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Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs 22

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Prefix-Free Parsing for Building Large Tunnelled Wheeler Gra...

22nd International Workshop on Algorithms in Bioinformatics, WABI 2022

作者： Goga, Adrián Baláž, Andrej Department of Computer Science Faculty of Mathematics Physics and Informatics Comenius University Bratislava Slovakia Department of Applied Informatics Faculty of Mathematics Physics and Informatics Comenius University Bratislava Slovakia

ISBN: (纸本)9783959772433

We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this area: Wheeler graphs (Gagie et al., 2017) and prefix-free parsing (PFP, Boucher et al., 2019). Wheeler graphs are a general framework encompassing several indexes based on the Burrows-Wheeler transform (BWT), such as the FM-index. Wheeler graphs admit a succinct representation which can be further compacted by employing the idea of tunnelling, which exploits redundancies in the form of parallel, equally-labelled paths called blocks that can be merged into a single path. The problem of finding the optimal set of blocks for tunnelling, i.e. the one that minimizes the size of the resulting Wheeler graph, is known to be NP-complete and remains the most computationally challenging part of the tunnelling process. To find an adequate set of blocks in less time, we propose a new method based on the prefix-free parsing (PFP). The idea of PFP is to divide the input text into phrases of roughly equal sizes that overlap by a fixed number of characters. The phrases are then sorted lexicographically. The original text is represented by a sequence of phrase ranks (the parse) and a list of all used phrases (the dictionary). In repetitive texts, the PFP representation of the text is generally much shorter than the original since individual phrases are used many times in the parse, thus reducing the size of the dictionary. To speed up the block selection for tunnelling, we apply the PFP to obtain the parse and the dictionary of the original text, tunnel the Wheeler graph of the parse using existing heuristics and subsequently use this tunnelled parse to construct a compact Wheeler graph of the original text. Compared with constructing a Wheeler graph from the original text without PFP, our method is much faster and uses less memory on collections of

关键词： Graphic methods

Ultrafast laser-induced dynamics of non-equilibrium electron spill-out in nanoplasmonic bilayers

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arXiv 2024年

作者： Avdizhiyan, Artur Janus, Weronika Szpytma, Marcin Lezak, Tomasz Przybylski, Marek Chrobak, Maciej Roddatis, Vladimir Stupakiewicz, Andrzej Razdolski, Ilya Faculty of Physics University of Bialystok Bialystok15-245 Poland Faculty of Physics and Applied Computer Science AGH University of Krakow Kraków Poland Academic Centre for Materials and Nanotechnology AGH University of Krakow Kraków Poland Helmholtz Centre Potsdam Telegrafenberg PotsdamD-14473 Germany

Contemporary quantum plasmonics captures subtle corrections to the properties of plasmonic nanoobjects in the equilibrium. Here, we demonstrate non-equiulbrium spill-out redistribution of the electronic density at the ultrafast timescale. As revealed by time-resolved 2D spectroscopy of nanoplasmonic Fe/Au bilayers, an injection of the laser-excited non-thermal electrons induces transient electron spill-out thus changing the plasma frequency. The response of the local electronic density switches the electronic density behaviour from spill-in to strong (an order of magnitude larger) spill-out at the femtosecond timescale. The superdiffusive transport of hot electrons and the lack of a direct laser heating indicate significantly non-thermal origin of the underlying physics. Our results demonstrate an ultrafast and non-thermal way to control surface plasmon dispersion through transient variations of the spatial electron distribution at the nanoscale. These findings expand quantum plasmonics into previously unexplored directions by introducing ultrashort timescales in the non-equilibrium electronic systems. © 2024, CC0.

关键词： Hazardous materials spills

Enhancing the Swanepoel method: precise envelope detection of thin-film transmission spectra

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Optics Express 2025年第6期33卷 13376-13400页

作者： Ballester, Manuel Marquez, Almudena P. Lopez-Tapia, Santiago Fernandez, Susana Bass, John Minkov, Dorian Wuersch, Christoph Willomitzer, Florian Marquez, Emilio Katsaggelos, Aggelos K. Computer Science Department Northwestern University EvanstonIL60208 United States Department of Mathematics Faculty of Science University of Cadiz Puerto Real11510 Spain Department of Electrical and Computer Engineering Northwestern University EvanstonIL60208 United States CIEMAT Avenida Complutense 40 Madrid28040 Spain Wyant College of Optical Sciences University of Arizona TucsonAZ85721 United States Sofia1000 Bulgaria Institute for Computational Engineering ICE OST Eastern Switzerland University of Applied Sciences Switzerland Department of Condensed-matter Physics Faculty of Science University of Cadiz Puerto Real11510 Spain

