@phdthesis{21401, abstract = {Runtime verification offers scalable solutions to improve the safety and reliability of systems. However, systems that require verification or monitoring by a third party to ensure compliance with a specification might contain sensitive information, causing privacy concerns when usual runtime verification approaches are used. Privacy is compromised if protected information about the system, or sensitive data that is processed by the system, is revealed. In addition, revealing the specification being monitored may undermine the essence of third-party verification. In this thesis, we propose a protocol for privacy-preserving runtime verification of systems against formal sequential specifications. We develop the protocol in two steps. In the first step, the monitor verifies whether the system satisfies the specification without learning anything else, though both parties are aware of the specification. In the second step, we extend the protocol to ensure that the system remains oblivious to the monitored specification, while the monitor learns only whether the system satisfies the specification and nothing more. Our protocol adapts and improves existing techniques used in cryptography, and more specifically, multi-party computation. The sequential specification defines the observation step of the monitor, whose granularity depends on the situation (e.g., banks may be monitored on a daily basis). Our protocol exchanges a single message per observation step, after an initialization phase. This design minimizes communication overhead, enabling relatively lightweight privacy-preserving monitoring. We implement our approach for monitoring specifications described by register automata and evaluate it experimentally. }, author = {Karimi, Mahyar}, issn = {2791-4585}, keywords = {Privacy-preserving verification, Runtime verification, Monitoring, Reactive functionalities, Cryptographic protocols}, pages = {60}, publisher = {Institute of Science and Technology Austria}, title = {{Privacy-preserving runtime verification}}, doi = {10.15479/AT-ISTA-21401}, year = {2026}, } @phdthesis{20964, author = {Vladimirtsev, Dmitrii}, issn = {2791-4585}, pages = {22}, publisher = {Institute of Science and Technology Austria}, title = {{Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels}}, doi = {10.15479/AT-ISTA-20964}, year = {2026}, } @phdthesis{19853, abstract = {The internal dynamical properties of red giant stars have been explored extensively in recent years as a result of the increase in high precision data availability from the space missions Kepler and TESS (Transiting Exoplanet Survey Satellite), and in this exploration, it has been discovered that some of these stars are not behaving as expected. Red giants are stars that have evolved off of the main sequence after having completed fusing hydrogen into helium in their core. Observational data shows that the cores are rotating significantly slower than models can recreate consistently across evolutionary stages. This discrepancy has prompted investigation into the efficiency of angular momentum transport mechanisms and mixing processes including meridional circulation, shear instability, internal gravity waves, Tayler-Spruit dynamo, fossil magnetic fields etc., to explain this behavior. Analyzing seismic oscillations in stars, via asteroseismology, is a powerful tool as it is the only way in which the deep stellar interior can be probed and subsequently characterized; this is possible as global oscillations modulating the stellar surface are effected by internal processes. For red giants, p-modes (pressure modes; resonating through the entire star) and g-modes (gravity-modes; resonating in the radiative interior) couple to create mixed modes. These mixed modes give access to the otherwise hidden stellar interior as g-modes couple to p-modes, delivering information from the interior to the surface. Internal magnetic signatures have been observationally confirmed in red giant stars via asteroseismology and characterized in two ways. One being that dipole mixed modes with ℓ = 1 will display a global asymmetric frequency shift of its azimuthal components; where the m = 0 and m = ±1 components of the ℓ = 1 dipole mode will be shifted by two different power laws, respectively. And the other being a reduced visibility of dipole mixed mode amplitudes in the power spectra, where stars presenting with this feature are denoted as suppressed. Several studies of the suppressed dipole mixed mode amplitudes have been carried out, but thus far, no dedicated studies of the asymmetric frequency shifts of suppressed red giants have been conducted; one reason being that the asymmetric frequency shifts cannot be characterized when the dipole mixed mode amplitudes are severely reduced in many of the suppressed stars. Sincefullysuppressedstarsdonothavedetectablemixed-modestoevaluate, partiallysuppressed stars, that is, red giant stars presenting with suppressed dipole mixed modes in select parts of their power spectra rather than across the entire spectra, will be the subject of this study as the respective mode amplitudes are still visible at high frequencies. As such, this study will search for asymmetric frequency shifts on the