[{"page":"9483-9498","oa_version":"None","year":"2022","language":[{"iso":"eng"}],"date_published":"2022-08-09T00:00:00Z","_id":"18211","date_created":"2024-10-08T12:47:53Z","publication":"Applied Intelligence","volume":53,"month":"08","type":"journal_article","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yaniv","full_name":"Nemcovsky, Yaniv","last_name":"Nemcovsky"},{"last_name":"Zheltonozhskii","full_name":"Zheltonozhskii, Evgenii","first_name":"Evgenii"},{"full_name":"Baskin, Chaim","last_name":"Baskin","first_name":"Chaim"},{"full_name":"Chmiel, Brian","last_name":"Chmiel","first_name":"Brian"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander"},{"full_name":"Mendelson, Avi","last_name":"Mendelson","first_name":"Avi"}],"intvolume":"        53","article_processing_charge":"No","scopus_import":"1","day":"09","issue":"8","citation":{"apa":"Nemcovsky, Y., Zheltonozhskii, E., Baskin, C., Chmiel, B., Bronstein, A. M., &#38; Mendelson, A. (2022). Adversarial robustness via noise injection in smoothed models. <i>Applied Intelligence</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10489-022-03423-5\">https://doi.org/10.1007/s10489-022-03423-5</a>","ama":"Nemcovsky Y, Zheltonozhskii E, Baskin C, Chmiel B, Bronstein AM, Mendelson A. Adversarial robustness via noise injection in smoothed models. <i>Applied Intelligence</i>. 2022;53(8):9483-9498. doi:<a href=\"https://doi.org/10.1007/s10489-022-03423-5\">10.1007/s10489-022-03423-5</a>","short":"Y. Nemcovsky, E. Zheltonozhskii, C. Baskin, B. Chmiel, A.M. Bronstein, A. Mendelson, Applied Intelligence 53 (2022) 9483–9498.","mla":"Nemcovsky, Yaniv, et al. “Adversarial Robustness via Noise Injection in Smoothed Models.” <i>Applied Intelligence</i>, vol. 53, no. 8, Springer Nature, 2022, pp. 9483–98, doi:<a href=\"https://doi.org/10.1007/s10489-022-03423-5\">10.1007/s10489-022-03423-5</a>.","ieee":"Y. Nemcovsky, E. Zheltonozhskii, C. Baskin, B. Chmiel, A. M. Bronstein, and A. Mendelson, “Adversarial robustness via noise injection in smoothed models,” <i>Applied Intelligence</i>, vol. 53, no. 8. Springer Nature, pp. 9483–9498, 2022.","chicago":"Nemcovsky, Yaniv, Evgenii Zheltonozhskii, Chaim Baskin, Brian Chmiel, Alex M. Bronstein, and Avi Mendelson. “Adversarial Robustness via Noise Injection in Smoothed Models.” <i>Applied Intelligence</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10489-022-03423-5\">https://doi.org/10.1007/s10489-022-03423-5</a>.","ista":"Nemcovsky Y, Zheltonozhskii E, Baskin C, Chmiel B, Bronstein AM, Mendelson A. 2022. Adversarial robustness via noise injection in smoothed models. Applied Intelligence. 53(8), 9483–9498."},"publication_identifier":{"eissn":["1573-7497"],"issn":["0924-669X"]},"publisher":"Springer Nature","quality_controlled":"1","title":"Adversarial robustness via noise injection in smoothed models","abstract":[{"text":"Deep neural networks are known to be vulnerable to malicious perturbations. Current methods for improving adversarial robustness make use of either implicit or explicit regularization, with the latter is usually based on adversarial training. Randomized smoothing, the averaging of the classifier outputs over a random distribution centered in the sample, has been shown to guarantee a classifier’s performance subject to bounded perturbations of the input. In this work, we study the application of randomized smoothing to improve performance on unperturbed data and increase robustness to adversarial attacks. We propose to combine smoothing along with adversarial training and randomization approaches, and find that doing so significantly improves the resilience compared to the baseline. We examine our method’s performance on common whitebox (FGSM, PGD) and black-box (transferable attack and NAttack) attacks on CIFAR-10 and CIFAR-100, and determine that for a low number of iterations, smoothing provides a significant performance boost that persists even for perturbations with a high attack norm, . For example, under a PGD-10 attack on CIFAR-10 using Wide-ResNet28-4, we achieve 60.3% accuracy for infinity norm ∞ = 8/255 and 13.1% accuracy for ∞ = 35/255 – outperforming previous art by 3% and 6%, respectively. We achieve nearly twice the accuracy on ∞ = 35/255 and even more so for perturbations with higher infinity norm. A reference implementation of the proposed method is provided. ","lang":"eng"}],"extern":"1","article_type":"original","date_updated":"2024-10-09T11:04:54Z","doi":"10.1007/s10489-022-03423-5","status":"public"},{"date_created":"2024-10-08T12:52:29Z","pmid":1,"external_id":{"pmid":["36539476"]},"_id":"18220","date_published":"2022-12-20T00:00:00Z","year":"2022","day":"20","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Scientific Reports","quality_controlled":"1","abstract":[{"lang":"eng","text":"Synonymous codons translate into the same amino acid. Although the identity of synonymous codons is often considered inconsequential to the final protein structure, there is mounting evidence for an association between the two. Our study examined this association using regression and classification models, finding that codon sequences predict protein backbone dihedral angles with a lower error than amino acid sequences, and that models trained with true dihedral angles have better classification of synonymous codons given structural information than models trained with random dihedral angles. Using this classification approach, we investigated local codon–codon dependencies and tested whether synonymous codon identity can be predicted more accurately from codon context than amino acid context alone, and most specifically which codon context position carries the most predictive power."}],"title":"Machine learning approaches demonstrate that protein structures carry information about their genetic coding","publisher":"Springer Nature","publication_identifier":{"issn":["2045-2322"]},"main_file_link":[{"url":"https://doi.org/10.1038/s41598-022-25874-z","open_access":"1"}],"status":"public","doi":"10.1038/s41598-022-25874-z","date_updated":"2024-10-14T09:46:06Z","DOAJ_listed":"1","article_type":"original","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":"        12","author":[{"full_name":"Ackerman-Schraier, Linor","last_name":"Ackerman-Schraier","first_name":"Linor"},{"full_name":"Rosenberg, Aviv A.","last_name":"Rosenberg","first_name":"Aviv A."},{"first_name":"Ailie","last_name":"Marx","full_name":"Marx, Ailie"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"}],"publication_status":"published","volume":12,"month":"12","citation":{"chicago":"Ackerman-Schraier, Linor, Aviv A. Rosenberg, Ailie Marx, and Alex M. Bronstein. “Machine Learning Approaches Demonstrate That Protein Structures Carry Information about Their Genetic Coding.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-25874-z\">https://doi.org/10.1038/s41598-022-25874-z</a>.","ieee":"L. Ackerman-Schraier, A. A. Rosenberg, A. Marx, and A. M. Bronstein, “Machine learning approaches demonstrate that protein structures carry information about their genetic coding,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022.","mla":"Ackerman-Schraier, Linor, et al. “Machine Learning Approaches Demonstrate That Protein Structures Carry Information about Their Genetic Coding.” <i>Scientific Reports</i>, vol. 12, 21968, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-25874-z\">10.1038/s41598-022-25874-z</a>.","ista":"Ackerman-Schraier L, Rosenberg AA, Marx A, Bronstein AM. 2022. Machine learning approaches demonstrate that protein structures carry information about their genetic coding. Scientific Reports. 12, 21968.","ama":"Ackerman-Schraier L, Rosenberg AA, Marx A, Bronstein AM. Machine learning approaches demonstrate that protein structures carry information about their genetic coding. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-25874-z\">10.1038/s41598-022-25874-z</a>","apa":"Ackerman-Schraier, L., Rosenberg, A. A., Marx, A., &#38; Bronstein, A. M. (2022). Machine learning approaches demonstrate that protein structures carry information about their genetic coding. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-25874-z\">https://doi.org/10.1038/s41598-022-25874-z</a>","short":"L. Ackerman-Schraier, A.A. Rosenberg, A. Marx, A.M. Bronstein, Scientific Reports 12 (2022)."