The Swanepoel method is a widely used optical technique for characterizing thin films through normal-incidence transmission measurements. A critical step in this approach involves extracting the upper and lower envelopes of the measured oscillatory spectrum. By analyzing the transmission spectrum and its corresponding envelopes, the Swanepoel procedure enables precise determination of the film refractive index and extinction coefficient. However, even minor inaccuracies in envelope construction can propagate significant errors into the final characterization results. To address this challenge, we present what we believe to be a novel physics-informed optimization algorithm for envelope detection. Our mathematical model reformulates the envelope detection problem as a global optimization task that enforces the physical properties of the Swanepoel envelopes. Extensive validation on fifty randomly generated transmission spectra demonstrates unprecedented accuracy: the method achieves root-mean-square errors (RMSE) below 0.10% for the upper envelope and 0.06% for the lower envelope (more than doubling the accuracy of current state-of-the-art approaches). Furthermore, the proposed model has been assessed with two experimental transmission spectra, demonstrating its robustness and accuracy with real noisy data. We have developed an open-source Python software package (see text below). This software includes not only our innovative envelope construction algorithm but also additional envelope drawing algorithms for comparison and an efficient implementation of the Swanepoel method, enabling complete optical characterization of thin films. © 2025 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.

关键词： Mean square error

Effect of transverse momentum conservation and flow on symmetric cumulants sc2,3 {4} and sc2,3,4 {6}

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arXiv 2025年

作者： Pei, Jia-Lin Ma, Guo-Liang Bzdak, Adam Institute of Modern Physics Fudan University Shanghai200433 China Shanghai Research Center for Theoretical Nuclear Physics NSFC and Fudan University Shanghai200438 China AGH University of Science and Technology Faculty of Physics and Applied Computer Science Kraków30-059 Poland

Symmetric cumulants can improve our understanding of the joint probability distribution function P (vm, vn, vk, . . ., Ψm, Ψn, Ψk, . . .), potentially offering new insights into the nature of the fluctuations of the quark-gluon plasma produced in relativistic heavy-ion collisions. In this work, the four-particle symmetric cumulants sc2,3 {4}, six-particle symmetric cumulants sc2,3,4 {6}, and the normalized cumulants nsc2,3 {4} and nsc2,3,4 {6} originating from transverse momentum conservation, collective flow, and the interplay between the two effects are calculated. Our results are consistent with the ATLAS data using the subevent cumulant method and the simulations using the realistic Monte Carlo models of iEBE-VISHNU and HIJING, facilitating a more profound understanding of the origins of these symmetric cumulants in small systems. © 2025, CC BY.

关键词： Distribution functions

Classification of Wheat Species Using Convolutional Neural Networks: A Comparative Study 8th

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Classification of Wheat Species Using Convolutional Neural ...

8th EAI International Conference on Future Access Enablers of Ubiquitous and Intelligent Infrastructures, FABULOUS 2024

作者： Kowalski, Piotr A. Jeczmionek, Ernest Charytanowicz, Malgorzata Lukasik, Szymon Niewczas, Jerzy Kulczycki, Piotr Faculty of Physics and Applied Computer Science AGH University of Krakow al. A. Mickiewicza 30 Cracow30-059 Poland Polish Academy of Sciences Systems Research Institute ul. Newelska 6 Warsaw01-447 Poland Doctoral School at AGH Krakow al. A. Mickiewicza 30 Cracow30-059 Poland Department of Computer Science Lublin University of Technology ul. Nadbystrzycka 36B Lublin20-618 Poland Department of Microstructure and Mechanics of Biomaterials Institute of Agrophysics PAS Doswiadczalna 4 Lublin20-290 Poland

ISBN: (纸本)9783031723926

This paper introduces a novel image dataset tailored for evaluating machine learning solutions, particularly focusing on deep neural networks. Derived from X-ray images of wheat grains, the dataset encompasses three distinct species: Kama, Rosa, and Canadian. We provide a comprehensive overview of the dataset’s structure and conduct experiments using ten pretrained deep neural networks to classify wheat species. The Seeds Image Data Set offers a competitive alternative to established object recognition benchmarks such as CIFAR-10, CIFAR-100, SVHN, and ImageNet. Its compact size streamlines computational processes, making it an efficient resource for exploratory data analysis. The dataset will be publicly available, serving as a foundational resource for future research endeavors in the field. © ICST Institute for computer sciences, Social Informatics and Telecommunications Engineering 2025.

关键词： Convolutional neural networks

Factorial cumulants from short-range correlations and global baryon number conservation

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arXiv 2022年

作者： Barej, Michal Bzdak, Adam AGH University of Science and Technology Faculty of Physics and Applied Computer Science Kraków30-059 Poland

We calculate the baryon factorial cumulants assuming arbitrary short-range correlations and the global baryon number conservation. The general factorial cumulant generating function is derived. Various relations between factorial cumulants subjected to baryon number conservation and the factorial cumulants without this constraint are presented. We observe that for n-th factorial cumulant, the short-range correlations of more than n particles are suppressed with the increasing number of particles. The recently published [1] relations between the cumulants in a finite acceptance with global baryon conservation and the grand-canonical susceptibilities are reproduced. © 2022, CC BY.