dipole mixed modes of partially suppressed red giant stars; the aim here is to investigate if both mode suppression and magnetic shifting of dipole mixed modes occur simultaneously. Thisstudywillbeconductedbycreatingapipelinetoestimatepriorsofasteroseismicparameters, use the priors to model the power spectra with the stellar modeling code sloscillations_ISTA, and perform a Bayesian fit of the parameters with the simulated data on the star KIC 6975038, a target with partially suppressed dipolar mode amplitudes identified in the literature, to fit its magnetic parameters. I present a novel method to model the stellar power spectra of partially suppressed red giants by application of a sigmoid profile to the ℓ= 1 dipolar mode component of the spectra. With the results of this study I aim at constraining the cause of this partial dipole mode amplitude suppression, allowing for more detailed studies regarding their astrophysical nature. Furthermore, the long term hope for the method used in this study will be to expand the sample of partially suppressed red giants and fit their asteroseismic parameters accordingly.}, author = {Smith, Kanah}, issn = {2791-4585}, keywords = {asteroseismology, stellar physics, red giant, magnetism, suppressed}, pages = {38}, publisher = {Institute of Science and Technology Austria}, title = {{Exploring internal magnetism in partially suppressed red giant stars}}, doi = {10.15479/AT-ISTA-19853}, year = {2025}, } @phdthesis{20735, abstract = {Left–right alternation is a defining feature of spinal locomotor circuits, yet the level of neuronal detail required to generate and maintain this pattern remains unclear. This thesis investigates how models spanning multiple levels of abstraction—from biophysically detailed Hodgkin–Huxley (HH) neurons to adaptive integrate–and–fire (I&F) formulations and synfire-chain modules—can account for the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole. The guiding hypothesis is that a small set of neuronal mechanisms is sufficient to reproduce the essential features of rhythmic alternation, and that moving between modeling scales helps distinguish core principles from biological detail. A minimal bilateral HH network comprising only four canonical neuron classes—excitatory descending interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory interneurons (aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce experimentally observed firing modes, the model demonstrated that rebound-prone dIN excitability, contralateral inhibition and modest electrical coupling are sufficient to generate stable alternating activity, even in very small networks. These results motivated the transition to simpler models capable of efficient analysis and scaling. Adaptive exponential I&F (AdEx) neurons were calibrated to physiological recordings using simulation-based inference, yielding tonic and phasic/rebound templates that preserved the key dynamical signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying single-spike responses and rebound firing in dINs. At network level, the I&F models robustly reproduced left–right alternation, while highlighting constraints on synaptic kinetics and adaptation needed to avoid multi-spike responses. Finally, a synfire-chain framework provided a complementary, timing-centric perspective, demonstrating how precise spike synchrony, synaptic delays and minimal inhibitory coupling can generate alternating left–right sequences in a feedforward setting. Together, these approaches converge on a common conclusion: rebound-prone ipsilateral excitation combined with precisely timed contralateral inhibition constitutes a sufficient substrate for alternating spinal rhythms. By integrating bottom-up and top-down modeling strategies, this thesis provides a unified, extensible framework for studying spinal pattern generation. The results show that essential locomotor dynamics can be captured across multiple abstraction levels, offering both mechanistic insight and practical tools for future data-driven investigations of spinal circuit development, robustness and modulation.}, author = {Wilson, Alexia C}, issn = {2791-4585}, pages = {110}, publisher = {Institute of Science and Technology Austria}, title = {{Modelling the spinal cord of a tadpole : Exploring different ways to model the spinal cord in the Xenopus frog}}, doi = {10.15479/AT-ISTA-20735}, year = {2025}, } @phdthesis{18588, abstract = {This thesis is an experimental work about two distinct research projects that evolved from a single project: non-equilibrium dynamics of an acoustically vibrated particle and microfabrication of particles with nano-scale 3D printing. The first project explores non equilibrium dynamics of a particle driven by ultrasonic vibrations. We design an experimental system consisting of an electromechanical vibration scheme to drive the particle’s vibrations and an imaging scheme to track its trajectories. We study the trajectories to determine how the particle’s dynamics evolve under the driven conditions, considering out of equilibrium systems in the context of equilibrium statistical mechanics. Using a Langevin framework and the Boltzmann factor, we characterize the particle’s dynamics as complex; the particle motion