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Uniform sampling from the set G(d) of graphs with a given degree-sequence d=(d1,…,dn)∈Nn is a classical problem in the study of random graphs. We consider an analogue for temporal graphs in which the edges are labeled with integer timestamps. The input to this generation problem is a tuple D=(d,T)∈Nn×N>0 and the task is to output a uniform random sample from the set G(D) of temporal graphs with degree-sequence d and timestamps in the interval [1,T]. By allowing repeated edges with distinct timestamps, G(D) can be non-empty even if G(d) is, and as a consequence, existing algorithms are difficult to apply.
We describe an algorithm for this generation problem which runs in expected time O(M) if Δ2+ϵ=O(M) for some constant ϵ>0 and T−Δ=Ω(T) where M=∑idi and Δ=maxidi. Our algorithm applies the switching method of McKay and Wormald [1] to temporal graphs: we first generate a random temporal multigraph and then remove self-loops and duplicated edges with switching operations which rewire the edges in a degree-preserving manner.
Uniform sampling from the set G(d) of graphs with a given degree-sequence d=(d1,…,dn)∈Nn is a classical problem in the study of random graphs. We consider an analogue for temporal graphs in which the edges are labeled with integer timestamps. The input to this generation problem is a tuple D=(d,T)∈Nn×N>0 and the task is to output a uniform random sample from the set G(D) of temporal graphs with degree-sequence d and timestamps in the interval [1,T]. By allowing repeated edges with distinct timestamps, G(D) can be non-empty even if G(d) is, and as a consequence, existing algorithms are difficult to apply.
We describe an algorithm for this generation problem which runs in expected time O(M) if Δ2+ϵ=O(M) for some constant ϵ>0 and T−Δ=Ω(T) where M=∑idi and Δ=maxidi. Our algorithm applies the switching method of McKay and Wormald [1] to temporal graphs: we first generate a random temporal multigraph and then remove self-loops and duplicated edges with switching operations which rewire the edges in a degree-preserving manner.
n this paper we study invasion probabilities and invasion times of cooperative parasites spreading in spatially structured host populations. The spatial structure of the host population is given by a random geometric graph on [0,1]n, n∈N, with a Poisson(N)-distributed number of vertices and in which vertices are connected over an edge when they have a distance of at most rN∈Θ(Nβ−1n) for some 0<β<1 and N→∞. At a host infection many parasites are generated and parasites move along edges to neighbouring hosts. We assume that parasites have to cooperate to infect hosts, in the sense that at least two parasites need to attack a host simultaneously. We find lower and upper bounds on the invasion probability of the parasites in terms of survival probabilities of branching processes with cooperation. Furthermore, we characterize the asymptotic invasion time.
An important ingredient of the proofs is a comparison with infection dynamics of cooperative parasites in host populations structured according to a complete graph, i.e. in well-mixed host populations. For these infection processes we can show that invasion probabilities are asymptotically equal to survival probabilities of branching processes with cooperation.
Furthermore, we build in the proofs on techniques developed in [BP22], where an analogous invasion process has been studied for host populations structured according to a configuration model.
We substantiate our results with simulations.
Parallel global edge switching for the uniform sampling of simple graphs with prescribed degrees
(2023)
The uniform sampling of simple graphs matching a prescribed degree sequence is an important tool in network science, e.g. to construct graph generators or null-models. Here, the Edge Switching Markov Chain (ES-MC) is a common choice. Given an arbitrary simple graph with the required degree sequence, ES-MC carries out a large number of small changes, called edge switches, to eventually obtain a uniform sample. In practice, reasonably short runs efficiently yield approximate uniform samples.
In this work, we study the problem of executing edge switches in parallel. We discuss parallelizations of ES-MC, but find that this approach suffers from complex dependencies between edge switches. For this reason, we propose the Global Edge Switching Markov Chain (G-ES-MC), an ES-MC variant with simpler dependencies. We show that G-ES-MC converges to the uniform distribution and design shared-memory parallel algorithms for ES-MC and G-ES-MC. In an empirical evaluation, we provide evidence that G-ES-MC requires not more switches than ES-MC (and often fewer), and demonstrate the efficiency and scalability of our parallel G-ES-MC implementation.
