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mgr inż. Krzysztof Pastuszak
Employment
- Assistant at Department of Algorithms and Systems Modelling
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total: 26
Catalog Publications
Year 2024
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Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data
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Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data
PublicationThe field of cancer diagnostics has been revolutionized by liquid biopsies, which offer a bridge between laboratory research and clinical settings. These tests are less invasive than traditional biopsies and more convenient than routine imaging methods. Liquid biopsies allow studying of tumor-derived markers in bodily fluids, enabling the development of more precise cancer diagnostic tests for screening, disease monitoring, and...
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Detection of circulating tumor cells by means of machine learning using Smart-Seq2 sequencing
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Detection of circulating tumor cells by means of machine learning using Smart-Seq2 sequencing
PublicationCirculating tumor cells (CTCs) are tumor cells that separate from the solid tumor and enter the bloodstream, which can cause metastasis. Detection and enumeration of CTCs show promising potential as a predictor for prognosis in cancer patients. Furthermore, single-cells sequencing is a technique that provides genetic information from individual cells and allows to classify them precisely and reliably. Sequencing data typically...
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Immune escape of B-cell lymphoblastic leukemic cells through a lineage switch to acute myeloid leukemia
PublicationAcute leukemia (AL) with a lineage switch (LS) is associated with poor prognosis. The predisposing factors of LS are unknown, apart from KMT2A rearrangements that have been reported to be associated with LS. Herein, we present two cases and review all 104 published cases to identify risk factors for LS. Most of the patients (75.5%) experienced a switch from the lymphoid phenotype to the myeloid phenotype. Eighteen patients (17.0%)...
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Improving platelet‐RNA‐based diagnostics: a comparative analysis of machine learning models for cancer detection and multiclass classification
PublicationLiquid biopsy demonstrates excellent potential in patient management by providing a minimally invasive and cost-effective approach to detecting and monitoring cancer, even at its early stages. Due to the complexity of liquid biopsy data, machine-learning techniques are increasingly gaining attention in sample analysis, especially for multidimensional data such as RNA expression profiles. Yet, there is no agreement in the community...
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Sleep alterations in treatment-resistant depression patients undergoing ketamine treatment
PublicationBackground This study examines self-reported sleep alterations in treatment-resistant depression (TRD) inpatients following intravenous ketamine administration. Methods This is a post-hoc analysis of a naturalistic observational study, which enrolled 28 inpatients with treatment-resistant major depressive disorder and analyzed self-reported sleep changes (items 1–4; ‘insomnia’, ‘nighttime restlessness’, ‘early morning waking’,...
Year 2023
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Longitudinal drug synergy assessment using convolutional neural network image-decoding of glioblastoma single-spheroid cultures
PublicationAbstract Background In recent years, drug combinations have become increasingly popular to improve therapeutic outcomes in various diseases, including difficult to cure cancers such as the brain cancer glioblastoma. Assessing the interaction between drugs over time is critical for predicting drug combination effectiveness and minimizing the risk of therapy resistance. However, as viability readouts of drug combination experiments...
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Long-term mortality after transcatheter aortic valve implantation for aortic stenosis in immunosuppression-treated patients: a propensity-matched multicentre retrospective registry-based analysis
PublicationIntroduction Data regarding patients with a previous medical record of immunosuppression treatment who have undergone transcatheter aortic valve implantation (TAVI) are limited and extremely inconclusive. Available studies are mostly short term observations; thus there is a lack of evidence on efficacy and safety of TAVI in this specific group of patients. Aim To compare the in-hospital and long-term outcomes between patients...
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Neural Graph Collaborative Filtering: Analysis of Possibilities on Diverse Datasets
PublicationThis paper continues the work by Wang et al. [17]. Its goal is to verify the robustness of the NGCF (Neural Graph Collaborative Filtering) technique by assessing its ability to generalize across different datasets. To achieve this, we first replicated the experiments conducted by Wang et al. [17] to ensure that their replication package is functional. We received sligthly better results for ndcg@20 and somewhat poorer results for...
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Neural Graph Collaborative Filtering: Analysis of Possibilities on Diverse Datasets
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Platelet RNA Sequencing Data Through the Lens of Machine Learning
PublicationLiquid biopsies offer minimally invasive diagnosis and monitoring of cancer disease. This biosource is often analyzed using sequencing, which generates highly complex data that can be used using machine learning tools. Nevertheless, validating the clinical applications of such methods is challenging. It requires: (a) using data from many patients; (b) verifying potential bias concerning sample collection; and (c) adding interpretability...
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Screening of predicted synergistic multi-target therapies in glioblastoma identifies new treatment strategies
PublicationAbstract Background IDH-wildtype glioblastoma (GBM) is a highly malignant primary brain tumor with a median survival of 15 months after standard of care, which highlights the need for improved therapy. Personalized combination therapy has shown to be successful in many other tumor types and could be beneficial for GBM patients. Methods We performed the largest drug combination screen to date in GBM, using a high-throughput effort...
Year 2022
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Efficacy of intralesional bleomycin in treatment resistant viral warts
PublicationIntroduction Optimal management of treatment-refractory viral warts caused by human papillomavirus is unknown. One of the treatment methods is intralesional bleomycin solution. Objective To determine risk factors for resistant viral warts (not responding to conventional treatments for ≥ 6 months), to determine the effectiveness and safety of intralesional bleomycin in a group of patients with viral warts resistant to conventional...