},"article_number":"21968","OA_type":"gold","extern":"1","OA_place":"publisher"},{"oa_version":"Published Version","language":[{"iso":"eng"}],"volume":13,"month":"05","publication_status":"published","author":[{"first_name":"Aviv A.","last_name":"Rosenberg","full_name":"Rosenberg, Aviv A."},{"last_name":"Marx","full_name":"Marx, Ailie","first_name":"Ailie"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730"}],"intvolume":"        13","scopus_import":"1","OA_type":"gold","article_number":"2815","citation":{"ista":"Rosenberg AA, Marx A, Bronstein AM. 2022. Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nature Communications. 13, 2815.","mla":"Rosenberg, Aviv A., et al. “Codon-Specific Ramachandran Plots Show Amino Acid Backbone Conformation Depends on Identity of the Translated Codon.” <i>Nature Communications</i>, vol. 13, 2815, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30390-9\">10.1038/s41467-022-30390-9</a>.","ieee":"A. A. Rosenberg, A. Marx, and A. M. Bronstein, “Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Rosenberg, Aviv A., Ailie Marx, and Alex M. Bronstein. “Codon-Specific Ramachandran Plots Show Amino Acid Backbone Conformation Depends on Identity of the Translated Codon.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30390-9\">https://doi.org/10.1038/s41467-022-30390-9</a>.","short":"A.A. Rosenberg, A. Marx, A.M. Bronstein, Nature Communications 13 (2022).","apa":"Rosenberg, A. A., Marx, A., &#38; Bronstein, A. M. (2022). Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30390-9\">https://doi.org/10.1038/s41467-022-30390-9</a>","ama":"Rosenberg AA, Marx A, Bronstein AM. Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30390-9\">10.1038/s41467-022-30390-9</a>"},"OA_place":"publisher","extern":"1","year":"2022","date_published":"2022-05-20T00:00:00Z","external_id":{"pmid":["35595777"]},"_id":"18221","pmid":1,"date_created":"2024-10-08T12:53:01Z","publication":"Nature Communications","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","day":"20","main_file_link":[{"url":"https://doi.org/10.1038/s41467-022-30390-9","open_access":"1"}],"publication_identifier":{"issn":["2041-1723"]},"publisher":"Springer Nature","quality_controlled":"1","abstract":[{"lang":"eng","text":"Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases."}],"title":"Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon","oa":1,"article_type":"original","DOAJ_listed":"1","status":"public","date_updated":"2024-10-14T09:49:02Z","doi":"10.1038/s41467-022-30390-9"},{"year":"2022","date_published":"2022-10-01T00:00:00Z","_id":"18222","date_created":"2024-10-08T12:53:20Z","publication":"Human Reproduction","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","main_file_link":[{"url":"https://doi.org/10.1093/humrep/deac171","open_access":"1"}],"publication_identifier":{"eissn":["1460-2350"],"issn":["0268-1161"]},"publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"STUDY QUESTION: What is the accuracy and agreement of embryologists when assessing the implantation probability of blastocysts using time-lapse imaging (TLI), and can it be improved with a data-driven algorithm?\r\n\r\nSUMMARY ANSWER: The overall interobserver agreement of a large panel of embryologists was moderate and prediction accuracy was modest, while the purpose-built artificial intelligence model generally resulted in higher performance metrics.\r\n\r\nWHAT IS KNOWN ALREADY: Previous studies have demonstrated significant interobserver variability amongst embryologists when assessing embryo quality. However, data concerning embryologists’ ability to predict implantation probability using TLI is still lacking. Emerging technologies based on data-driven tools have shown great promise for improving embryo selection and predicting clinical outcomes.\r\n\r\nSTUDY DESIGN, SIZE, DURATION: TLI video files of 136 embryos with known implantation data were retrospectively collected from two clinical sites between 2018 and 2019 for the performance assessment of 36 embryologists and comparison with a deep neural network (DNN).\r\n\r\nPARTICIPANTS/MATERIALS, SETTING, METHODS: We recruited 39 embryologists from 13 different countries. All participants were blinded to clinical outcomes. A total of 136 TLI videos of embryos that reached the blastocyst stage were used for this experiment. Each embryo’s likelihood of successfully implanting was assessed by 36 embryologists, providing implantation probability grades (IPGs) from 1 to 5, where 1 indicates a very low likelihood of implantation and 5 indicates a very high likelihood. Subsequently, three embryologists with over 5 years of experience provided Gardner scores. All 136 blastocysts were categorized into three quality groups based on their Gardner scores. Embryologist predictions were then converted into predictions of implantation (IPG ≥ 3) and no implantation (IPG ≤ 2). Embryologists’ performance and agreement were assessed using Fleiss kappa coefficient. A 10-fold cross-validation DNN was developed to provide IPGs for TLI video files. The model’s performance was compared to that of the embryologists.\r\n\r\nMAIN RESULTS AND THE ROLE OF CHANCE: Logistic regression was employed for the following confounding variables: country of residence, academic level, embryo scoring system, log years of experience and experience using TLI. None were found to have a statistically significant impact on embryologist performance at α = 0.05. The average implantation prediction accuracy for the embryologists was 51.9% for all embryos (N = 136). The average accuracy of the embryologists when assessing top quality and poor quality embryos (according to the Gardner score categorizations) was 57.5% and 57.4%, respectively, and 44.6% for fair quality embryos. Overall interobserver agreement was moderate (κ = 0.56, N = 136). The best agreement was achieved in the poor + top quality group (κ = 0.65, N = 77), while the agreement in the fair quality group was lower (κ = 0.25, N = 59). The DNN showed an overall accuracy rate of 62.5%, with accuracies of 62.2%, 61% and 65.6% for the poor, fair and top quality groups, respectively. The AUC for the DNN was higher than that of the embryologists overall (0.70 DNN vs 0.61 embryologists) as well as in all of the Gardner groups (DNN vs embryologists—Poor: 0.69 vs 0.62; Fair: 0.67 vs 0.53; Top: 0.77 vs 0.54).\r\n\r\nLIMITATIONS, REASONS FOR CAUTION: Blastocyst assessment was performed using video files acquired from time-lapse incubators, where each video contained data from a single focal plane. Clinical data regarding the underlying cause of infertility and endometrial thickness before the transfer was not available, yet may explain implantation failure and lower accuracy of IPGs. Implantation was defined as the presence of a gestational sac, whereas the detection of fetal heartbeat is a more robust marker of embryo viability. The raw data were anonymized to the extent that it was not possible to quantify the number of unique patients and cycles included in the study, potentially masking the effect of bias from a limited patient pool. Furthermore, the lack of demographic data makes it difficult to draw conclusions on how representative the dataset was of the wider population. Finally, embryologists were required to assess the implantation potential, not embryo quality. Although this is not the traditional approach to embryo evaluation, morphology/morphokinetics as a means of assessing embryo quality is believed to be strongly correlated with viability and, for some methods, implantation potential.\r\n\r\nWIDER IMPLICATIONS OF THE FINDINGS: Embryo selection is a key element in IVF success and continues to be a challenge. Improving the predictive ability could assist in optimizing implantation success rates and other clinical outcomes and could minimize the financial and emotional burden on the patient. This study demonstrates moderate agreement rates between embryologists, likely due to the subjective nature of embryo assessment. In particular, we found that average embryologist accuracy and agreement were significantly lower for fair quality embryos when compared with that for top and poor quality embryos. Using data-driven algorithms as an assistive tool may help IVF professionals increase success rates and promote much needed standardization in the IVF clinic. Our results indicate a need for further research regarding technological advancement in this field."