is not purely diffusive. We extract physical parameters like spring constant, effective temperature, damping coefficient and resonance frequency. In the second project, we explore and develop techniques in the design and microfabrication of particles across scales. Microfabrication involves building structures at the micron or submicron scale. These designed miniaturized patterns, objects, or devices are useful in biophysics, pharmacology, medical biology, and nanotechnology. We specifically apply two-photon polymerization, a form of 3D nano printing. We print millimetric particles, characterizing different designs to evaluate and showcase the resolution, aspect ratio integrity and print quality of the printing process. We also design and fabricate a microsensor to deflect under applicable force of order 0.1 pN. We present fundamental concepts needed to design the microsensor, showcasing 3D printing at considerably smaller scales down to the µm or below.}, author = {Mweka, Cecelia N}, issn = {2791-4585}, pages = {61}, publisher = {Institute of Science and Technology Austria}, title = {{Non equilibrium dynamics of driven individual particles and 3D printing across scales}}, doi = {10.15479/at:ista:18588}, year = {2024}, } @phdthesis{18301, abstract = {Physics simulation in computer graphics can bring triangle meshes into topologically invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh.}, author = {Etemadihaghighi, Arian}, issn = {2791-4585}, keywords = {surface tracking, non-manifold, hole-filling, topology change, multi-material, solid-modeling}, pages = {39}, publisher = {Institute of Science and Technology Austria}, title = {{Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking}}, doi = {10.15479/at:ista:18301}, year = {2024}, } @phdthesis{15352, abstract = {Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological disorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common assumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in seizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have proven unsuccessful in treating seizure progression. One potential reason could be that the therapies only focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial response, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons have been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship between microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that several studies investigate microglia dynamics in ex vivo slice models, which can severely affect the microglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo studies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term consequences on microglia activity leaving out the direct consequences of acute seizure activity on microglia dynamics. Here, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to directly monitor and correlate the onset of seizure activity with microglia response. To induce seizures, we take advantage of the kainic acid (KA) model, which represents similar neuropathological and electroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After confirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we investigated whether these changes also reached the primary visual cortex (V1) as a secondary generalized seizure activity. Indeed, we found that microglia changed their morphology at high doses of KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording, our initial attempts under the microscope suffered from extensive electrical noise, which overlaid the actual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio was sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of microglia, we had to optimize the imaging parameters, so that we would be able to detect microglial processes in a sufficient resolution to track their process changes. Finally, we combined both methodologies with the KA model. We confirmed that KA induced seizure activity and found first indication that those correlate with microglia volume changes. Overall, we have developed a first methodological approach, which allows the analysis of the acute effects of seizure onset on microglia. Future studies will have to continue to optimize the drift during imaging recording and the post-image analysis. }, author = {Murmann, Julie Stefanie}, issn = {2791-4585}, pages = {54}, publisher = {Institute of Science and Technology Austria}, title = {{Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording}}, doi = {10.15479/at:ista:15352}, year = {2024}, } @phdthesis{17368, abstract = {Recent advancements in molecular diagnostic techniques have enabled the collection of multiple types of omics data from patients, including genomics, epigenomics, proteomics, and transcriptomics. However, we lack effective methods for integrating all these different data types and combining them with clinical outcomes to study the molecular mechanisms that govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian regression method that can handle general omics data for survival analysis of time-to-event phenotypes. Our method can: (1) accommodate incomplete data by allowing censored individuals, (2) use continuous time-to-event data to test associations of markers with a phenotype and (3) estimate effects jointly while allowing