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Catalog Publications
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TreeCmp: Comparison of Trees in Polynomial Time
PublicationMetryki filogenetyczne umożliwiają ocenę jakości wyników analizy filogenetycznej oraz wiarygodności algorytmów przeprowadzających taką analizę. Aplikacja TreeCmp oferuje efektywne, wielomianowe implementacje ośmiu takich metryk (dla drzew nieukorzenionych i zawierających korzeń) zdefiniowanych dla dowolnych filogenez (nie koniecznie binarnych). Program ten jako pierwszy umożliwia wyznaczanie nowych metryk, definiowanych w oparciu...
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How to meet when you forget: log-space rendezvous in arbitrary graphs
PublicationTwo identical (anonymous) mobile agents start from arbitrary nodes in an a priori unknown graph and move synchronously from node to node with the goal of meeting. This rendezvous problem has been thoroughly studied, both for anonymous and for labeled agents, along with another basic task, that of exploring graphs by mobile agents. The rendezvous problem is known to be not easier than graph exploration. A well-known recent result...
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Taking advantage of symmetries: Gathering of many asynchronous oblivious robots on a ring
PublicationOne of the recently considered models of robot-based computing makes use of identical, memoryless mobile units placed in nodes of an anonymous graph. The robots operate in Look-Compute-Move cycles; in one cycle, a robot takes a snapshot of the current configuration (Look), takes a decision whether to stay idle or to move to one of the nodes adjacent to its current position (Compute), and in the latter case makes an instantaneous...
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Fast collaborative graph exploration
PublicationWe study the following scenario of online graph exploration. A team of k agents is initially located at a distinguished vertex r of an undirected graph. At every time step, each agent can traverse an edge of the graph. All vertices have unique identifiers, and upon entering a vertex, an agent obtains the list of identifiers of all its neighbors. We ask how many time steps are required to complete exploration, i.e., to make sure...
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Constructing a map of an anonymous graph: applications of universal sequences
PublicationWe study the problem of mapping an unknown environmentrepresented as an unlabelled undirected graph. A robot (or automaton)starting at a single vertex of the graph G has to traverse the graph and return to its starting point building a map of the graph in the process. We are interested in the cost of achieving this task (whenever possible) in terms of the number of edge traversal made by the robot. Another optimization criteria...
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On a matching distance between rooted phylogenetic trees
PublicationThe Robinson–Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach...
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Drawing maps with advice
PublicationRozważamy następujący problem obliczeniowy. Agent zostaje umieszczony w wierzchołku nieznanego mu grafu. Wierzchołki grafu są nierozróżnialne, natomiast krawędzie posiadają numery portów. Zadaniem agenta jest wyznaczenie mapy, tzn. obliczenie izomorficznej kopii grafu, lub obliczenie dowolnego drzewa spinającego grafu. Bez dodatkowej informacji zadań tych nie można wykonać. W artykule wyznaczamy oszacowania na minimalną liczbę...
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Euler tour lock-in problem in the rotor-router model
PublicationW pracy rozważano model eksploracji grafu nieskierowanego przez pojedynczego agenta, w którym sterowanie agentem odbywa się zgodnie z zasadą ''rotor-router'' (inaczej: ''Propp machine''). Porównano czas stabilizacji agenta do trajektorii w postaci cyklu Eulera dla różnych klas grafów, prowadząc rozważania w kontekście teorii gier. Przydział początkowych portów i wskaźników w modelu jest traktowany jako rozgrywka pomiędzy graczem...
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Connections between Mutually Unbiased Bases and Quantum Random Access Codes
PublicationWe present a new quantum communication complexity protocol, the promise--Quantum Random Access Code, which allows us to introduce a new measure of unbiasedness for bases of Hilbert spaces. The proposed measure possesses a clear operational meaning and can be used to investigate whether a specific number of mutually unbiased bases exist in a given dimension by employing Semi--Definite Programming techniques.
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A graph coloring approach to scheduling of multiprocessor tasks on dedicated machines with availability constraints
PublicationWe address a generalization of the classical 1- and 2-processor unit execution time scheduling problem on dedicated machines. In our chromatic model of scheduling machines have non-simultaneous availability times and tasks have arbitrary release times and due dates. Also, the versatility of our approach makes it possible to generalize all known classical criteria of optimality. Under these stipulations we show that the problem...