Stimulated emission depletion (STED) microscopy is a super-resolution technique that surpasses the diffraction limit and has contributed to the study of dynamic processes in living cells. However, high laser intensities induce fluorophore photobleaching and sample phototoxicity, limiting the number of fluorescence images obtainable from a living cell. Here, we address these challenges by using ultra-low irradiation intensities and a neural network for image restoration, enabling extensive imaging of single living cells. The endoplasmic reticulum (ER) was chosen as the target structure due to its dynamic nature over short and long timescales. The reduced irradiation intensity combined with denoising permitted continuous ER dynamics observation in living cells for up to 7 hours with a temporal resolution of seconds. This allowed for quantitative analysis of ER structural features over short (seconds) and long (hours) timescales within the same cell, and enabled fast 3D live-cell STED microscopy. Overall, the combination of ultra-low irradiation with image restoration enables comprehensive analysis of organelle dynamics over extended periods in living cells.
Heavy quarks are useful probes to investigate the properties of the Quark-Gluon Plasma (QGP) produced in heavy-ion collisions at the LHC, since they are produced in initial hard scattering processes. To single out the signals that are characteristic of the QGP, it is nevertheless crucial to understand the primordial heavy-quark production in vacuum, and to disentangle hot from cold nuclear matter effects. Moreover, observations of collective effects in high-multiplicity pp and p-Pb collisions show surprising similarities with those in heavy-ion collisions. Heavy-flavour production in such collisions could give further insight into the underlying processes. The heavy-flavour production can be studied with e+e− pairs from correlated semileptonic decays of heavy-flavour hadrons. Compared to single heavy-flavour measurements, the dielectron yield contains information about the initial kinematical correlations between the charm and anti-charm quarks, which is otherwise not accessible, and is sensitive to soft heavy-flavour production. We report results on correlated e+e− pairs in pp collisions recorded by the ALICE detector at different collision energies. The production of heavy quarks is discussed by comparing the yield of dielectrons from heavy-flavour hadron decays as a function of invariant mass, pair transverse momentum and distance of closest approach to the primary vertex with different Monte Carlo event generators. The heavy-flavour production cross sections are also presented. Results from high-multiplicity pp collisions at √s=13 TeV and the status of the p-Pb analysis at √sNN=5.02 TeV are reported as well.
The production yields of antideuterons and antiprotons are measured in pp collisions at a center-of-mass energy of √s=13 TeV, as a function of transverse momentum (pT) and rapidity (y), for the first time up to |y|=0.7. The measured spectra are used to study the pT and rapidity dependence of the coalescence parameter B2, which quantifies the coalescence probability of antideuterons. The pT and rapidity dependence of the obtained B2 is extrapolated for pT>1.7 GeV/c and |y|>0.7 using the phenomenological antideuteron production model implemented in PYTHIA 8.3 as well as a baryon coalescence afterburner model based on EPOS 3. Such measurements are of interest to the astrophysics community, since they can be used for the calculation of the flux of antinuclei from cosmic rays, in combination with coalescence models.
Measurement of beauty production via non-prompt charm hadrons in p-Pb collisions at √sNN = 5.02 TeV
(2024)
The production cross sections of D0, D+, and Λ+c hadrons originating from beauty-hadron decays (i.e. non-prompt) were measured for the first time at midrapidity in proton−lead (p−Pb) collisions at the center-of-mass energy per nucleon pair of √sNN=5.02 TeV. Nuclear modification factors (RpPb) of non-prompt D0, D+, and Λ+c are calculated as a function of the transverse momentum (pT) to investigate the modification of the momentum spectra measured in p−Pb collisions with respect to those measured in proton−proton (pp) collisions at the same energy. The RpPb measurements are compatible with unity and with the measurements in the prompt charm sector, and do not show a significant pT dependence. The pT-integrated cross sections and pT-integrated RpPb of non-prompt D0 and D+ mesons are also computed by extrapolating the visible cross sections down to pT = 0. The non-prompt D-meson RpPb integrated over pT is compatible with unity and with model calculations implementing modification of the parton distribution functions of nucleons bound in nuclei with respect to free nucleons. The non-prompt Λ+c/D0 and D+/D0 production ratios are computed to investigate hadronisation mechanisms of beauty quarks into mesons and baryons. The measured ratios as a function of pT display a similar trend to that measured for charm hadrons in the same collision system.
