arXiv subjects

Krzysztof Rzecki

Publications and source records attributed to Krzysztof Rzecki.

14 recordsLinked to original sources

arXiv2026

Computational Methods and Challenges in Cell-Free DNA Analysis for Multi-Cancer Early Detection

Cell-free DNA (cfDNA) is a promising avenue for non-invasive multicancer early detection (MCED), in that, it can enable multiple cancer detection simultaneously from a single blood draw, with particular sensitivity to cancers that currently lack established screening programs. Here we review the computational methods developed between 2022 and 2025 for cfDNA-based MCED. We focus on how fragmentomics and epigenetic features are extracted and analyzed to detect cancer at early stages. We first briefly outline the biological basis of cfDNA signals, then review classical statistical and machine learning approaches alongside deep learning frameworks including autoencoder-based models. For each method we discuss biological interpretability, validation strategy, and readiness for clinical integration. Furthermore, we categorize the current challenges into technical, computational, and methodological while outlining open problems in the field. This review shows that multimodal ensemble approaches have the strongest promise for clinical integration and the highest readiness. However, for better assessment of future work and side-by-side comparison, standardization of evaluation protocols and reporting results will be crucial.

cs.LG↗

arXiv2024

Recent Developments within The Cosmic Ray Extremely Distributed Observatory (CREDO)

This contribution presents the recent research developments within the Cosmic Ray Extremely Distributed Observatory (CREDO) in the search for resolution of various scientific puzzles, ranging from fundamental physical questions to applications like the determination of earthquake precursors. The state-of-the art theoretical, numerical and computational aspects of these phenomena are addressed, as well as recent experimental developments for detection.

astro-ph.HE↗

arXiv2023

Simulation of the isotropic ultra-high energy photons flux in the solar magnetic field and a comparison with observations made by the HAWC and Fermi-LAT observatories

In this contribution we study the possibility of the formation of cosmic ray ensembles (CRE) created by the interaction of ultra-high energy (UHE) photons with the magnetic field of the Sun. The lack of observation of those UHE and the difficulties for their identification given the current methodologies motivates this study. We performed simulations using the PRESHOWER program in order to simulate the expected extensive air showers which might be spatially correlated generated upon entering the Earth's atmosphere. We found characteristic features like very thing and extremely elongates cascades of secondary photons with their corresponding energies spanning the entire cosmic range spectrum. Shower footprints are as large as hundreds of kilometres. An application of this study is the scenario of gamma-ray emission from the vicinity of the Sun as a result of ultra-high energy photon cascading in the solar magnetic field in order to understand recent observations made by the HAWC and Fermi-LAT observatories.

astro-ph.HE↗

arXiv2023

Manifolds.jl: An Extensible Julia Framework for Data Analysis on Manifolds

We present the Julia package Manifolds$.$jl, providing a fast and easy-to-use library of Riemannian manifolds and Lie groups. This package enables working with data defined on a Riemannian manifold, such as the circle, the sphere, symmetric positive definite matrices, or one of the models for hyperbolic spaces. We introduce a common interface, available in ManifoldsBase$.$jl, with which new manifolds, applications, and algorithms can be implemented. We demonstrate the utility of Manifolds$.$jl using Bézier splines, an optimization task on manifolds, and principal component analysis on nonlinear data. In a benchmark, Manifolds$.$jl outperforms all comparable packages for low-dimensional manifolds in speed; over Python and Matlab packages, the improvement is often several orders of magnitude, while over C/C++ packages, the improvement is two-fold. For high-dimensional manifolds, it outperforms all packages except for Tensorflow-Riemopt, which is specifically tailored for high-dimensional manifolds.

cs.MS↗

arXiv2022

Simulation of the isotropic ultra-high energy photons flux in the solar magnetic field

Both the lack of observation of ultra-high energy (UHE) photons and the limitations of the state-of-the-art methodology being applied for their identification motivate studies on alternative approaches to the relevant simulations and the related observational strategies. One of such new approaches is proposed in this report and it concerns new observables allowing indirect identification of UHE photons through cosmic ray phenomena composed of many spatially correlated extensive air showers or primary cosmic rays observed at one time. The study is based on simulations of interactions of UHE photons with the magnetic field of the Sun using the PRESHOWER program with some essential modifications. One of the expected results of such interactions is a generation of cosmic ray ensembles (CRE) in the form of very thin and very elongated cascades of secondary photons of energies spanning the whole cosmic ray energy spectrum. Upon entering the Earth's atmosphere, these cascades or their parts may generate uniquely characteristic walls of spatially correlated extensive air showers, and the effect is expected also in cases when primary UHE photons are not directed towards the Earth. Particle distributions in these multi-primary UHE photon footprints are expected to have thicknesses of the order of meters and elongations reaching even hundreds of millions kilometers, making them potentially observable with a global, multi-experiment approach, including re-exploring of the historical data, with the expected event rate exceeding the capabilities of even very large cosmic ray observatories. The methods described in this report allow for simulating potentially observable quantities related to CRE induced by UHE photons: densities, energy spectra and geographical orientations of particles at the top of the Earth's atmosphere.