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Cost minimization in wireless networks with a bounded and unbounded number of interfaces
PublicationPraca dotyczy problemu minimalizacji energii poprzez selektywne odłączanie urządzeń komunikacyjnych w wielointerfejsowych sieciach bezprzewodowych w taki sposób, by zapewnić realizację wymaganego grafu połączeń. Sformułowano problem optymalizacyjny, podano wyniki dotyczące jego trudności i zaproponowano algorytmy optymalizacyjne. Rozważono zarówno wariant, w którym liczba interfejsów komunikacyjnych jest parametrem stałym (narzuconym...
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Monitoring of the Process of System Information Broadcasting in Time
PublicationOne of the problems of quantum physics is how a measurement turns quantum, noncopyable data, towards copyable classical knowledge. We use the quantum state discrimination in a central system model to show how its evolution leads to the broadcasting of the information, and how orthogonalization and decoherence factors allow us to monitor the distance of the state in question to the one perfectly broadcasting information, in any...
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Taking advantage of symmetries: gathering of asynchronous oblivious robots on a ring
PublicationW pracy rozważano problem rendezvous (spotkania, zebrania) dla zbioru bezpamięciowych robotów umieszczonych na wierzchołkach cyklu nieskierowanego, niewyposażonych w urządzenia komunikacyjne. Przyjęto model systemu rozproszonego występujący w literaturze pod nazwą asynchronicznego systemu z cyklami Look-Compute-Move. Problem istnienia rozwiązania rozwiązano dla wszystkich konfiguracji poczatkowych składających się z więcej niż...
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Experimentally feasible semi-device-independent certification of four-outcome positive-operator-valued measurements
PublicationRecently the quantum information science community devoted a lot of attention to the theoretical and practical aspects of generalized measurements, the formalism of all possible quantum operations leading to acquisition of classical information. On the other hand, due to imperfections present in quantum devices, and limited thrust to them, a trend of formulating quantum information tasks in a semi-device-independent manner emerged....
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Edge ranking and searching in partial orders
PublicationArtykuł jest poświęcony problemowi konstrukcji optymalnej (wymagającej minimalnej ilości porównań/zapytań) strategii wyszukiwania elementu w częściowym porządku. W pracy wskazano związki pomiędzy tym problemem oraz uporządkowanym kolorowaniem krawędzi grafów, co implikuje liniowy algorytm dla częściowych porządków o strukturze drzewa. Pokazano również, że znalezienie optymalnej strategii jest problemem obliczeniowo trudnym dla...
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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,...
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From Pathwidth to Connected Pathwidth
PublicationW pracy przedstawiono dowód faktu, że spójna szerokość ścieżkowa grafu wynosi co najwyżek 2k+1, gdzie k jest jego szerokością ścieżkową. Dowód jest konstruktywny, tzn., został skonstruowany algorytm, który dla podanej na wejściu dekompozycji grafu o szerekości k zwraca dekompozycję spóją o szerekości co najwyżej 2k+1.
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On the complexity of distributed graph coloring with local minimality constraints
PublicationArtykuł traktuje o zachłannym kolorowaniu grafów w modelu rozproszonym. Omówiono algorytmy rozproszone, dające w wyniku pokolorowanie spełniające warunki dla pokolorowań sekwencyjnych typu S oraz Largest-First (LF). Udowodniono również, że każda rozproszona implementacja algorytmu S wymaga co najmniej Omega(log n / log log n) rund, a algorytmu LF co najmniej Omega (n^{1/2}) rund, gdzie n oznacza liczbę wierzchołków grafu.
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Experimental certification of an informationally complete quantum measurement in a device-independent protocol
PublicationMinimal informationally complete positive operator-valued measures (MIC-POVMs) are special kinds of measurement in quantum theory in which the statistics of their d2-outcomes are enough to reconstruct any d-dimensional quantum state. For this reason, MIC-POVMs are referred to as standard measurements for quantum information.Here, we report an experiment with entangled photon pairs that certifies, for what we believe is the first...