Particle production as a function of charged-particle flattenicity in pp collisions at √s = 13 TeV
(2024)
This paper reports the first measurement of the transverse momentum (pT) spectra of primary charged pions, kaons, (anti)protons, and unidentified particles as a function of the charged-particle flattenicity in pp collisions at s√=13 TeV. Flattenicity is a novel event shape observable that is measured in the pseudorapidity intervals covered by the V0 detector, 2.8<η<5.1 and −3.7<η<−1.7. According to QCD-inspired phenomenological models, it shows sensitivity to multiparton interactions and is less affected by biases towards larger pT due to local multiplicity fluctuations in the V0 acceptance than multiplicity. The analysis is performed in minimum-bias (MB) as well as in high-multiplicity events up to pT=20 GeV/c. The event selection requires at least one charged particle produced in the pseudorapidity interval |η|<1. The measured pT distributions, average pT, kaon-to-pion and proton-to-pion particle ratios, presented in this paper, are compared to model calculations using PYTHIA 8 based on color strings and EPOS LHC. The modification of the pT-spectral shapes in low-flattenicity events that have large event activity with respect to those measured in MB events develops a pronounced peak at intermediate pT (2<pT<8 GeV/c), and approaches the vicinity of unity at higher pT. The results are qualitatively described by PYTHIA, and they show different behavior than those measured as a function of charged-particle multiplicity based on the V0M estimator.
A Large Ion Collider Experiment (ALICE) is a high-energy physics experiment, designed to study heavy ion collisions at the European Organization for Nuclear Research (CERN)Large Hadron Collider (LHC). ALICE is built to study the fundamental properties of matter as it existed shortly after the big bang. This requires reading out millions of sensors with high frequency, enabling high statistics for physics analysis, resulting in a considerable computing demand concerning network throughput and processing power. With the ALICE Run 3 upgrade [14], requirements for a High Throughput Computing
(HTC) online processing cluster increased significantly, due to more than an order of magnitude more data than in Run 2, resulting in a processing input rate of up to 900 GB/s. Online (real-time) event reconstruction allows for the compression of the data stream to 130 GB/s, which is stored on disk for physics analysis.
This thesis presents the implementation of the ALICE Event Processing Node (EPN) compute farm, to cope with the Run 3 online computing challenges. Building a Data Centre tailored to ALICE requirements for the Run 3 and Run 4 EPN farm. Providing the operational conditions for a dynamic compute environment of a High Performance Computing (HPC) cluster, with significant load changes in a short time span, when starting or stopping a data-taking run. EPN servers provide the required computing resources for online reconstruction and data compression. The farm includes network connectivity towards First Level Processors (FLPs), requiring reliable throughput of 900 GB/s between FLPs and EPNs and connectivity from the internal InfiniBand network to the CERN Exabyte Object Storage (EOS) Ethernet network, with more than 100 GB/s.
The results of operating the EPN computing infrastructure during the first year of Run 3 LHC collisions are described in the context of the ALICE experiment. The EPN farm was delivering the expected performance for ALICE data-taking. Data Centre environmental conditions remained stable during the last more than two years, in particular during starting and stopping runs, which include significant changes in IT load. Several unforeseen external circumstances lead to increasing demands for the Online Offline System (O2). Higher data rates than anticipated required network performance to exceed the initial design specifications, for the throughput between FLPs and EPNs. In particular, the high throughput from an internal EPN InfiniBand network towards the storage Ethernet network was one of the challenges to overcome.
Natural Language Processing (NLP) for big data requires an efficient and sophisticated infrastructure to complete tasks both fast and correctly. Providing an intuitive and lightweight interaction with a framework that abstracts and simplifies complex tasks assists in reaching this goal. This bachelor thesis extends the NLP framework Docker Unified UIMA Interface (DUUI) by an API and a web-based graphical user interface to control and manage pipelines for automated analysis of large quantities of natural language. The extension aims to reduce the entry barrier into the field as well as to accelerate the creation and management of pipelines according to UIMA standards. Pipelines can be executed in the browser or using the web API directly and then monitored on a document level. The evaluation in usability and user experience indicates that the implementation benefits the framework by making its usage more user friendly, lightweight, and intuitive while also making the management of pipelines more efficient.