关键词： Hadrons

Cumulants from short-range correlations and baryon number conservation - next-to-leading order

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arXiv 2022年

作者： Barej, Michal Bzdak, Adam AGH University of Science and Technology Faculty of Physics and Applied Computer Science Kraków30-059 Poland

We calculate the baryon number cumulants within acceptance with short-range correlations and global baryon number conservation in terms of cumulants in the whole system without baryon conservation. We extract leading and next-to-leading order terms of the large baryon number limit approximation. Our results extend the findings of Refs. [1, 2]. These approximations are checked to be very close to the exact results. © 2022, CC BY.

关键词： Hadrons

Ask the experts: Sourcing a high-quality nutrition counseling dataset through Human-AI collaboration

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Ask the experts: Sourcing a high-quality nutrition counselin...

2024 Conference on Empirical Methods in Natural Language Processing, EMNLP 2024

作者： Balloccu, Simone Reiter, Ehud Li, Karen Jia-Hui Sargsyan, Rafael Kumar, Vivek Recupero, Diego Reforgiato Riboni, Daniele Dusek, Ondrej Charles University Faculty of Mathematics and Physics Institute of Formal and Applied Linguistics Prague Czech Republic Department of Computing Science University of Aberdeen United Kingdom FI CODE University of Bundeswehr Munich Germany Department of Mathematics and Computer Science University of Cagliari Italy

ISBN: (纸本)9798891761681

Large Language Models (LLMs) are being employed by end-users for various tasks, including sensitive ones such as health counseling, disregarding potential safety concerns. It is thus necessary to understand how adequately LLMs perform in such domains. We conduct a case study on ChatGPT in nutrition counseling, a popular use-case where the model supports a user with their dietary struggles. We crowdsource real-world diet-related struggles, then work with nutrition experts to generate supportive text using ChatGPT. Finally, experts evaluate the safety and text quality of ChatGPT's output. The result is the HAI-Coaching dataset, containing ∼2.4K crowdsourced dietary struggles and ∼97K corresponding ChatGPT-generated and expert-annotated supportive texts. We analyse ChatGPT's performance, discovering potentially harmful behaviours, especially for sensitive topics like mental health. Finally, we use HAI-Coaching to test open LLMs on various downstream tasks, showing that even the latest models struggle to achieve good performance. HAI-Coaching is available at https://***/uccollab/hai-coaching/. © 2024 Association for Computational Linguistics.

关键词： Computational linguistics

Analysis of Virtual Reality Based on the Internet of Things on Human Psychology ‘Internet of Thoughts’ (IoThs) for Rich Content Extraction applied Natural Language Processing and Deep Learning 20th

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Analysis of Virtual Reality Based on the Internet of Things ...

20th International Conference on Smart Living and Public Health, ICOST 2023

作者： Mah, Pascal Muam Skalna, Iwona Pelech-Pilichowski, Tomasz Derlecki, Tomasz Nasr, Mahmoud Munyeshuri, Eric Amuzang, Gilly Njoh Itoe, Micheal Blake Somaah Tah, Ning Frida Department of Technical Informatics and Telecommunications AGH University of Science and Technology Krakow Poland Department of Business Informatics and Management Engineering AGH University of Science and Technology Krakow Poland Institute of Computer Science AGH University of Science and Technology Krakow Poland Department of Economics and Management Industry AGH University of Science and Technology Krakow Poland Department of Biomedical Engineering AGH University of Science and Technology Krakow Poland Department of Engineering Mathematics and Physics Faculty of Engineering and Technology Future University Cairo Egypt Department of Production Engineering and Logistics Enterprise Silesian University of Technology Gliwice Poland Department of Logistics Management Silesian University of Technology Gliwice Poland

ISBN: (纸本)9783031439490

In the past decade, a lot of challenges to access, assess, and to acquire the needed technological opportunities to teach computers what naturally comes from the human brain and to understand how we naturally react when we rely on technology. The ability to document human thoughts, reactions and behavior to computers has led to the coming of NLP, AI, Dl, & ML. Aim to understand the influence of IoT on humans with the use of DL to achieve content correctness and accuracy with virtual technology. Studies show that the way we think, react, and do the things we think "Internet of thoughts" reflect our personality. The way we think determines the way we react and the way we do things are based on how we think. Technology advancement has reinforced a lot of changes in humans which makes humans vulnerable to personal content exposure misappropriation due to the continuously changing nature of humanity and language. The study uses NLP, DL and behavior-oriented drive and influential function and results show that IoT based on VR influences human psychology "Internet of Thoughts". © 2023, The Author(s).

关键词： Internet of things