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Significance of Dermoscopy in Association with Clinical Features in Differentiation of Basal Cell Carcinoma and Benign Trichoblastic Tumours
PublicationBackground: Although basal cell carcinoma (BCC) can, in the majority of cases, be diagnosed based on clinical and dermoscopic assessment, a potential overlap with benign adnexal skin tumours seems to exist, including trichoblastic tumours (TT). Methods: Retrospective analysis of clinical and dermoscopic features of benign TT and BCC cases was performed to develop a diagnostic algorithm with a potential utility in clinical practice....
Year 2021
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Bortezomib induces methylation changes in neuroblastoma cells that appear to play a significant role in resistance development to this compound
PublicationThe anticancer activity of bortezomib (BTZ) has been increasingly studied in a number of indications and promising results for the use of this treatment have been shown in neuroblastoma. As BTZ treatment is usually administered in cycles, the development of resistance and side effects in patients undergoing therapy with BTZ remains a major challenge for the clinical usage of this compound. Common resistance development also means...
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Diagnostic Accuracy of Liquid Biopsy in Endometrial Cancer
PublicationBackground: Liquid biopsy is a minimally invasive collection of a patient body fluid sample. In oncology, they offer several advantages compared to traditional tissue biopsies. However, the potential of this method in endometrial cancer (EC) remains poorly explored. We studied the utility of tumor educated platelets (TEPs) and circulating tumor DNA (ctDNA) for preoperative EC diagnosis, including histology determination. Methods:...
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Graphs hard-to-process for greedy algorithm MIN
PublicationWe compare results of selected algorithms that approximate the independence number in terms of the quality of constructed solutions. Furthermore, we establish smallest hard- to-process graphs for the greedy algorithm MIN.
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imPlatelet classifier: image‐converted RNA biomarker profiles enable blood‐based cancer diagnostics
PublicationLiquid biopsies offer a minimally invasive sample collection, outperforming traditional biopsies employed for cancer evaluation. The widely used material is blood, which is the source of tumor-educated platelets. Here, we developed the imPlatelet classifier, which converts RNA-sequenced platelet data into images in which each pixel corresponds to the expression level of a certain gene. Biological knowledge from the Kyoto Encyclopedia...
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Interval Edge Coloring of Bipartite Graphs with Small Vertex Degrees
PublicationAn edge coloring of a graph G is called interval edge coloring if for each v ∈ V(G) the set of colors on edges incident to v forms an interval of integers. A graph G is interval colorable if there is an interval coloring of G. For an interval colorable graph G, by the interval chromatic index of G, denoted by χ'_i(G), we mean the smallest number k such that G is interval colorable with k colors. A bipartite graph G is called (α,β)-biregular...
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Modelling of dark fermentation of glucose and sour cabbage
PublicationIn the article, modified Anaerobic Digestion Models 1 (ADM-1) was tested for modelling dark fermentation for hydrogen production. The model refitting was done with the Euler method. The new model was based on sets of differential equations. The model was checked for hydrogen production from sour cabbage in batch and semi-batch in 5 g VSS (volatile solid suspension)/L and at the semi-batch process from glucose at 5 and 10 g VSS/L....
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Sztuczna inteligencja w onkologii - nowe narzędzia do diagnostyki i medycyny spersonalizowanej
Publicationstatnie dekady doprowadziły do rozwoju zaawansowanych technologii badawczych, cechujących się wysoką przepustowością. Zmienia to oblicze medycyny, doprowadzając do generowania ogromnej ilości danych. Z każdym kolejnym rokiem przybywa pacjentów onkologicznych, a zebrane informacje o pacjentach przekraczają możliwości lekarzy i naukowców w zakresie samodzielnej analizy tzw. big data. Właśnie dlatego świat nauki coraz częściej zwraca...
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Towards Cancer Patients Classification Using Liquid Biopsy
PublicationLiquid biopsy is a useful, minimally invasive diagnostic and monitoring tool for cancer disease. Yet, developing accurate methods, given the potentially large number of input features, and usually small datasets size remains very challenging. Recently, a novel feature parameterization based on the RNA-sequenced platelet data which uses the biological knowledge from the Kyoto Encyclopedia of Genes and Genomes, combined with a classifier...
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Transcriptomic landscape of blood platelets in healthy donors
PublicationBlood platelet RNA-sequencing is increasingly used among the scientific community. Aberrant platelet transcriptome is common in cancer or cardiovascular disease, but reference data on platelet RNA content in healthy individuals are scarce and merit complex investigation. We sought to explore the dynamics of platelet transcriptome. Datasets from 204 healthy donors were used for the analysis of splice variants, particularly with...
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Transcriptomic landscape of blood platelets in healthy donors
PublicationBACKGROUND Blood platelet RNA-sequencing is increasingly used among the scientific community. Aberrant platelet transcriptome is common in cancer or cardiovascular disease, but reference data on platelet RNA content in healthy individuals are scarce and merit complex investigation. METHODS We sought to explore the dynamics of platelet transcriptome. Datasets from 204 healthy donors were used for the analysis of splice variants,...
Year 2017
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No-Wait & No-Idle Open Shop Minimum Makespan Scheduling with Bioperational Jobs
PublicationIn the open shop scheduling with bioperational jobs each job consists of two unit operations with a delay between the end of the first operation and the beginning of the second one. No-wait requirement enforces that the delay between operations is equal to 0. No-idle means that there is no idle time on any machine. We model this problem by the interval incidentor (1, 1)-coloring (IIR(1, 1)-coloring) of a graph with the minimum...
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