Graph4Med: a web application and a graph database for visualizing and analyzing medical databases
(2022)
Background: Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databases is challenging since these are often based on a relational schema and cannot be used to easily extract information for cohort analysis and visualization. As a consequence, valuable information regarding cohort distribution or patient similarity may be missed. With the rapid advancement of biomedical technologies, new forms of data from methods such as Next Generation Sequencing (NGS) or chromosome microarray (array CGH) are constantly being generated; hence it can be expected that the amount and complexity of medical data will rise and bring relational database systems to a limit.
Description: We present Graph4Med, a web application that relies on a graph database obtained by transforming a relational database. Graph4Med provides a straightforward visualization and analysis of a selected patient cohort. Our use case is a database of pediatric Acute Lymphoblastic Leukemia (ALL). Along routine patients’ health records it also contains results of latest technologies such as NGS data. We developed a suitable graph data schema to convert the relational data into a graph data structure and store it in Neo4j. We used NeoDash to build a dashboard for querying and displaying patients’ cohort analysis. This way our tool (1) quickly displays the overview of patients’ cohort information such as distributions of gender, age, mutations (fusions), diagnosis; (2) provides mutation (fusion) based similarity search and display in a maneuverable graph; (3) generates an interactive graph of any selected patient and facilitates the identification of interesting patterns among patients.
Conclusion: We demonstrate the feasibility and advantages of a graph database for storing and querying medical databases. Our dashboard allows a fast and interactive analysis and visualization of complex medical data. It is especially useful for patients similarity search based on mutations (fusions), of which vast amounts of data have been generated by NGS in recent years. It can discover relationships and patterns in patients cohorts that are normally hard to grasp. Expanding Graph4Med to more medical databases will bring novel insights into diagnostic and research.
Interacting with the environment to process sensory information, generate perceptions, and shape behavior engages neural networks in brain areas with highly varied representations, ranging from unimodal sensory cortices to higher-order association areas. Recent work suggests a much greater degree of commonality across areas, with distributed and modular networks present in both sensory and non-sensory areas during early development. However, it is currently unknown whether this initially common modular structure undergoes an equally common developmental trajectory, or whether such a modular functional organization persists in some areas—such as primary visual cortex—but not others. Here we examine the development of network organization across diverse cortical regions in ferrets of both sexes using in vivo widefield calcium imaging of spontaneous activity. We find that all regions examined, including both primary sensory cortices (visual, auditory, and somatosensory—V1, A1, and S1, respectively) and higher order association areas (prefrontal and posterior parietal cortices) exhibit a largely similar pattern of changes over an approximately 3 week developmental period spanning eye opening and the transition to predominantly externally-driven sensory activity. We find that both a modular functional organization and millimeter-scale correlated networks remain present across all cortical areas examined. These networks weakened over development in most cortical areas, but strengthened in V1. Overall, the conserved maintenance of modular organization across different cortical areas suggests a common pathway of network refinement, and suggests that a modular organization—known to encode functional representations in visual areas—may be similarly engaged in highly diverse brain areas.
Significance Different areas of the mature brain encode vastly different representations of the world. This study shows that a modular functional organization where nearby neurons participate in similar functional networks is shared across different brain areas not only during early development, but also as the brain matures where it remains a shared feature that shapes neural activity. The largely conserved trajectory of developmental changes across brain areas suggests that similar circuit mechanisms may drive this maturation. This implies that the large literature on developing cortical circuits, which is largely focused on sensory areas, may also apply more broadly, and that perturbations during development that impinge on any such shared mechanisms may produce deficits that extend across multiple brain systems.