astro-ph.HE↗

arXiv2022

Advancing the Landscape of Multimessenger Science in the Next Decade

The last decade has brought about a profound transformation in multimessenger science. Ten years ago, facilities had been built or were under construction that would eventually discover the nature of objects in our universe could be detected through multiple messengers. Nonetheless, multimessenger science was hardly more than a dream. The rewards for our foresight were finally realized through IceCube's discovery of the diffuse astrophysical neutrino flux, the first observation of gravitational waves by LIGO, and the first joint detections in gravitational waves and photons and in neutrinos and photons. Today we live in the dawn of the multimessenger era. The successes of the multimessenger campaigns of the last decade have pushed multimessenger science to the forefront of priority science areas in both the particle physics and the astrophysics communities. Multimessenger science provides new methods of testing fundamental theories about the nature of matter and energy, particularly in conditions that are not reproducible on Earth. This white paper will present the science and facilities that will provide opportunities for the particle physics community renew its commitment and maintain its leadership in multimessenger science.

astro-ph.HE↗

arXiv2021

Simulations of Cosmic Ray Ensembles originated nearby the Sun

Cosmic Ray Ensembles (CRE) are yet not observed groups of cosmic rays with a common primary interaction vertex or the same parent particle. One of the processes capable of initiating identifiable CRE is an interaction of an ultra-high energy (UHE) photon with the solar magnetic field which results in an electron pair production and the subsequent synchrotron radiation. The resultant electromagnetic cascade forms a very characteristic line-like front of a very small width ($\sim$ meters), stretching from tens of thousands to even many millions of kilometers. In this contribution we present the results of applying a toy model to simulate detections of such CRE at the ground level with an array of ideal detectors of different dimensions. The adopted approach allows us to assess the CRE detection feasibility for a specific configuration of a detector array. The process of initiation and propagation of an electromagnetic cascade originated from an UHE photon passing near the Sun, as well as the resultant particle distribution on ground, were simulated using the CORSIKA program with the PRESHOWER option, both modified accordingly. The studied scenario results in photons forming a cascade that extends even over tens of millions of kilometers when it arrives at the top of the Earth's atmosphere, and the photon energies span practically the whole cosmic ray energy spectrum. The topology of the signal consists of very extended CRE shapes, and the characteristic, very much elongated disk-shape of the particle distribution on ground illustrates the potential for identification of CRE of this type.

astro-ph.HE↗

arXiv2021

Machine learning aided noise filtration and signal classification for CREDO experiment

The wealth of smartphone data collected by the Cosmic Ray Extremely Distributed Observatory(CREDO) greatly surpasses the capabilities of manual analysis. So, efficient means of rejectingthe non-cosmic-ray noise and identification of signals attributable to extensive air showers arenecessary. To address these problems we discuss a Convolutional Neural Network-based method ofartefact rejection and complementary method of particle identification based on common statisticalclassifiers as well as their ensemble extensions. These approaches are based on supervised learning,so we need to provide a representative subset of the CREDO dataset for training and validation.According to this approach over 2300 images were chosen and manually labeled by 5 judges.The images were split into spot, track, worm (collectively named signals) and artefact classes.Then the preprocessing consisting of luminance summation of RGB channels (grayscaling) andbackground removal by adaptive thresholding was performed. For purposes of artefact rejectionthe binary CNN-based classifier was proposed which is able to distinguish between artefacts andsignals. The classifier was fed with input data in the form of Daubechies wavelet transformedimages. In the case of cosmic ray signal classification, the well-known feature-based classifierswere considered. As feature descriptors, we used Zernike moments with additional feature relatedto total image luminance. For the problem of artefact rejection, we obtained an accuracy of 99%. For the 4-class signal classification, the best performing classifiers achieved a recognition rate of 88%.

physics.ins-det↗

arXiv2020

Cosmic Ray Extremely Distributed Observatory

The Cosmic Ray Extremely Distributed Observatory (CREDO) is a newly formed, global collaboration dedicated to observing and studying cosmic rays (CR) and cosmic ray ensembles (CRE): groups of a minimum of two CR with a common primary interaction vertex or the same parent particle. The CREDO program embraces testing known CR and CRE scenarios, and preparing to observe unexpected physics, it is also suitable for multi-messenger and multi-mission applications. Perfectly matched to CREDO capabilities, CRE could be formed both within classical models (e.g. as products of photon-photon interactions), and exotic scenarios (e.g. as results of decay of Super Heavy Dark Matter particles). Their fronts might be significantly extended in space and time, and they might include cosmic rays of energies spanning the whole cosmic ray energy spectrum, with a footprint composed of at least two extensive air showers with correlated arrival directions and arrival times. Since CRE are mostly expected to be spread over large areas and, because of the expected wide energy range of the contributing particles, CRE detection might only be feasible when using available cosmic ray infrastructure collectively, i.e. as a globally extended network of detectors. Thus, with this review article, the CREDO Collaboration invites the astroparticle physics community to actively join or to contribute to the research dedicated to CRE, and in particular to share any cosmic ray data useful for the specific CRE detection strategies.

astro-ph.HE↗

arXiv2019

Recognition and classification of the cosmic-ray events in images captured by CMOS/CCD cameras