}],"title":"Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity?","quality_controlled":"1","oa":1,"article_type":"original","status":"public","date_updated":"2024-10-14T09:54:40Z","doi":"10.1093/humrep/deac171","page":"2275-2290","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"10","volume":37,"publication_status":"published","author":[{"first_name":"Daniel E","full_name":"Fordham, Daniel E","last_name":"Fordham"},{"first_name":"Dror","last_name":"Rosentraub","full_name":"Rosentraub, Dror"},{"last_name":"Polsky","full_name":"Polsky, Avital L","first_name":"Avital L"},{"first_name":"Talia","full_name":"Aviram, Talia","last_name":"Aviram"},{"first_name":"Yotam","full_name":"Wolf, Yotam","last_name":"Wolf"},{"first_name":"Oriel","last_name":"Perl","full_name":"Perl, Oriel"},{"full_name":"Devir, Asnat","last_name":"Devir","first_name":"Asnat"},{"first_name":"Shahar","last_name":"Rosentraub","full_name":"Rosentraub, Shahar"},{"last_name":"Silver","full_name":"Silver, David H","first_name":"David H"},{"last_name":"Gold Zamir","full_name":"Gold Zamir, Yael","first_name":"Yael"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","last_name":"Bronstein","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"last_name":"Lara Lara","full_name":"Lara Lara, Miguel","first_name":"Miguel"},{"last_name":"Ben Nagi","full_name":"Ben Nagi, Jara","first_name":"Jara"},{"last_name":"Alvarez","full_name":"Alvarez, Adrian","first_name":"Adrian"},{"full_name":"Munné, Santiago","last_name":"Munné","first_name":"Santiago"}],"intvolume":"        37","scopus_import":"1","issue":"10","OA_type":"free access","citation":{"ista":"Fordham DE, Rosentraub D, Polsky AL, Aviram T, Wolf Y, Perl O, Devir A, Rosentraub S, Silver DH, Gold Zamir Y, Bronstein AM, Lara Lara M, Ben Nagi J, Alvarez A, Munné S. 2022. Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity? Human Reproduction. 37(10), 2275–2290.","mla":"Fordham, Daniel E., et al. “Embryologist Agreement When Assessing Blastocyst Implantation Probability: Is Data-Driven Prediction the Solution to Embryo Assessment Subjectivity?” <i>Human Reproduction</i>, vol. 37, no. 10, Oxford University Press, 2022, pp. 2275–90, doi:<a href=\"https://doi.org/10.1093/humrep/deac171\">10.1093/humrep/deac171</a>.","chicago":"Fordham, Daniel E, Dror Rosentraub, Avital L Polsky, Talia Aviram, Yotam Wolf, Oriel Perl, Asnat Devir, et al. “Embryologist Agreement When Assessing Blastocyst Implantation Probability: Is Data-Driven Prediction the Solution to Embryo Assessment Subjectivity?” <i>Human Reproduction</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/humrep/deac171\">https://doi.org/10.1093/humrep/deac171</a>.","ieee":"D. E. Fordham <i>et al.</i>, “Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity?,” <i>Human Reproduction</i>, vol. 37, no. 10. Oxford University Press, pp. 2275–2290, 2022.","short":"D.E. Fordham, D. Rosentraub, A.L. Polsky, T. Aviram, Y. Wolf, O. Perl, A. Devir, S. Rosentraub, D.H. Silver, Y. Gold Zamir, A.M. Bronstein, M. Lara Lara, J. Ben Nagi, A. Alvarez, S. Munné, Human Reproduction 37 (2022) 2275–2290.","apa":"Fordham, D. E., Rosentraub, D., Polsky, A. L., Aviram, T., Wolf, Y., Perl, O., … Munné, S. (2022). Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity? <i>Human Reproduction</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/humrep/deac171\">https://doi.org/10.1093/humrep/deac171</a>","ama":"Fordham DE, Rosentraub D, Polsky AL, et al. Embryologist agreement when assessing blastocyst implantation probability: Is data-driven prediction the solution to embryo assessment subjectivity? <i>Human Reproduction</i>. 2022;37(10):2275-2290. doi:<a href=\"https://doi.org/10.1093/humrep/deac171\">10.1093/humrep/deac171</a>"},"OA_place":"publisher","extern":"1"},{"publisher":"Springer Nature","quality_controlled":"1","abstract":[{"lang":"eng","text":"The term silent mutation is commonly used to describe (1) a change in the DNA sequence that does not result in an observable effect on the organism’s phenotype; and (2) a synonymous mutation where the nucleotide change leaves the translated amino acid sequence unchanged. When Christian Anfinsen showed that a folded and active protein could be denatured to lose structure and activity and then subsequently renatured to regain the same structure and activity it appeared that the native, thermodynamically stable, structure of a protein depends only on the amino acid sequence and solution conditions (Anfinsen and Haber 1961). This experiment suggested that, once translated, proteins carry no memory of the genetic sequence and led to one of the most erroneous assumptions in modern science; synonymous codons were long considered silent, a mutation of the type that has no effect on an organism’s phenotype."}],"title":"Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease","OA_type":"closed access","citation":{"short":"A.A. Rosenberg, A.M. Bronstein, A. Marx, in:, Z.E. Sauna, C. Kimchi-Sarfaty (Eds.), Single Nucleotide Polymorphisms, Springer Nature, Cham, 2022, pp. 37–47.","apa":"Rosenberg, A. A., Bronstein, A. M., &#38; Marx, A. (2022). Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease. In Z. E. Sauna &#38; C. Kimchi-Sarfaty (Eds.), <i>Single Nucleotide Polymorphisms</i> (pp. 37–47). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-05616-1_3\">https://doi.org/10.1007/978-3-031-05616-1_3</a>","ama":"Rosenberg AA, Bronstein AM, Marx A. Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease. In: Sauna ZE, Kimchi-Sarfaty C, eds. <i>Single Nucleotide Polymorphisms</i>. Cham: Springer Nature; 2022:37-47. doi:<a href=\"https://doi.org/10.1007/978-3-031-05616-1_3\">10.1007/978-3-031-05616-1_3</a>","ista":"Rosenberg AA, Bronstein AM, Marx A. 2022.Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease. In: Single Nucleotide Polymorphisms. , 37–47.","mla":"Rosenberg, Aviv A., et al. “Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease.” <i>Single Nucleotide Polymorphisms</i>, edited by Zuben E. Sauna and Chava Kimchi-Sarfaty, Springer Nature, 2022, pp. 37–47, doi:<a href=\"https://doi.org/10.1007/978-3-031-05616-1_3\">10.1007/978-3-031-05616-1_3</a>.","chicago":"Rosenberg, Aviv A., Alex M. Bronstein, and Ailie Marx. “Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease.” In <i>Single Nucleotide Polymorphisms</i>, edited by Zuben E. Sauna and Chava Kimchi-Sarfaty, 37–47. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-05616-1_3\">https://doi.org/10.1007/978-3-031-05616-1_3</a>.","ieee":"A. A. Rosenberg, A. M. Bronstein, and A. Marx, “Recording Silence – Accurate Annotation of the Genetic Sequence Is Required to Better Understand How Synonymous Coding Affects Protein Structure and Disease,” in <i>Single Nucleotide Polymorphisms</i>, Z. E. Sauna and C. Kimchi-Sarfaty, Eds. Cham: Springer Nature, 2022, pp. 37–47."},"publication_identifier":{"isbn":["9783031056147"],"eisbn":["9783031056161"]},"doi":"10.1007/978-3-031-05616-1_3","status":"public","date_updated":"2024-10-14T09:58:21Z","extern":"1","date_published":"2022-08-10T00:00:00Z","editor":[{"full_name":"Sauna, Zuben E.","last_name":"Sauna","first_name":"Zuben E."},{"first_name":"Chava","last_name":"Kimchi-Sarfaty","full_name":"Kimchi-Sarfaty, Chava"}],"_id":"18223","date_created":"2024-10-08T12:53:44Z","page":"37-47","oa_version":"None","year":"2022","language":[{"iso":"eng"}],"place":"Cham","article_processing_charge":"No","day":"10","scopus_import":"1","month":"08","publication":"Single Nucleotide Polymorphisms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"book_chapter","author":[{"first_name":"Aviv A.","full_name":"Rosenberg, Aviv A.","last_name":"Rosenberg"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","last_name":"Bronstein","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"},{"full_name":"Marx, Ailie","last_name":"Marx","first_name":"Ailie"}]},{"article_processing_charge":"No","day":"01","publication":"Pattern Recognition Letters","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2022-08-01T00:00:00Z","_id":"18224","external_id":{"arxiv":["1906.01905"]},"date_created":"2024-10-08T12:54:03Z","year":"2022","date_updated":"2024-10-14T10:58:20Z","doi":"10.1016/j.patrec.2022.06.012","status":"public","arxiv":1,"oa":1,"article_type":"original","publisher":"Elsevier","quality_controlled":"1","abstract":[{"text":"Learning from one or few visual examples is one of the key capabilities of humans since early infancy, but is still a significant