The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at centre-of-momentum energy of s√=13 TeV collected during the LHC Run 2 data-taking period. The measurement is performed by combining the measurements of the electromagnetic calorimeter EMCal and the central tracking detectors ITS and TPC, covering a pseudorapidity range of |ηγ|<0.67 and a transverse momentum range of 7<pγT<200 GeV/c. The result extends to lower pγT and xγT=2pγT/s√ ranges, the lowest xγT of any isolated photon measurements to date, extending significantly those measured by the ATLAS and CMS experiments towards lower pγT at the same collision energy with a small overlap between the measurements. The measurement is compared with next-to-leading order perturbative QCD calculations and the results from the ATLAS and CMS experiments as well as with measurements at other collision energies. The measurement and theory prediction are in agreement with each other within the experimental and theoretical uncertainties.
Assessing communicative accommodation in the context of large language models : a semiotic approach
(2023)
Recently, significant strides have been made in the ability of transformer-based chatbots to hold natural conversations. However, despite a growing societal and scientific relevancy, there are few frameworks systematically deriving what it means for a chatbot conversation to be natural. The present work approaches this question through the phenomenon of communicative accommodation/interactive alignment. While there is existing research suggesting that humans adapt communicatively to technologies, the aim of this work is to explore the accommodation of AI-chatbots to an interlocutor. Its research interest is twofold: Firstly, the structural ability of the transformer-architecture to support accommodative behavior is assessed using a frame constructed in accordance with existing accommodationtheories.
This results in hypotheses to be tested empirically. Secondly, since effective accommodation produces the same outcomes, regardless of technical implementation, a behavioral experiment is proposed. Existing quantifications of accommodation are reconciled,
extended, and modified to apply them to nonhuman-interlocutors. Thus, a measurement scheme is suggested which evaluates textual data from text-only, double-blind interactions between chatbots and humans, chatbots and chatbots and humans and humans. Using the generated human-to-human convergence data as a reference, the degree of artificial accommodation can be evaluated. Accommodation as a central facet of artificial interactivity can thus be evaluated directly against its theoretical paradigm, i.e. human interaction. In case that subsequent examinations show that chatbots effectively do not accommodate, there may be a new form of algorithmic bias, emerging from the aggregate accommodation towards chatbots but not towards humans. Thus, existing, hegemonic semantics could be cemented through chatbot-learning. Meanwhile, the ability to effectively accommodate would render chatbots vastly more susceptible to misuse.
The first measurement of the impact-parameter dependent angular anisotropy in the decay of coherently photoproduced ρ0 mesons is presented. The ρ0 mesons are reconstructed through their decay into a pion pair. The measured anisotropy corresponds to the amplitude of the cos(2ϕ) modulation, where ϕ is the angle between the two vectors formed by the sum and the difference of the transverse momenta of the pions, respectively. The measurement was performed by the ALICE Collaboration at the LHC using data from ultraperipheral Pb−Pb collisions at a center-of-mass energy of sNN−−−√ = 5.02 TeV per nucleon pair. Different impact-parameter regions are selected by classifying the events in nuclear-breakup classes. The amplitude of the cos(2ϕ) modulation is found to increase by about one order of magnitude from large to small impact parameters. Theoretical calculations, which describe the measurement, explain the cos(2ϕ) anisotropy as the result of a quantum interference effect at the femtometer scale that arises from the ambiguity as to which of the nuclei is the source of the photon in the interaction.
Investigating strangeness enhancement with multiplicity in pp collisions using angular correlations
(2024)
A study of strange hadron production associated with hard scattering processes and with the underlying event is conducted to investigate the origin of the enhanced production of strange hadrons in small collision systems characterised by large charged-particle multiplicities. For this purpose, the production of the single-strange meson K0S and the double-strange baryon Ξ± is measured, in each event, in the azimuthal direction of the highest-pT particle (``trigger" particle), related to hard scattering processes, and in the direction transverse to it in azimuth, associated with the underlying event, in pp collisions at s√=5.02 TeV and s√=13 TeV using the ALICE detector at the LHC. The per-trigger yields of K0S and Ξ± are dominated by the transverse-to-leading production (i.e., in the direction transverse to the trigger particle), whose contribution relative to the toward-leading production is observed to increase with the event charged-particle multiplicity. The transverse-to-leading and the toward-leading Ξ±/K0S yield ratios increase with the multiplicity of charged particles, suggesting that strangeness enhancement with multiplicity is associated with both hard scattering processes and the underlying event. The relative production of Ξ± with respect to K0S is higher in transverse-to-leading processes over the whole multiplicity interval covered by the measurement. The K0S and Ξ± per-trigger yields and yield ratios are compared with predictions of three different phenomenological models, namely PYTHIA 8.2 with the Monash tune, PYTHIA 8.2 with ropes and EPOS LHC. The comparison shows that none of them can quantitatively describe either the transverse-to-leading or the toward-leading yields of K0S and Ξ±.