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Improving Accuracy of Contactless Respiratory Rate Estimation by Enhancing Thermal Sequences with Deep Neural Networks
PublicationEstimation of vital signs using image processing techniques have already been proved to have a potential for supporting remote medical diagnostics and replacing traditional measurements that usually require special hardware and electrodes placed on a body. In this paper, we further extend studies on contactless Respiratory Rate (RR) estimation from extremely low resolution thermal imagery by enhancing acquired sequences using Deep...
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Exploiting multi-interface networks: Connectivity and Cheapest Paths
PublicationLet G = (V,E) be a graph which models a set of wireless devices (nodes V) that can communicate by means of multiple radio interfaces, according to proximity and common interfaces (edges E). The problem of switching on (activating) the minimum cost set of interfaces at the nodes in order to guarantee the coverage of G was recently studied. A connection is covered (activated) when the endpoints of the corresponding edge share at...
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Exploiting Multi-Interface Networks: Connectivity and Cheapest Paths
PublicationRozważano zagadnienie minimalizacji energii w sieciach bezprzewodowych bez infrastruktury, w których niektóre węzły są wyposażone w więcej, niż jeden interfejs. W przyjętym modelu sieci podano nowe algorytmy przybliżone oraz wyniki dotyczące złożoności obliczeniowej dla dwóch problemów: aktywacji najtańszej spójnej podsieci spinającej oraz aktywacji ścieżki pomiędzy ustaloną parą węzłów.
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Complementarity between entanglement-assisted and quantum distributed random access code
PublicationCollaborative communication tasks such as random access codes (RACs) employing quantum resources have manifested great potential in enhancing information processing capabilities beyond the classical limitations. The two quantum variants of RACs, namely, quantum random access code (QRAC) and the entanglement-assisted random access code (EARAC), have demonstrated equal prowess for a number of tasks. However, there do exist specific...
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Leader election for anonymous asynchronous agents in arbitrary networks
PublicationWe consider the problem of leader election among mobile agents operating in an arbitrary network modeled as an undirected graph. Nodes of the network are unlabeled and all agents are identical. Hence the only way to elect a leader among agents is by exploiting asymmetries in their initial positions in the graph. Agents do not know the graph or their positions in it, hence they must gain this knowledge by navigating in the graph...
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Visual TreeCmp : Comprehensive Comparison of Phylogenetic Trees on the Web
Publication1. We present Visual TreeCmp—a package of applications for comparing phylogenetic tree sets. 2. Visual TreeCmp includes a graphical web interface allowing the visualization of compared trees and command line application extended by comparison methods recently proposed in the literature. 3. The phylogenetic tree similarity analysis in Visual TreeCmp can be performed using eighteen metrics, of which 11 are dedicated to rooted trees...
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Universal Augmentation Schemes for Network Navigability
PublicationRozważano problem uzupełniania grafu (reprezentującego np. sieci społeczne) poprzez dodanie w każdym węźle jednego dodatkowego skierowanego połączenia (długodystansowego). Dokładniej, dla każdego węzła definiuje się listę prawdopodobieństw istnienia połączenia wychodzącego z danego węzła do wszystkich pozostałych węzłów; wartości tych prawdopodobieństw muszą sumować się do jedności. Routing zachłanny w takiej sieci polega na przekazywaniu...
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Approximating the maximum 2- and 3-edge-colorable subgraph problems
PublicationDla ustalonej wartości parametru k>=2, problem maksymalnego podgrafu krawędziowo k-kolorowalnego polega na wskazaniu k rozłącznych skojarzeń w grafie prostym, a kryterium optymalizacji jest maksymalizacja całkowitej liczby użytych krawędzi. W pracy podano algorytmy 5/6- i 4/5-przybliżone odpowiednio dla przypadków k=2 i k=3, poprawiając wyniki znane z literatury.