challenge for modern AI systems. While considerable progress has been achieved in few-shot learning from a few image examples, much less attention has been given to the verbal descriptions that are usually provided to infants when they are presented with a new object. In this paper, we focus on the role of additional semantics that can significantly facilitate few-shot visual learning. Building upon recent advances in few-shot learning with additional semantic information, we demonstrate that further improvements are possible by combining multiple and richer semantics (category labels, attributes, and natural language descriptions). Using these ideas, we offer the community new results on the popular miniImageNet and CUB few-shot benchmarks, comparing favorably to the previous state-of-the-art results for both visual only and visual plus semantics-based approaches. We also performed an ablation study investigating the components and design choices of our approach. Code available on github.com/EliSchwartz/mutiple-semantics.","lang":"eng"}],"title":"Baby steps towards few-shot learning with multiple semantics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.01905"}],"publication_identifier":{"issn":["0167-8655"]},"intvolume":"       160","scopus_import":"1","volume":160,"month":"08","publication_status":"published","author":[{"first_name":"Eli","last_name":"Schwartz","full_name":"Schwartz, Eli"},{"first_name":"Leonid","last_name":"Karlinsky","full_name":"Karlinsky, Leonid"},{"first_name":"Rogerio","full_name":"Feris, Rogerio","last_name":"Feris"},{"last_name":"Giryes","full_name":"Giryes, Raja","first_name":"Raja"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730"}],"page":"142-147","oa_version":"Preprint","language":[{"iso":"eng"}],"OA_place":"repository","extern":"1","citation":{"ama":"Schwartz E, Karlinsky L, Feris R, Giryes R, Bronstein AM. Baby steps towards few-shot learning with multiple semantics. <i>Pattern Recognition Letters</i>. 2022;160:142-147. doi:<a href=\"https://doi.org/10.1016/j.patrec.2022.06.012\">10.1016/j.patrec.2022.06.012</a>","apa":"Schwartz, E., Karlinsky, L., Feris, R., Giryes, R., &#38; Bronstein, A. M. (2022). Baby steps towards few-shot learning with multiple semantics. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2022.06.012\">https://doi.org/10.1016/j.patrec.2022.06.012</a>","short":"E. Schwartz, L. Karlinsky, R. Feris, R. Giryes, A.M. Bronstein, Pattern Recognition Letters 160 (2022) 142–147.","ieee":"E. Schwartz, L. Karlinsky, R. Feris, R. Giryes, and A. M. Bronstein, “Baby steps towards few-shot learning with multiple semantics,” <i>Pattern Recognition Letters</i>, vol. 160. Elsevier, pp. 142–147, 2022.","chicago":"Schwartz, Eli, Leonid Karlinsky, Rogerio Feris, Raja Giryes, and Alex M. Bronstein. “Baby Steps towards Few-Shot Learning with Multiple Semantics.” <i>Pattern Recognition Letters</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.patrec.2022.06.012\">https://doi.org/10.1016/j.patrec.2022.06.012</a>.","mla":"Schwartz, Eli, et al. “Baby Steps towards Few-Shot Learning with Multiple Semantics.” <i>Pattern Recognition Letters</i>, vol. 160, Elsevier, 2022, pp. 142–47, doi:<a href=\"https://doi.org/10.1016/j.patrec.2022.06.012\">10.1016/j.patrec.2022.06.012</a>.","ista":"Schwartz E, Karlinsky L, Feris R, Giryes R, Bronstein AM. 2022. Baby steps towards few-shot learning with multiple semantics. Pattern Recognition Letters. 160, 142–147."}},{"extern":"1","OA_place":"publisher","citation":{"short":"G. Pai, A.M. Bronstein, R. Talmon, R. Kimmel, Image and Vision Computing 123 (2022).","ama":"Pai G, Bronstein AM, Talmon R, Kimmel R. Deep isometric maps. <i>Image and Vision Computing</i>. 2022;123. doi:<a href=\"https://doi.org/10.1016/j.imavis.2022.104461\">10.1016/j.imavis.2022.104461</a>","apa":"Pai, G., Bronstein, A. M., Talmon, R., &#38; Kimmel, R. (2022). Deep isometric maps. <i>Image and Vision Computing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.imavis.2022.104461\">https://doi.org/10.1016/j.imavis.2022.104461</a>","ista":"Pai G, Bronstein AM, Talmon R, Kimmel R. 2022. Deep isometric maps. Image and Vision Computing. 123, 104461.","chicago":"Pai, Gautam, Alex M. Bronstein, Ronen Talmon, and Ron Kimmel. “Deep Isometric Maps.” <i>Image and Vision Computing</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.imavis.2022.104461\">https://doi.org/10.1016/j.imavis.2022.104461</a>.","ieee":"G. Pai, A. M. Bronstein, R. Talmon, and R. Kimmel, “Deep isometric maps,” <i>Image and Vision Computing</i>, vol. 123. Elsevier, 2022.","mla":"Pai, Gautam, et al. “Deep Isometric Maps.” <i>Image and Vision Computing</i>, vol. 123, 104461, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.imavis.2022.104461\">10.1016/j.imavis.2022.104461</a>."},"article_number":"104461","author":[{"full_name":"Pai, Gautam","last_name":"Pai","first_name":"Gautam"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730"},{"last_name":"Talmon","full_name":"Talmon, Ronen","first_name":"Ronen"},{"full_name":"Kimmel, Ron","last_name":"Kimmel","first_name":"Ron"}],"publication_status":"published","month":"07","volume":123,"scopus_import":"1","intvolume":"       123","language":[{"iso":"eng"}],"oa_version":"Published Version","article_type":"original","oa":1,"status":"public","date_updated":"2024-10-14T11:03:26Z","doi":"10.1016/j.imavis.2022.104461","publication_identifier":{"issn":["0262-8856"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.imavis.2022.104461","open_access":"1"}],"abstract":[{"text":"Isometric feature mapping is an established time-honored algorithm in manifold learning and non-linear dimensionality reduction. Its prominence can be attributed to the output of a coherent global low-dimensional representation of data by preserving intrinsic distances. In order to enable an efficient and more applicable isometric feature mapping, a diverse set of sophisticated advancements have been proposed to the original algorithm to incorporate important factors like sparsity of computation, conformality, topological constraints and spectral geometry. However, a significant shortcoming of most approaches is the dependence on large-scale dense-spectral decompositions and the inability to generalize to points far away from the sampling of the manifold.\r\nIn this paper, we explore an unsupervised deep learning approach for computing distance-preserving maps for non-linear dimensionality reduction. We demonstrate that our framework is general enough to incorporate all previous advancements and show a significantly improved local and non-local generalization of the isometric mapping. Our approach involves training with only a few landmark points and avoids the need for population of dense matrices as well as computing their spectral decomposition.","lang":"eng"}],"quality_controlled":"1","title":"Deep isometric maps","publisher":"Elsevier","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Image and Vision Computing","day":"01","article_processing_charge":"No","year":"2022","date_created":"2024-10-08T12:54:22Z","_id":"18225","date_published":"2022-07-01T00:00:00Z"},{"year":"2022","_id":"18226","date_published":"2022-06-06T00:00:00Z","date_created":"2024-10-08T12:54:43Z","publication":"Optica","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"06","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1364/OPTICA.451115","open_access":"1"}],"publication_identifier":{"issn":["2334-2536"]},"title":"Inverse design of spontaneous parametric downconversion for generation of high-dimensional qudits","abstract":[{"text":"Spontaneous parametric downconversion (SPDC) in quantum optics is an invaluable resource for the realization of high-dimensional qudits with spatial modes of light. One of the main open challenges is how to directly generate a desirable qudit state in the SPDC process. This problem can be addressed through advanced computational learning methods; however, due to difficulties in modeling the SPDC process by a fully differentiable algorithm, progress has been limited. Here, we overcome these limitations and introduce a physically constrained and differentiable model, validated against experimental results for shaped pump beams and structured crystals, capable of learning the relevant interaction parameters in the process. We avoid any restrictions induced by the stochastic nature of our physical model and integrate the