Muons and other ionizing radiation produced by cosmic rays and radiative decays affect CMOS/CCD sensor. When particles colliding with sensors atoms cause specific kind of noise on images recorded by cameras. We present a concept and preliminary implementation of method for recognizing those events and algorithms for image processing and their classification by machine learning. Our method consists of analyzing the shape of traces present in images recorded by a camera sensor and metadata related to an image like camera model, GPS location of camera, vertical and horizontal orientation of a camera sensor, timestamp of image acquisition, and other events recognized near-by sensors. The so created feature vectors are classified as either a muon-like event, an electron-like event or the other event, possibly noise. For muon-like events our method estimates azimuth of a muon track. Source of the data is database of CREDO (Cosmic-Ray Extremely Distributed Observatory) project and ESO (European Southern Observatory) archives. The telescope dark frames from ESO are analysed. CREDO project collected so far over 2 millions images of events from many kinds of cameralike: smartphones camera, laptop webcams and Internet of Things cameras localised around the globe.

astro-ph.IM↗

arXiv2019

A communication solution for portable detectors of the Cosmic Ray Extremely Distributed Observatory

The search for Cosmic-Ray Ensembles (CRE), groups of correlated cosmic rays that might be distributed over very large areas, even of the size of the planet, requires a globally spread and dense network of detectors, as proposed by the Cosmic-Ray Extremely Distributed Observatory (CREDO) Collaboration. This proposal motivates an effort towards exploring the potential of using even very much diversified detection technologies within one system, with detection units located even in hard-to-reach places, where, nevertheless, the sensors could work independently - without human intervention. For these reasons we have developed a dedicated communication solution enabling the connection of many different types of detectors, in a range of environments. The proposed data transmission system uses radio waves as an information carrier on the 169MHz frequency band in a contrast to the typical commercially used frequencies in a IoT systems (868MHz). The connectivity within the system is based on the star topology, which ensures the least energy consumption. The solution is now being prepared to being implemented using the prototype detection system based on the CosmicWatch open hardware design: a portable, pocket size, and economy particle detector using the scintillation technique. Our prototype detector is equipped with a dedicated software that integrates it with the already operational CREDO server system.

astro-ph.IM↗

arXiv2019

Search for ultra-high energy photons: observing the preshower effect with gamma-ray telescopes

Ultra-high energy photons constitute one of the most important pieces of the astroparticle physics problems. Their observation may provide new insight on several phenomena such as supermassive particle annihilation or the GZK effect. Because of the absence of any significant photon identification by a leading experiments such as the Pierre Auger Observatory, we consider a screening phenomenon called preshower effect which could efficiently affect ultra-high energy photon propagation. This effect is a consequence of photon interactions with the geomagnetic field and results in large electromagnetic cascade of particles several thousands kilometers above the atmosphere. This collection of particles, called cosmic-ray ensembles (CRE), may reach the atmosphere and produce the well-known air showers. In this paper we propose to use gamma-ray telescopes to look for air showers induced by CRE. Possible sources of ultra-high energy photons include the GZK effect and Super Heavy Dark Matter particles. Simulations involving the preshower effect and detectors response are performed and properties of these peculiar air showers are investigated. The use of boosted decision trees to obtain the best cosmic-ray ensemble/hadron separation, the aperture and event rate predictions for a few models of photon production are also presented.

astro-ph.IM↗

arXiv2019

Cosmic Ray Extremely Distributed Observatory: Status and perspectives of a global cosmic ray detection framework

The Cosmic-Ray Extremely Distributed Observatory (CREDO) is a project dedicated to global studies of extremely extended cosmic-ray phenomena, the cosmic-ray ensembles (CRE), beyond the capabilities of existing detectors and observatories. Up to date cosmic-ray research has been focused on detecting single air showers, while the search for ensembles of cosmic-rays, which may spread over a significant fraction of the Earth, is a scientific terra incognita. The key idea of CREDO is to combine existing cosmic-ray detectors (large professional arrays, educational instruments, individual detectors, such as smartphones, etc.) into a worldwide network, thus enabling a global analysis. The second goal of CREDO involves a large number of participants (citizen science!), assuring the geographical spread of the detectors and managing manpower necessary to deal with vast amount of data to search for evidence for cosmic-ray ensembles. In this paper the status and perspectives of the project are presented.

astro-ph.IM↗

arXiv2019

Cosmic ray ensembles from ultra-high energy photons propagating in the galactic and intergalactic space

Propagation of ultra-high energy photons in the galactic and intergalactic space gives rise to cascades comprising thousands of photons. Using Monte Carlo simulations, we investigate the development of such cascades in the solar magnetosphere, and find that the photons in the cascades are distributed over hundreds of kilometers as they arrive at the top of the Earth's atmosphere. We also perform similar study for cascades starting as far as 10 Mpc away from us using relevant magnetic field models. A few photons correlated in time are expected to arrive at the Earth from the latter type of cascade. We present our simulation results and discuss the prospects for detection of these cascades with the Cosmic-Ray Extremely Distributed Observatory.

astro-ph.HE↗