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What Can Be Observed Locally? Round based models for quantum distributed computing
PublicationW pracy rozważono zagadnienie lokalności w kontekście informacji kwantowej w obliczeniach rozproszonych. Rozważono dwa kwantowe rozszerzenia modelu LOCAL Liniala, otrzymane poprzez: (1) inicjalizację systemu w kwantowym stanie splątanym, (2) zastosowanie kwantowych kanałów komunikacyjnych. Dla obydwu typów rozszerzeń zaproponowano przykłady problemów, których złożoność rundowa ulega redukcji w porównaniu do oryginalnego modelu...
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Connected searching of weighted trees
PublicationW pracy pokazano, że problem spójnego przeszukiwania drzew ważonych jest silnie NP-zupełny. Problem pozostaje trudnym dla drzew z jednym wierzchołkiem o stopniu większym niż 2. Ponadto, przedstawiony został wielomianowy optymalny algorytm dla klasy drzew z ograniczonym stopniem.
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Trees having many minimal dominating sets
PublicationWe provide an algorithm for listing all minimal dominating sets of a tree of order n in time O(1.4656^n). This leads to that every tree has at most 1.4656^n minimal dominating sets. We also give an infinite family of trees of odd and even order for which the number of minimal dominating sets exceeds 1.4167^n, thus exceeding 2^{n/2}. This establishes a lower bound on the running time of an algorithm for listing all minimal dominating...
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Graph Decomposition for Memoryless Periodic Exploration
PublicationWe consider a general framework in which a memoryless robot periodically explores all the nodes of a connected anonymous graph by following local information available at each vertex. For each vertex v, the endpoints of all edges adjacent to v are assigned unique labels within the range 1 to deg (v) (the degree of v). The generic exploration strategy is implemented using a right-hand-rule transition function: after entering vertex...
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The complexity of zero-visibility cops and robber
PublicationWe consider the zero-visibility cops & robber game restricted to trees. We produce a characterisation of trees of copnumber k and We consider the computational complexity of the zero-visibility Cops and Robber game. We present a heavily modified version of an already-existing algorithm that computes the zero-visibility copnumber of a tree in linear time and we show that the corresponding decision problem is NP-complete on a nontrivial...
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Zero-visibility cops and robber and the pathwidth of a graph
PublicationWe examine the zero-visibility cops and robber graph searching model, which differs from the classical cops and robber game in one way: the robber is invisible. We show that this model is not monotonic. We show that the zero-visibility copnumber of a graph is bounded above by its pathwidth and cannot be bounded below by any nontrivial function of the pathwidth. As well, we define a monotonic version of this game and show that the...
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Collaborative Exploration of Trees by Energy-Constrained Mobile Robots
PublicationWe study the problem of exploration of a tree by mobile agents (robots) that have limited energy. The energy constraint bounds the number of edges that can be traversed by a single agent. We use a team of agents to collectively explore the tree and the objective is to minimize the size of this team. The agents start at a single node, the designated root of the tree and the height of the tree is assumed to be less than the energy...
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Synchronous black hole search in directed graphs
PublicationThe paper considers a team of robots which has to explore a graph G, where some nodes can be harmful. Robots are initially located at the so-called home base node. The dangerous nodes are the so-called black hole nodes, and once a robot enters in one of them, it is destroyed. The goal is to find a strategy in order to explore G in such a way that minimum number of robots is wasted. The exploration ends if there is at least one...
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System information propagation for composite structures
PublicationWe study in details decoherence process of a spin register, coupled to a spin environment. We use recently developed methods of information transfer study in open quantum systems to analyze information flow between the register and its environment. We show that there are regimes when not only the register decoheres effectively to a classical bit string, but this bit string is redundantly encoded in the environment, making it available...
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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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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Turbine stage design aided by artificial intelligence methods
PublicationZaproponowano ogólny, wydajny system wspomagania projektowania palisad , stopni i grupy stopni turbinowych. Zastosowane algorytmy wykorzystują algorytmy genetyczne, sieci neuronowe i obliczenia równoległe. Uzyskane rozwiązania projektowe są wysoko zoptymalizowane pod względem sprawności, a czas ich uzyskania jest o kilka rzędów wielkości mniejszy, niż przy zastosowaniu obliczeń CFD.