dynamic equations governing the evolution under the SPDC Hamiltonian. We solve the inverse problem of designing a nonlinear quantum optical system that achieves the desired quantum state of downconverted photon pairs. The desired states are defined using either the second-order correlations between different spatial modes or by specifying the required density matrix. By learning nonlinear photonic crystal structures as well as different pump shapes, we successfully show how to generate maximally entangled states. Furthermore, we simulate all-optical coherent control over the generated quantum state by actively changing the profile of the pump beam. Our work can be useful for applications such as novel designs of high-dimensional quantum key distribution and quantum information processing protocols. In addition, our method can be readily applied for controlling other degrees of freedom of light in the SPDC process, such as spectral and temporal properties, and may even be used in condensed-matter systems having a similar interaction Hamiltonian.","lang":"eng"}],"quality_controlled":"1","publisher":"Optica Publishing Group","oa":1,"article_type":"original","doi":"10.1364/optica.451115","status":"public","date_updated":"2024-10-14T11:07:29Z","oa_version":"Published Version","page":"602-615","language":[{"iso":"eng"}],"volume":9,"month":"06","author":[{"first_name":"Eyal","full_name":"Rozenberg, Eyal","last_name":"Rozenberg"},{"first_name":"Aviv","last_name":"Karnieli","full_name":"Karnieli, Aviv"},{"first_name":"Ofir","last_name":"Yesharim","full_name":"Yesharim, Ofir"},{"first_name":"Joshua","last_name":"Foley-Comer","full_name":"Foley-Comer, Joshua"},{"full_name":"Trajtenberg-Mills, Sivan","last_name":"Trajtenberg-Mills","first_name":"Sivan"},{"first_name":"Daniel","last_name":"Freedman","full_name":"Freedman, Daniel"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730"},{"full_name":"Arie, Ady","last_name":"Arie","first_name":"Ady"}],"publication_status":"published","scopus_import":"1","intvolume":"         9","issue":"6","OA_type":"hybrid","citation":{"apa":"Rozenberg, E., Karnieli, A., Yesharim, O., Foley-Comer, J., Trajtenberg-Mills, S., Freedman, D., … Arie, A. (2022). Inverse design of spontaneous parametric downconversion for generation of high-dimensional qudits. <i>Optica</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/optica.451115\">https://doi.org/10.1364/optica.451115</a>","ama":"Rozenberg E, Karnieli A, Yesharim O, et al. Inverse design of spontaneous parametric downconversion for generation of high-dimensional qudits. <i>Optica</i>. 2022;9(6):602-615. doi:<a href=\"https://doi.org/10.1364/optica.451115\">10.1364/optica.451115</a>","short":"E. Rozenberg, A. Karnieli, O. Yesharim, J. Foley-Comer, S. Trajtenberg-Mills, D. Freedman, A.M. Bronstein, A. Arie, Optica 9 (2022) 602–615.","mla":"Rozenberg, Eyal, et al. “Inverse Design of Spontaneous Parametric Downconversion for Generation of High-Dimensional Qudits.” <i>Optica</i>, vol. 9, no. 6, Optica Publishing Group, 2022, pp. 602–15, doi:<a href=\"https://doi.org/10.1364/optica.451115\">10.1364/optica.451115</a>.","chicago":"Rozenberg, Eyal, Aviv Karnieli, Ofir Yesharim, Joshua Foley-Comer, Sivan Trajtenberg-Mills, Daniel Freedman, Alex M. Bronstein, and Ady Arie. “Inverse Design of Spontaneous Parametric Downconversion for Generation of High-Dimensional Qudits.” <i>Optica</i>. Optica Publishing Group, 2022. <a href=\"https://doi.org/10.1364/optica.451115\">https://doi.org/10.1364/optica.451115</a>.","ieee":"E. Rozenberg <i>et al.</i>, “Inverse design of spontaneous parametric downconversion for generation of high-dimensional qudits,” <i>Optica</i>, vol. 9, no. 6. Optica Publishing Group, pp. 602–615, 2022.","ista":"Rozenberg E, Karnieli A, Yesharim O, Foley-Comer J, Trajtenberg-Mills S, Freedman D, Bronstein AM, Arie A. 2022. Inverse design of spontaneous parametric downconversion for generation of high-dimensional qudits. Optica. 9(6), 602–615."},"OA_place":"publisher","extern":"1"},{"oa_version":"None","page":"15653-15670","language":[{"iso":"eng"}],"year":"2022","_id":"18227","date_published":"2022-05-01T00:00:00Z","date_created":"2024-10-08T12:55:04Z","publication":"Multimedia Tools and Applications","month":"05","volume":81,"author":[{"first_name":"Peipei","last_name":"Kang","full_name":"Kang, Peipei"},{"first_name":"Zehang","full_name":"Lin, Zehang","last_name":"Lin"},{"first_name":"Zhenguo","last_name":"Yang","full_name":"Yang, Zhenguo"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander"},{"first_name":"Qing","last_name":"Li","full_name":"Li, Qing"},{"first_name":"Wenyin","full_name":"Liu, Wenyin","last_name":"Liu"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","scopus_import":"1","day":"01","article_processing_charge":"No","intvolume":"        81","issue":"11","publication_identifier":{"eissn":["1573-7721"],"issn":["1380-7501"]},"citation":{"chicago":"Kang, Peipei, Zehang Lin, Zhenguo Yang, Alex M. Bronstein, Qing Li, and Wenyin Liu. “Deep Fused Two-Step Cross-Modal Hashing with Multiple Semantic Supervision.” <i>Multimedia Tools and Applications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11042-022-12187-6\">https://doi.org/10.1007/s11042-022-12187-6</a>.","ieee":"P. Kang, Z. Lin, Z. Yang, A. M. Bronstein, Q. Li, and W. Liu, “Deep fused two-step cross-modal hashing with multiple semantic supervision,” <i>Multimedia Tools and Applications</i>, vol. 81, no. 11. Springer Nature, pp. 15653–15670, 2022.","mla":"Kang, Peipei, et al. “Deep Fused Two-Step Cross-Modal Hashing with Multiple Semantic Supervision.” <i>Multimedia Tools and Applications</i>, vol. 81, no. 11, Springer Nature, 2022, pp. 15653–70, doi:<a href=\"https://doi.org/10.1007/s11042-022-12187-6\">10.1007/s11042-022-12187-6</a>.","ista":"Kang P, Lin Z, Yang Z, Bronstein AM, Li Q, Liu W. 2022. Deep fused two-step cross-modal hashing with multiple semantic supervision. Multimedia Tools and Applications. 81(11), 15653–15670.","ama":"Kang P, Lin Z, Yang Z, Bronstein AM, Li Q, Liu W. Deep fused two-step cross-modal hashing with multiple semantic supervision. <i>Multimedia Tools and Applications</i>. 2022;81(11):15653-15670. doi:<a href=\"https://doi.org/10.1007/s11042-022-12187-6\">10.1007/s11042-022-12187-6</a>","apa":"Kang, P., Lin, Z., Yang, Z., Bronstein, A. M., Li, Q., &#38; Liu, W. (2022). Deep fused two-step cross-modal hashing with multiple semantic supervision. <i>Multimedia Tools and Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11042-022-12187-6\">https://doi.org/10.1007/s11042-022-12187-6</a>","short":"P. Kang, Z. Lin, Z. Yang, A.M. Bronstein, Q. Li, W. Liu, Multimedia Tools and Applications 81 (2022) 15653–15670."},"title":"Deep fused two-step cross-modal hashing with multiple semantic supervision","quality_controlled":"1","abstract":[{"text":"Existing cross-modal hashing methods ignore the informative multimodal joint information and cannot fully exploit the semantic labels. In this paper, we propose a deep fused two-step cross-modal hashing (DFTH) framework with multiple semantic supervision. In the first step, DFTH learns unified hash codes for instances by a fusion network. Semantic label and similarity reconstruction have been introduced to acquire binary codes that are informative, discriminative and semantic similarity preserving. In the second step, two modality-specific hash networks are learned under the supervision of common hash codes reconstruction, label reconstruction, and intra-modal and inter-modal semantic similarity reconstruction. The modality-specific hash networks can generate semantic preserving binary codes for out-of-sample queries. To deal with the vanishing gradients of binarization, continuous differentiable tanh is introduced to approximate the discrete sign function, making the networks able to back-propagate by automatic gradient computation. Extensive experiments on MIRFlickr25K and NUS-WIDE show the superiority of DFTH over state-of-the-art methods.","lang":"eng"}],"publisher":"Springer Nature","article_type":"original","extern":"1","doi":"10.1007/s11042-022-12187-6","date_updated":"2024-10-14T11:10:00Z","status":"public"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.10994"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031198205"],"eissn":["1611-3349"],"eisbn":["9783031198212"]},"abstract":[{"lang":"eng","text":"We present Self-Classifier – a novel self-supervised end-to-end classification learning approach. Self-Classifier learns labels and representations simultaneously in a single-stage end-to-end manner by optimizing for same-class prediction of two augmented views of the same sample. To guarantee non-degenerate solutions (i.e., solutions where all labels are assigned to the same class) we propose a mathematically motivated variant of the cross-entropy loss that has a uniform prior asserted on the predicted labels. In our theoretical analysis, we prove that degenerate solutions are not in the set of optimal solutions of our approach. Self-Classifier is simple to implement and scalable. Unlike other popular unsupervised classification and contrastive representation learning approaches, it does not require any form of pre-training, expectation-maximization, pseudo-labeling, external clustering, a second network, stop-gradient operation, or negative pairs. Despite its simplicity, our approach sets a new state of the art for unsupervised classification of ImageNet; and even achieves comparable to state-of-the-art results for unsupervised representation learning. Code is available at https://github.com/elad-amrani/self-classifier."