[{"abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.","lang":"eng"}],"type":"preprint","related_material":{"record":[{"id":"8155","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Grah, Rok","last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"oa_version":"Preprint","date_updated":"2023-09-07T13:13:26Z","date_created":"2020-04-23T10:12:51Z","_id":"7675","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","status":"public","title":"Normative models of enhancer function","article_processing_charge":"No","day":"09","month":"04","date_published":"2020-04-09T00:00:00Z","doi":"10.1101/2020.04.08.029405","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"oa":1,"citation":{"ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020)."},"publication":"bioRxiv","project":[{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}]},{"doi":"10.15479/AT:ISTA:7460","language":[{"iso":"eng"}],"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"publication_identifier":{"issn":["2663-337X"]},"month":"02","related_material":{"record":[{"id":"6608","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Ölsböck, Katharina","last_name":"Ölsböck","first_name":"Katharina","orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:15:30Z","date_created":"2020-02-06T14:56:53Z","year":"2020","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2020-07-14T12:47:58Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2020-02-10T00:00:00Z","citation":{"chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460"},"page":"155","has_accepted_license":"1","article_processing_charge":"No","day":"10","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"oa_version":"Published Version","file":[{"creator":"koelsboe","file_size":76195184,"content_type":"application/pdf","file_name":"thesis_ist-final_noack.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:43:54Z","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","file_id":"7461","relation":"main_file"},{"relation":"source_file","file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:52:45Z","access_level":"closed","description":"latex source files, figures","file_name":"latex-files.zip","content_type":"application/x-zip-compressed","file_size":122103715,"creator":"koelsboe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7460","status":"public","title":"The hole system of triangulated shapes","ddc":["514"],"abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6677"}]},"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"}],"date_created":"2020-05-26T14:08:55Z","date_updated":"2023-09-07T13:15:55Z","ec_funded":1,"file_date_updated":"2020-07-14T12:48:04Z","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"doi":"10.15479/AT:ISTA:7896","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05","_id":"7896","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"On the average-case hardness of total search problems","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"checksum":"b39e2e1c376f5819b823fb7077491c64","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T14:08:13Z","file_id":"7897","relation":"main_file","creator":"dernst","file_size":1622742,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Thesis_Kamath.pdf"},{"file_name":"Thesis_Kamath.zip","access_level":"closed","creator":"dernst","content_type":"application/x-zip-compressed","file_size":15301529,"file_id":"7898","relation":"source_file","date_created":"2020-05-26T14:08:23Z","date_updated":"2020-07-14T12:48:04Z","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"citation":{"ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020."},"page":"126","date_published":"2020-05-25T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"25"},{"month":"03","publication_identifier":{"isbn":["9781728165530"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2004.12623","open_access":"1"}],"external_id":{"arxiv":["2004.12623"]},"quality_controlled":"1","conference":{"end_date":"2020-03-05","start_date":"2020-03-01","location":" Snowmass Village, CO, United States","name":"WACV: Winter Conference on Applications of Computer Vision"},"doi":"10.1109/WACV45572.2020.9093288","language":[{"iso":"eng"}],"article_number":"1716-1725","year":"2020","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"IEEE","author":[{"last_name":"Royer","first_name":"Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"deleted","id":"8331"},{"relation":"dissertation_contains","status":"public","id":"8390"}]},"date_created":"2020-06-07T22:00:53Z","date_updated":"2023-09-07T13:16:17Z","scopus_import":1,"day":"01","article_processing_charge":"No","publication":"IEEE Winter Conference on Applications of Computer Vision","citation":{"chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093288.","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” IEEE Winter Conference on Applications of Computer Vision, 1716–1725, IEEE, 2020, doi:10.1109/WACV45572.2020.9093288.","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","apa":"Royer, A., & Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093288","ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093288"},"date_published":"2020-03-01T00:00:00Z","type":"conference","abstract":[{"text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures.","lang":"eng"}],"_id":"7936","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Localizing grouped instances for efficient detection in low-resource scenarios","oa_version":"Preprint"},{"article_number":"2180-2189","year":"2020","publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"}],"author":[{"orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer","first_name":"Amélie","full_name":"Royer, Amélie"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"deleted","id":"8331"},{"status":"public","relation":"dissertation_contains","id":"8390"}]},"date_created":"2020-06-07T22:00:53Z","date_updated":"2023-09-07T13:16:17Z","month":"03","publication_identifier":{"isbn":["9781728165530"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/2008.11995"}],"external_id":{"arxiv":["2008.11995"]},"oa":1,"quality_controlled":"1","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","end_date":"2020-03-05","location":"Snowmass Village, CO, United States","start_date":"2020-03-01"},"doi":"10.1109/WACV45572.2020.9093635","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7937","status":"public","title":"A flexible selection scheme for minimum-effort transfer learning","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"2020 IEEE Winter Conference on Applications of Computer Vision","citation":{"chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635.","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635.","apa":"Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635","ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in 2020 IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.","ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635"},"date_published":"2020-03-01T00:00:00Z"}]