@inproceedings{12854, abstract = {The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis. At SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.}, author = {Chalupa, Marek and Henzinger, Thomas A}, booktitle = {Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783031308192}, issn = {1611-3349}, location = {Paris, France}, pages = {535--540}, publisher = {Springer Nature}, title = {{Bubaak: Runtime monitoring of program verifiers}}, doi = {10.1007/978-3-031-30820-8_32}, volume = {13994}, year = {2023}, } @unpublished{12846, abstract = {We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.}, author = {Chern, Albert and Ishida, Sadashige}, booktitle = {arXiv}, title = {{Area formula for spherical polygons via prequantization}}, doi = {10.48550/arXiv.2303.14555}, year = {2023}, } @inproceedings{12856, abstract = {As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both. We present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems. We implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.}, author = {Chalupa, Marek and Mühlböck, Fabian and Muroya Lei, Stefanie and Henzinger, Thomas A}, booktitle = {Fundamental Approaches to Software Engineering}, isbn = {9783031308253}, issn = {1611-3349}, location = {Paris, France}, pages = {260--281}, publisher = {Springer Nature}, title = {{Vamos: Middleware for best-effort third-party monitoring}}, doi = {10.1007/978-3-031-30826-0_15}, volume = {13991}, year = {2023}, } @misc{12407, abstract = {As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both. We present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems. We implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.}, author = {Chalupa, Marek and Mühlböck, Fabian and Muroya Lei, Stefanie and Henzinger, Thomas A}, issn = {2664-1690}, keywords = {runtime monitoring, best effort, third party}, pages = {38}, publisher = {Institute of Science and Technology Austria}, title = {{VAMOS: Middleware for Best-Effort Third-Party Monitoring}}, doi = {10.15479/AT:ISTA:12407}, year = {2023}, } @inbook{12866, abstract = {Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation. Decades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.}, author = {Currin, Christopher and Beyer, Chad}, booktitle = {Encyclopedia of Child and Adolescent Health}, editor = {Halpern-Felsher, Bonnie}, isbn = {9780128188736}, pages = {86--98}, publisher = {Elsevier}, title = {{Altered childhood brain development in autism and epilepsy}}, doi = {10.1016/b978-0-12-818872-9.00129-1}, year = {2023}, } @phdthesis{12809, abstract = {Understanding the mechanisms of learning and memory formation has always been one of the main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic conditioning experiments to study the neural mechanisms governing behavioral adaptation. What was not known back then was that the part of the brain that is largely responsible for this type of associative learning is the cerebellum. Since then, plenty of theories on cerebellar learning have emerged. Despite their differences, one thing they all have in common is that learning relies on synaptic and intrinsic plasticity. The goal of my PhD project was to unravel the molecular mechanisms underlying synaptic plasticity in two synapses that have been shown to be implicated in motor learning, in an effort to understand how learning and memory formation are processed in the cerebellum. One of the earliest and most well-known cerebellar theories postulates that motor learning largely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse. However, the discovery of other types of plasticity in the cerebellar circuitry, like long-term potentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs), and plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the popularity of the idea that multiple sites of plasticity might be involved in learning. Still a lot remains unknown about the molecular mechanisms responsible for these types of plasticity and whether they occur during physiological learning. In the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid type glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC LTP. We have found that on the last day of adaptation there is no learning trace in form of VGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of PF-PC synapses. These data seem to support the view that learning is only stored in the cerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei. Next, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We have found behavior-induced MLI potentiation in form of release probability increase that could be explained by the increase of VGCCs at the presynaptic side. Our results strengthen the idea of distributed cerebellar plasticity contributing to learning and provide a novel mechanism for release probability increase. }, author = {Alcarva, Catarina}, issn = {2663 - 337X}, pages = {115}, publisher = {Institute of Science and Technology Austria}, title = {{Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning}}, doi = {10.15479/at:ista:12809}, year = {2023}, } @article{12668, abstract = {Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. Results: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. Conclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.}, author = {Zhao, Long and Yang, Yiman and Chen, Jinchao and Lin, Xuelei and Zhang, Hao and Wang, Hao and Wang, Hongzhe and Bie, Xiaomin and Jiang, Jiafu and Feng, Xiaoqi and Fu, Xiangdong and Zhang, Xiansheng and Du, Zhuo and Xiao, Jun}, issn = {1474-760X}, journal = {Genome Biology}, publisher = {Springer Nature}, title = {{Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat}}, doi = {10.1186/s13059-022-02844-2}, volume = {24}, year = {2023}, } @inproceedings{13048, abstract = {In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.}, author = {Lieutier, André and Wintraecken, Mathijs}, booktitle = {Proceedings of the 55th Annual ACM Symposium on Theory of Computing}, isbn = {9781450399135}, location = {Orlando, FL, United States}, pages = {1768--1776}, publisher = {Association for Computing Machinery}, title = {{Hausdorff and Gromov-Hausdorff stable subsets of the medial axis}}, doi = {10.1145/3564246.3585113}, year = {2023}, } @inproceedings{13053, abstract = {Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .}, author = {Peste, Elena-Alexandra and Vladu, Adrian and Kurtic, Eldar and Lampert, Christoph and Alistarh, Dan-Adrian}, booktitle = {11th International Conference on Learning Representations }, location = {Kigali, Rwanda }, title = {{CrAM: A Compression-Aware Minimizer}}, year = {2023}, } @inproceedings{13143, abstract = {GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime. In this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic. Our approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.}, author = {Hoffmann, Charlotte and Hubáček, Pavel and Kamath, Chethan and Pietrzak, Krzysztof Z}, booktitle = {Public-Key Cryptography - PKC 2023}, isbn = {9783031313677}, issn = {1611-3349}, location = {Atlanta, GA, United States}, pages = {530--553}, publisher = {Springer Nature}, title = {{Certifying giant nonprimes}}, doi = {10.1007/978-3-031-31368-4_19}, volume = {13940}, year = {2023}, }