for independent groups of biological markers. Extensive simulations using planted signals on real data demonstrate that our model accurately retrieves the true parameters of the model while controlling for false discoveries and maintaining the expected prediction accuracy. We address data correlations by estimating the effects jointly, even between omic groups, while also estimating the individual variance explained by each group. We apply our model to two datasets. Using 18,000 individuals from the Generation Scotland study we model the association of time at onset of Type 2 Diabetes, Stroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG methylation probes. We find that large proportions of variation in disease onset times can be attributed to methylation as measured in whole blood at baseline in individuals without disease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer dataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic mutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when fitting the 5 groups together, almost all variation attributable to "omics" data is explained by DNA methylation. When considering progression times, both methylation and gene expression explain a large part of the variance. We found 2 genes that are significantly associated (95% posterior inclusion probability) with cancer survival time, conditional on all other genome-wide omics data variation. Owing to the vast variability of mechanisms characterizing different cancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken together, we showed the applicability of our multi-omics BayesW model to a wide-range of biological questions in multi-omics data. }, author = {Villanueva Marijuan, Ariadna}, issn = {2791-4585}, keywords = {Epigenetics, Multi-omics, Bayesian regression}, pages = {60}, publisher = {Institute of Science and Technology Austria}, title = {{Bayesian linear regression for analyzing general omics data with time-to-event phenotypes}}, doi = {10.15479/at:ista:17368}, year = {2024}, } @phdthesis{13331, abstract = {The extension of extremal combinatorics to the setting of exterior algebra is a work in progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms. }, author = {Köse, Seyda}, issn = {2791-4585}, pages = {26}, publisher = {Institute of Science and Technology Austria}, title = {{Exterior algebra and combinatorics}}, doi = {10.15479/at:ista:13331}, year = {2023}, } @phdthesis{12800, abstract = {The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. }, author = {Julseth, Mara}, issn = {2791-4585}, pages = {21}, publisher = {Institute of Science and Technology Austria}, title = {{The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone}}, doi = {10.15479/at:ista:12800}, year = {2023}, } @phdthesis{14226, abstract = {We introduce the notion of a Faustian interchange in a 1-parameter family of smooth functions to generalize the medial axis to critical points of index larger than 0. We construct and implement a general purpose algorithm for approximating such generalized medial axes.}, author = {Stephenson, Elizabeth R}, issn = {2791-4585}, pages = {43}, publisher = {Institute of Science and Technology Austria}, title = {{Generalizing medial axes with homology switches}}, doi = {10.15479/at:ista:14226}, year = {2023}, } @phdthesis{12531, abstract = {All visual experiences of the vertebrates begin with light being converted into electrical signals by the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the mammal retina, and they transmit visual information to the rest of the brain. It has been shown that RGCs vary in their morphology and genetic profiles, moreover they can be unambiguously grouped into subtypes that share the same morphological and/or molecular properties. However, in terms of RGCs function, it remains unclear how many distinct types there are and what response properties their typology relies on. Even given the recent studies that successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the question remains whether the found subtypes persist across the entire retina. In this work, using a novel imaging method, we show that, when sampled from a large portion of the retina, RGCs can not be clearly divided into functional subtypes. We found that in photopic conditions, which implies more prominent natural scene statistic differences across the visual field, response properties can be exhibited by cells differently depending on their location in the retina, which leads to formation of a gradient of features rather than distinct classes. This finding suggests that RGCs follow a global organization across the visual field of the animal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.}, author = {Kirillova, Kseniia}, issn = {2791-4585}, pages = {46}, publisher = {Institute of Science and Technology Austria}, title = {{Panoramic functional gradients across the mouse retina}}, doi = {10.15479/at:ista:12531}, year = {2023}, } @phdthesis{10422, abstract = {Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems.}, author = {Piankov, Anton}, issn = {2791-4585}, publisher = {Institute of Science and Technology Austria}, title = {{Towards designer materials using customizable particle shape}}, doi = {10.15479/at:ista:10422}, year = {2021}, }