}],"quality_controlled":"1","title":"Self-supervised classification network","publisher":"Springer Nature","oa":1,"status":"public","doi":"10.1007/978-3-031-19821-2_7","date_updated":"2024-10-15T07:04:39Z","arxiv":1,"year":"2022","external_id":{"arxiv":["2103.10994"]},"_id":"18229","date_published":"2022-10-23T00:00:00Z","date_created":"2024-10-08T12:55:44Z","publication":"17th European Conference on Computer Vision","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","article_processing_charge":"No","citation":{"short":"E. Amrani, L. Karlinsky, A.M. Bronstein, in:, 17th European Conference on Computer Vision, Springer Nature, 2022, pp. 116–132.","apa":"Amrani, E., Karlinsky, L., &#38; Bronstein, A. M. (2022). Self-supervised classification network. In <i>17th European Conference on Computer Vision</i> (Vol. 13691, pp. 116–132). Tel Aviv, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-19821-2_7\">https://doi.org/10.1007/978-3-031-19821-2_7</a>","ama":"Amrani E, Karlinsky L, Bronstein AM. Self-supervised classification network. In: <i>17th European Conference on Computer Vision</i>. Vol 13691. Springer Nature; 2022:116-132. doi:<a href=\"https://doi.org/10.1007/978-3-031-19821-2_7\">10.1007/978-3-031-19821-2_7</a>","ista":"Amrani E, Karlinsky L, Bronstein AM. 2022. Self-supervised classification network. 17th European Conference on Computer Vision. ECCV: European Conference on Computer Vision, LNCS, vol. 13691, 116–132.","mla":"Amrani, Elad, et al. “Self-Supervised Classification Network.” <i>17th European Conference on Computer Vision</i>, vol. 13691, Springer Nature, 2022, pp. 116–32, doi:<a href=\"https://doi.org/10.1007/978-3-031-19821-2_7\">10.1007/978-3-031-19821-2_7</a>.","ieee":"E. Amrani, L. Karlinsky, and A. M. Bronstein, “Self-supervised classification network,” in <i>17th European Conference on Computer Vision</i>, Tel Aviv, Israel, 2022, vol. 13691, pp. 116–132.","chicago":"Amrani, Elad, Leonid Karlinsky, and Alex M. Bronstein. “Self-Supervised Classification Network.” In <i>17th European Conference on Computer Vision</i>, 13691:116–32. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-19821-2_7\">https://doi.org/10.1007/978-3-031-19821-2_7</a>."},"related_material":{"link":[{"relation":"software","url":"https://github.com/elad-amrani/self-classifier"}]},"alternative_title":["LNCS"],"extern":"1","oa_version":"None","page":"116-132","language":[{"iso":"eng"}],"volume":13691,"month":"10","conference":{"start_date":"2022-10-23","location":"Tel Aviv, Israel","end_date":"2022-10-27","name":"ECCV: European Conference on Computer Vision"},"author":[{"full_name":"Amrani, Elad","last_name":"Amrani","first_name":"Elad"},{"first_name":"Leonid","last_name":"Karlinsky","full_name":"Karlinsky, Leonid"},{"orcid":"0000-0001-9699-8730","last_name":"Bronstein","full_name":"Bronstein, Alexander","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"}],"publication_status":"published","scopus_import":"1","intvolume":"     13691"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publication_status":"published","conference":{"name":"MICRO: Symposium on Microarchitecture","end_date":"2022-10-05","start_date":"2022-10-01","location":"Chicago, IL, United States"},"author":[{"first_name":"Nishil","full_name":"Talati, Nishil","last_name":"Talati"},{"first_name":"Haojie","last_name":"Ye","full_name":"Ye, Haojie"},{"full_name":"Vedula, Sanketh","last_name":"Vedula","first_name":"Sanketh"},{"first_name":"Kuan-Yu","full_name":"Chen, Kuan-Yu","last_name":"Chen"},{"last_name":"Chen","full_name":"Chen, Yuhan","first_name":"Yuhan"},{"full_name":"Liu, Daniel","last_name":"Liu","first_name":"Daniel"},{"first_name":"Yichao","last_name":"Yuan","full_name":"Yuan, Yichao"},{"first_name":"David","last_name":"Blaauw","full_name":"Blaauw, David"},{"first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","last_name":"Bronstein","full_name":"Bronstein, Alexander"},{"last_name":"Mudge","full_name":"Mudge, Trevor","first_name":"Trevor"},{"last_name":"Dreslinski","full_name":"Dreslinski, Ronald","first_name":"Ronald"}],"month":"10","publication":"55th IEEE/ACM International Symposium on Microarchitecture","article_processing_charge":"No","day":"01","scopus_import":"1","year":"2022","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2024-10-08T12:56:03Z","date_published":"2022-10-01T00:00:00Z","_id":"18230","extern":"1","status":"public","doi":"10.1109/micro56248.2022.00089","date_updated":"2024-10-15T07:14:02Z","citation":{"chicago":"Talati, Nishil, Haojie Ye, Sanketh Vedula, Kuan-Yu Chen, Yuhan Chen, Daniel Liu, Yichao Yuan, et al. “Mint: An Accelerator for Mining Temporal Motifs.” In <i>55th IEEE/ACM International Symposium on Microarchitecture</i>. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/micro56248.2022.00089\">https://doi.org/10.1109/micro56248.2022.00089</a>.","ieee":"N. Talati <i>et al.</i>, “Mint: An accelerator for mining temporal motifs,” in <i>55th IEEE/ACM International Symposium on Microarchitecture</i>, Chicago, IL, United States, 2022.","mla":"Talati, Nishil, et al. “Mint: An Accelerator for Mining Temporal Motifs.” <i>55th IEEE/ACM International Symposium on Microarchitecture</i>, Institute of Electrical and Electronics Engineers, 2022, doi:<a href=\"https://doi.org/10.1109/micro56248.2022.00089\">10.1109/micro56248.2022.00089</a>.","ista":"Talati N, Ye H, Vedula S, Chen K-Y, Chen Y, Liu D, Yuan Y, Blaauw D, Bronstein AM, Mudge T, Dreslinski R. 2022. Mint: An accelerator for mining temporal motifs. 55th IEEE/ACM International Symposium on Microarchitecture. MICRO: Symposium on Microarchitecture.","ama":"Talati N, Ye H, Vedula S, et al. Mint: An accelerator for mining temporal motifs. In: <i>55th IEEE/ACM International Symposium on Microarchitecture</i>. Institute of Electrical and Electronics Engineers; 2022. doi:<a href=\"https://doi.org/10.1109/micro56248.2022.00089\">10.1109/micro56248.2022.00089</a>","apa":"Talati, N., Ye, H., Vedula, S., Chen, K.-Y., Chen, Y., Liu, D., … Dreslinski, R. (2022). Mint: An accelerator for mining temporal motifs. In <i>55th IEEE/ACM International Symposium on Microarchitecture</i>. Chicago, IL, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/micro56248.2022.00089\">https://doi.org/10.1109/micro56248.2022.00089</a>","short":"N. Talati, H. Ye, S. Vedula, K.-Y. Chen, Y. Chen, D. Liu, Y. Yuan, D. Blaauw, A.M. Bronstein, T. Mudge, R. Dreslinski, in:, 55th IEEE/ACM International Symposium on Microarchitecture, Institute of Electrical and Electronics Engineers, 2022."