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Increased Certification of Semi-device Independent Random Numbers using Many Inputs and More Postprocessing
PublicationQuantum communication with systems of dimension larger than two provides advantages in information processing tasks. Examples include higher rates of key distribution and random number generation. The main disadvantage of using such multi-dimensional quantum systems is the increased complexity of the experimental setup. Here, we analyze a not-so-obvious problem: the relation between randomness certification and computational requirements...
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The Potential of Greed for Independence
PublicationThe well-known lower bound on the independence number of a graph due to Caro and Wei can be established as a performance guarantee of two natural and simple greedy algorithms or of a simple randomized algorithm. We study possible generalizations and improvements of these approaches using vertex weights and discuss conditions on so-called potential functions p(G) : V(G) -> N_0 defined on the vertex set of a graph G for which suitably...
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On the size of identifying codes in triangle-free graphs
PublicationIn an undirected graph G, a subset C⊆V(G) such that C is a dominating set of G, and each vertex in V(G) is dominated by a distinct subset of vertices from C, is called an identifying code of G. The concept of identifying codes was introduced by Karpovsky, Chakrabarty and Levitin in 1998. For a given identifiable graph G, let gammaID(G) be the minimum cardinality of an identifying code in G. In this paper, we show that for any connected...
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Scheduling of unit-length jobs with cubic incompatibility graphs on three uniform machines
PublicationWe consider the problem of scheduling n identical jobs on 3 uniform machines with speeds s1, s2, and s3 to minimize the schedule length. We assume that jobs are subject to some kind of mutual exclusion constraints, modeled by a cubic incompatibility graph. We how that if the graph is 2-chromatic then the problem can be solved in O(n^2) time. If the graph is 3-chromatic, the problem becomes NP-hard even if s1>s2=s3.
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Steering is an essential feature of non-locality in quantum theory
PublicationA physical theory is called non-local when observers can produce instantaneous effects over distant systems. Non-local theories rely on two fundamental effects: local uncertainty relations and steering of physical states at a distance. In quantum mechanics, the former one dominates the other in a well-known class of non-local games known as XOR games. In particular, optimal quantum strategies for XOR games are completely determined...
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Self-stabilizing algorithms for graph coloring with improved performance guarantees
PublicationW pracy rozważa się rozproszony model obliczeń, w którym struktura systemu jest reprezentowana przez graf bezpośrednich połączeń komunikacyjnych. W tym modelu podajemy nowy samostabilizujący algorytm kolorowania grafów oparty na konstrukcji drzewa spinającego. Zgodnie z naszą wiedzą jest to pierwszy algorytm z gwarantowaną wielomianową liczbą ruchów, który dokładnie koloruje grafy dwudzielne.
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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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Security of Cryptocurrencies: A View on the State-of-the-Art Research and Current Developments
Publication[Context] The goal of security is to protect digital assets, devices, and services from being disrupted, exploited or stolen by unauthorized users. It is also about having reliable information available at the right time. [Motivation] Since the inception in 2009 of the first cryptocurrency, few studies have been undertaken to analyze and review the state-of-the-art research and current developments with respect to the security...
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Cooperative mobile guards in grids
PublicationPraca dotyczy problemu strzeżenia dwuwymiarowych krat ortogonalnych, przy założeniu, że obszar widoczności strażnika obejmuje jedną ulicę oraz wszystkie ulice ją przecinające. Rozważano wariant straży słabo współpracujących, w którym dodatkowo każdy strażnik musi widzieć przynajmniej jednego innego strażnika. Podano dowód NP-trudności problemu optymalizacyjnego w przypadku ogólnym, algorytm dokładny o złożoności O(n log n) dla...
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Synchronization helps robots to detect black holes in directed graphs
PublicationPraca zawiera nowe wyniki dla problemu poszukiwania czarnej dziury w grafie skierowanym przez zbiór agentów. Czarna dziura jest węzłem niszczącym wszystkich wchodzącej do niej agentów. Pokazano, że w przypadku, gdy stopień wejściowy czarnej dziury wynosi D, do przeszukania grafu skierowanego w modelu synchronicznym wystarcza O(D 2^D) agentów. Wartość ta jest bliska znanemu z literatury oszacowaniu dolnemu Omega (2^D). W pracy pokazano...