The transverse momentum (pT) differential production cross section of the promptly-produced charm-strange baryon Ξ0c (and its charge conjugate Ξ0c¯¯¯¯¯¯) is measured at midrapidity via its hadronic decay into π+Ξ− in p−Pb collisions at a centre-of-mass energy per nucleon−nucleon collision sNN−−−√ = 5.02 TeV with the ALICE detector at the LHC. The Ξ0c nuclear modification factor (RpPb), calculated from the cross sections in pp and p−Pb collisions, is presented and compared with the RpPb of Λ+c baryons. The ratios between the pT-differential production cross section of Ξ0c baryons and those of D0 mesons and Λ+c baryons are also reported and compared with results at forward and backward rapidity from the LHCb Collaboration. The measurements of the production cross section of prompt Ξ0c baryons are compared with a model based on perturbative QCD calculations of charm-quark production cross sections, which includes only cold nuclear matter effects in p−Pb collisions, and underestimates the measurement by a factor of about 50. This discrepancy is reduced when the data is compared with a model in which hadronisation is implemented via quark coalescence. The pT-integrated cross section of prompt Ξ0c-baryon production at midrapidity extrapolated down to pT = 0 is also reported. These measurements offer insights and constraints for theoretical calculations of the hadronisation process. Additionally, they provide inputs for the calculation of the charm production cross section in p−Pb collisions at midrapidity.
Measurements of (anti)deuteron and (anti)3He production in the rapidity range |y|< 0.5 as a function of the transverse momentum and event multiplicity in Xe−Xe collisions at a center-of-mass energy per nucleon−nucleon pair of sNN−−−√ = 5.44 TeV are presented. The coalescence parameters B2 and B3 are measured as a function of the transverse momentum per nucleon. The ratios between (anti)deuteron and (anti)3He yields and those of (anti)protons and pions are reported as a function of the mean charged-particle multiplicity density, and compared with two implementations of the statistical hadronization model (SHM) and with coalescence predictions. The elliptic flow of (anti)deuterons is measured for the first time in Xe−Xe collisions and shows features similar to those already observed in Pb−Pb collisions, i.e., the mass ordering at low transverse momentum and the meson−baryon grouping at intermediate transverse momentum. The production of nuclei is particularly sensitive to the chemical freeze-out temperature of the system created in the collision, which is extracted from a grand-canonical-ensemble-based thermal fit, performed for the first time including light nuclei along with light-flavor hadrons in Xe−Xe collisions. The extracted chemical freeze-out temperature Tchem = (154.2 ± 1.1) MeV in Xe−Xe collisions is similar to that observed in Pb−Pb collisions and close to the crossover temperature predicted by lattice QCD calculations.
First measurements of hadron(h)−Λ azimuthal angular correlations in p−Pb collisions at sNN−−−√ = 5.02 TeV using the ALICE detector at the LHC are presented. These correlations are used to separate the production of associated Λ baryons into three different kinematic regions, namely those produced in the direction of the trigger particle (near-side), those produced in the opposite direction (away-side), and those whose production is uncorrelated with the jet-axis (underlying event). The per-trigger associated Λ yields in these regions are extracted, along with the near- and away-side azimuthal peak widths, and the results are studied as a function of associated particle pT and event multiplicity. Comparisons with the DPMJET event generator and previous measurements of the ϕ(1020) meson are also made. The final results indicate that strangeness production in the highest multiplicity p−Pb collisions is enhanced relative to low multiplicity collisions in the jet-like regions, as well as the underlying event. The production of Λ relative to charged hadrons is also enhanced in the underlying event when compared to the jet-like regions. Additionally, the results hint that strange quark production in the away-side of the jet is modified by soft interactions with the underlying event.