},"publication_identifier":{"eisbn":["9781665462723"]},"publisher":"Institute of Electrical and Electronics Engineers","title":"Mint: An accelerator for mining temporal motifs","abstract":[{"text":"A variety of complex systems, including social and communication networks, financial markets, biology, and neuroscience are modeled using temporal graphs that contain a set of nodes and directed timestamped edges. Temporal motifs in temporal graphs are generalized from subgraph patterns in static graphs in that they also account for edge ordering and time duration, in addition to the graph structure. Mining temporal motifs is a fundamental problem used in several application domains. However, existing software frameworks offer suboptimal performance due to high algorithmic complexity and irregular memory accesses of temporal motif mining.This paper presents Mint—a novel accelerator architecture and a programming model for mining temporal motifs efficiently. We first divide this workload into three fundamental tasks: search, book-keeping, and backtracking. Based on this, we propose a task-centric programming model that enables decoupled, asynchronous execution. This model unlocks massive opportunities for parallelism, and allows storing task context information on-chip. To best utilize the proposed programming model, we design a domain-specific hardware accelerator using its data path and memory subsystem design to cater to the unique workload characteristics of temporal motif mining. To further improve performance, we propose a novel optimization called search index memoization that significantly reduces memory traffic. We comprehensively compare the performance of Mint with state-of-the-art temporal motif mining software frameworks (both approximate and exact) running on both CPU and GPU, and show 9×−2576× benefit in performance.","lang":"eng"}],"quality_controlled":"1"},{"extern":"1","OA_place":"repository","citation":{"mla":"Zheltonozhskii, Evgenii, et al. “Contrast to Divide: Self-Supervised Pre-Training for Learning with Noisy Labels.” <i>IEEE/CVF Winter Conference on Applications of Computer Vision</i>, Institute of Electrical and Electronics Engineers, 2022, pp. 387–97, doi:<a href=\"https://doi.org/10.1109/wacv51458.2022.00046\">10.1109/wacv51458.2022.00046</a>.","chicago":"Zheltonozhskii, Evgenii, Chaim Baskin, Avi Mendelson, Alex M. Bronstein, and Or Litany. “Contrast to Divide: Self-Supervised Pre-Training for Learning with Noisy Labels.” In <i>IEEE/CVF Winter Conference on Applications of Computer Vision</i>, 387–97. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/wacv51458.2022.00046\">https://doi.org/10.1109/wacv51458.2022.00046</a>.","ieee":"E. Zheltonozhskii, C. Baskin, A. Mendelson, A. M. Bronstein, and O. Litany, “Contrast to divide: Self-supervised pre-training for learning with noisy labels,” in <i>IEEE/CVF Winter Conference on Applications of Computer Vision</i>, Waikoloa, HI, United States, 2022, pp. 387–397.","ista":"Zheltonozhskii E, Baskin C, Mendelson A, Bronstein AM, Litany O. 2022. Contrast to divide: Self-supervised pre-training for learning with noisy labels. IEEE/CVF Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 387–397.","apa":"Zheltonozhskii, E., Baskin, C., Mendelson, A., Bronstein, A. M., &#38; Litany, O. (2022). Contrast to divide: Self-supervised pre-training for learning with noisy labels. In <i>IEEE/CVF Winter Conference on Applications of Computer Vision</i> (pp. 387–397). Waikoloa, HI, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/wacv51458.2022.00046\">https://doi.org/10.1109/wacv51458.2022.00046</a>","ama":"Zheltonozhskii E, Baskin C, Mendelson A, Bronstein AM, Litany O. Contrast to divide: Self-supervised pre-training for learning with noisy labels. In: <i>IEEE/CVF Winter Conference on Applications of Computer Vision</i>. Institute of Electrical and Electronics Engineers; 2022:387-397. doi:<a href=\"https://doi.org/10.1109/wacv51458.2022.00046\">10.1109/wacv51458.2022.00046</a>","short":"E. Zheltonozhskii, C. Baskin, A. Mendelson, A.M. Bronstein, O. Litany, in:, IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2022, pp. 387–397."},"OA_type":"green","related_material":{"link":[{"url":"https://github.com/ContrastToDivide/C2D","relation":"software"}]},"publication_status":"published","author":[{"full_name":"Zheltonozhskii, Evgenii","last_name":"Zheltonozhskii","first_name":"Evgenii"},{"first_name":"Chaim","full_name":"Baskin, Chaim","last_name":"Baskin"},{"full_name":"Mendelson, Avi","last_name":"Mendelson","first_name":"Avi"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","full_name":"Bronstein, Alexander"},{"first_name":"Or","last_name":"Litany","full_name":"Litany, Or"}],"conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","location":"Waikoloa, HI, United States","start_date":"2022-01-03","end_date":"2022-01-08"},"month":"02","scopus_import":"1","language":[{"iso":"eng"}],"page":"387-397","oa_version":"Preprint","arxiv":1,"date_updated":"2024-10-15T07:27:12Z","status":"public","doi":"10.1109/wacv51458.2022.00046","publication_identifier":{"eisbn":["9781665409155"]},"publisher":"Institute of Electrical and Electronics Engineers","title":"Contrast to divide: Self-supervised pre-training for learning with noisy labels","quality_controlled":"1","abstract":[{"lang":"eng","text":"The success of learning with noisy labels (LNL) methods relies heavily on the success of a warm-up stage where standard supervised training is performed using the full (noisy) training set. In this paper, we identify a \"warm-up obstacle\": the inability of standard warm-up stages to train high quality feature extractors and avert memorization of noisy labels. We propose \"Contrast to Divide\" (C2D), a simple framework that solves this problem by pre-training the feature extractor in a self-supervised fashion. Using self-supervised pre-training boosts the performance of existing LNL approaches by drastically reducing the warm-up stage's susceptibility to noise level, shortening its duration, and improving extracted feature quality. C2D works out of the box with existing methods and demonstrates markedly improved performance, especially in the high noise regime, where we get a boost of more than 27% for CIFAR-100 with 90% noise over the previous state of the art. In real-life noise settings, C2D trained on mini-WebVision outperforms previous works both in WebVision and ImageNet validation sets by 3% top-1 accuracy. We perform an in-depth analysis of the framework, including investigating the performance of different pre-training approaches and estimating the effective upper bound of the LNL performance with semi-supervised learning. Code for reproducing our experiments is available at https://github.com/ContrastToDivide/C2D."}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"IEEE/CVF Winter Conference on Applications of Computer Vision","article_processing_charge":"No","day":"15","year":"2022","date_created":"2024-10-08T12:56:20Z","date_published":"2022-02-15T00:00:00Z","_id":"18231","external_id":{"arxiv":["2103.13646"]}},{"date_published":"2022-01-01T00:00:00Z","_id":"18232","date_created":"2024-10-08T12:56:38Z","page":"33-54","oa_version":"None","year":"2022","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"        52","day":"01","scopus_import":"1","volume":52,"month":"01","publication":"Applied Intelligence","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","author":[{"last_name":"Kang","full_name":"Kang, Peipei","first_name":"Peipei"},{"first_name":"Zehang","full_name":"Lin, Zehang","last_name":"Lin"},{"first_name":"Zhenguo","full_name":"Yang, Zhenguo","last_name":"Yang"},{"full_name":"Fang, Xiaozhao","last_name":"Fang","first_name":"Xiaozhao"},{"full_name":"Bronstein, Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander"},{"last_name":"Li","full_name":"Li, Qing","first_name":"Qing"},{"first_name":"Wenyin","last_name":"Liu","full_name":"Liu, Wenyin"}],"publisher":"Springer Nature","quality_controlled":"1","title":"Intra-class low-rank regularization for supervised and semi-supervised cross-modal retrieval","abstract":[{"lang":"eng","text":"Cross-modal retrieval aims to retrieve related items across different modalities, for example, using an image query to retrieve related text. The existing deep methods ignore both the intra-modal and inter-modal intra-class low-rank structures when fusing various modalities, which decreases the retrieval performance. In this paper, two deep models (denoted as ILCMR and Semi-ILCMR) based on intra-class low-rank regularization are proposed for supervised and semi-supervised cross-modal retrieval, respectively. Specifically, ILCMR integrates the image network and text network into a unified framework to learn a common feature space by imposing three regularization terms to fuse the cross-modal data. First, to align them in the label space, we utilize semantic consistency regularization to convert the data representations to probability distributions over the classes. Second, we introduce an intra-modal low-rank regularization, which encourages the intra-class samples that originate from the same space to be more relevant in the common feature space. Third, an inter-modal low-rank regularization is applied to reduce the cross-modal discrepancy. To enable the low-rank regularization to be optimized using automatic gradients during network back-propagation, we propose the rank-r approximation and specify the explicit gradients for theoretical completeness. In addition to the three regularization terms that rely on label information incorporated by ILCMR, we propose Semi-ILCMR in the semi-supervised regime, which introduces a low-rank constraint before projecting the general representations into the common feature space. Extensive experiments on four public cross-modal datasets demonstrate the superiority of ILCMR and Semi-ILCMR over other state-of-the-art methods."