Piotr Wieczorek

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Querying Best Paths in Graph Databases.

Foundations of Software Technology and Theoretical Computer Science (2017)

Jakub Michaliszyn Jan Otop Piotr Wieczorek

Expressive power

CLARITY

Formalism (music)

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[Preliminary approach towards construction of peptide libraries as potential tools for diagnosis of malignant thyroid tumors].

Endokrynologia Polska (2006)

Waldemar Balcerzak Wiktor Bednarz Paweł Domosławski Robert Olewiński J. Kolesińska

Cancer of thyroid gland is the most common malignancy of the endocrine system. The treatment improvement could be achieved by early diagnosis. The aim of the study was to identify cancer specific antigenes with use of peptide libraries.The material from 6 patients with thyroid cancer (4 with papillary cancer, 1 with follicular cancer and 1 with oxyphilic tumor) were analyzed. It was performed with use of lipophylic peptide libraries by direct comparison of staining of specimens prepared from normal and malignant tissue.Preliminary results confirm practical value of peptide libraries in early diagnostics of thyroid cancer.It is important to optimize construction of peptide libraries by using different staining agents hydrolyzed by proteases.

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Data Exchange, Integration, and Streams

Paolo Guagliardo Piotr Wieczorek

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Citations (6)

Inference of Shape Expression Schemas Typed RDF Graphs

arXiv (Cornell University) (2021)

Benoît Groz Aurélien Lemay Sławek Staworko Piotr Wieczorek

We consider the problem of constructing a Shape Expression Schema (ShEx) that describes the structure of a given input RDF graph. We employ the framework of grammatical inference, where the objective is to find an inference algorithm that is both sound i.e., always producing a schema that validates the input RDF graph, and complete i.e., able to produce any schema, within a given class of schemas, provided that a sufficiently informative input graph is presented. We study the case where the input graph is typed i.e., every node is given with its types. We limit our attention to a practical fragment ShEx0 of Shape Expressions Schemas that has an equivalent graphical representation in the form of shape graphs. We investigate the problem of constructing a canonical representative of a given shape graph. Finally, we present a sound and complete algorithm for shape graphs thus showing that ShEx0 is learnable from typed graphs.

Schema (genetic algorithms)

RDF Schema

10.48550/arxiv.2107.04891

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On Injective Embeddings of Tree Patterns

arXiv (Cornell University) (2012)

Jakub Michaliszyn Anca Muscholl Sławek Staworko Piotr Wieczorek Zhilin Wu

We study three different kinds of embeddings of tree patterns: weakly-injective, ancestor-preserving, and lca-preserving. While each of them is often referred to as injective embedding, they form a proper hierarchy and their computational properties vary (from P to NP-complete). We present a thorough study of the complexity of the model checking problem i.e., is there an embedding of a given tree pattern in a given tree, and we investigate the impact of various restrictions imposed on the tree pattern: bound on the degree of a node, bound on the height, and type of allowed labels and edges.

Tree (set theory)

10.48550/arxiv.1204.4948

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