}],"publication_identifier":{"issn":["0924-669X"],"eissn":["1573-7497"]},"citation":{"chicago":"Kang, Peipei, Zehang Lin, Zhenguo Yang, Xiaozhao Fang, Alex M. Bronstein, Qing Li, and Wenyin Liu. “Intra-Class Low-Rank Regularization for Supervised and Semi-Supervised Cross-Modal Retrieval.” <i>Applied Intelligence</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10489-021-02308-3\">https://doi.org/10.1007/s10489-021-02308-3</a>.","ieee":"P. Kang <i>et al.</i>, “Intra-class low-rank regularization for supervised and semi-supervised cross-modal retrieval,” <i>Applied Intelligence</i>, vol. 52. Springer Nature, pp. 33–54, 2022.","mla":"Kang, Peipei, et al. “Intra-Class Low-Rank Regularization for Supervised and Semi-Supervised Cross-Modal Retrieval.” <i>Applied Intelligence</i>, vol. 52, Springer Nature, 2022, pp. 33–54, doi:<a href=\"https://doi.org/10.1007/s10489-021-02308-3\">10.1007/s10489-021-02308-3</a>.","ista":"Kang P, Lin Z, Yang Z, Fang X, Bronstein AM, Li Q, Liu W. 2022. Intra-class low-rank regularization for supervised and semi-supervised cross-modal retrieval. Applied Intelligence. 52, 33–54.","ama":"Kang P, Lin Z, Yang Z, et al. Intra-class low-rank regularization for supervised and semi-supervised cross-modal retrieval. <i>Applied Intelligence</i>. 2022;52:33-54. doi:<a href=\"https://doi.org/10.1007/s10489-021-02308-3\">10.1007/s10489-021-02308-3</a>","apa":"Kang, P., Lin, Z., Yang, Z., Fang, X., Bronstein, A. M., Li, Q., &#38; Liu, W. (2022). Intra-class low-rank regularization for supervised and semi-supervised cross-modal retrieval. <i>Applied Intelligence</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10489-021-02308-3\">https://doi.org/10.1007/s10489-021-02308-3</a>","short":"P. Kang, Z. Lin, Z. Yang, X. Fang, A.M. Bronstein, Q. Li, W. Liu, Applied Intelligence 52 (2022) 33–54."},"date_updated":"2024-10-15T07:30:00Z","doi":"10.1007/s10489-021-02308-3","status":"public","extern":"1","article_type":"original"},{"corr_author":"1","citation":{"chicago":"Katsaros, Georgios, and Daniel Jirovec. “Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:18291\">https://doi.org/10.15479/AT:ISTA:18291</a>.","ieee":"G. Katsaros and D. Jirovec, “Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences.” Institute of Science and Technology Austria, 2022.","mla":"Katsaros, Georgios, and Daniel Jirovec. <i>Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18291\">10.15479/AT:ISTA:18291</a>.","ista":"Katsaros G, Jirovec D. 2022. Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18291\">10.15479/AT:ISTA:18291</a>.","ama":"Katsaros G, Jirovec D. Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18291\">10.15479/AT:ISTA:18291</a>","apa":"Katsaros, G., &#38; Jirovec, D. (2022). Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18291\">https://doi.org/10.15479/AT:ISTA:18291</a>","short":"G. Katsaros, D. Jirovec, (2022)."},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","title":"Dynamics of Hole Singlet-Triplet Qubits with Large 𝑔-Factor Differences","file":[{"date_updated":"2024-10-09T19:31:35Z","success":1,"checksum":"3128dffbd09267b93c2d0b1425fd3ba2","file_id":"18292","content_type":"application/x-zip-compressed","relation":"main_file","date_created":"2024-10-09T19:31:35Z","file_size":25566516,"creator":"gkatsaro","access_level":"open_access","file_name":"SOIPaper.zip"},{"success":1,"checksum":"df077d2f4652afeb3bf100068e88aa48","content_type":"text/plain","file_id":"18442","date_updated":"2024-10-14T18:11:45Z","file_name":"Readme.txt","relation":"main_file","date_created":"2024-10-14T18:11:45Z","file_size":6776,"access_level":"open_access","creator":"gkatsaro"}],"related_material":{"record":[{"relation":"research_paper","id":"10920","status":"public"}]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"date_updated":"2025-04-15T07:15:24Z","status":"public","doi":"10.15479/AT:ISTA:18291","year":"2022","oa_version":"None","file_date_updated":"2024-10-14T18:11:45Z","date_created":"2024-10-09T19:35:03Z","license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2022-03-01T00:00:00Z","_id":"18291","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","type":"research_data","author":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GeKa"}],"month":"03","article_processing_charge":"No","day":"01"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Communications in Mathematical Physics","day":"01","article_processing_charge":"No","year":"2022","date_created":"2026-06-19T07:46:39Z","_id":"22043","external_id":{"arxiv":["2009.06746"]},"date_published":"2022-02-01T00:00:00Z","article_type":"original","oa":1,"arxiv":1,"doi":"10.1007/s00220-021-04280-y","date_updated":"2026-06-25T07:41:51Z","status":"public","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2009.06746"}],"title":"Orbital stability of KdV multisolitons in H-1","abstract":[{"text":"We prove that multisoliton solutions of the Korteweg–de Vries equation are orbitally stable in H^-1(R). We introduce a variational characterization of multisolitons that remains meaningful at such low regularity and show that all optimizing sequences converge to the manifold of multisolitons. The proximity required at the initial time is uniform across the entire manifold of multisolitons; this had not been demonstrated previously, even in H^-1.","lang":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","author":[{"first_name":"Rowan","last_name":"Killip","full_name":"Killip, Rowan"},{"id":"056daca0-b8d1-11f0-964f-f91054abf8ca","first_name":"Monica","full_name":"Visan, Monica","last_name":"Visan"}],"publication_status":"published","volume":389,"month":"02","scopus_import":"1","intvolume":"       389","language":[{"iso":"eng"}],"oa_version":"Preprint","page":"1445-1473","das_tickbox":"1","extern":"1","OA_place":"repository","citation":{"ieee":"R. Killip and M. Vişan, “Orbital stability of KdV multisolitons in H-1,” <i>Communications in Mathematical Physics</i>, vol. 389, no. 3. Springer Nature, pp. 1445–1473, 2022.","chicago":"Killip, Rowan, and Monica Vişan. “Orbital Stability of KdV Multisolitons in H-1.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00220-021-04280-y\">https://doi.org/10.1007/s00220-021-04280-y</a>.","mla":"Killip, Rowan, and Monica Vişan. “Orbital Stability of KdV Multisolitons in H-1.” <i>Communications in Mathematical Physics</i>, vol. 389, no. 3, Springer Nature, 2022, pp. 1445–73, doi:<a href=\"https://doi.org/10.1007/s00220-021-04280-y\">10.1007/s00220-021-04280-y</a>.","ista":"Killip R, Vişan M. 2022. Orbital stability of KdV multisolitons in H-1. Communications in Mathematical Physics. 389(3), 1445–1473.","ama":"Killip R, Vişan M. Orbital stability of KdV multisolitons in H-1. <i>Communications in Mathematical Physics</i>. 2022;389(3):1445-1473. doi:<a href=\"https://doi.org/10.1007/s00220-021-04280-y\">10.1007/s00220-021-04280-y</a>","apa":"Killip, R., &#38; Vişan, M. (2022). Orbital stability of KdV multisolitons in H-1. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-021-04280-y\">https://doi.org/10.1007/s00220-021-04280-y</a>","short":"R. Killip, M. Vişan, Communications in Mathematical Physics 389 (2022) 1445–1473."},"issue":"3","OA_type":"green"},{"month":"09","volume":63,"author":[{"full_name":"Navarro, Francisco","last_name":"Navarro","first_name":"Francisco"},{"first_name":"Cayetana","full_name":"Recio-Blitz, Cayetana","last_name":"Recio-Blitz"},{"first_name":"Ricardo","last_name":"Rodríguez-Cielos","full_name":"Rodríguez-Cielos, Ricardo"},{"first_name":"Jaime","full_name":"Otero, Jaime","last_name":"Otero"},{"full_name":"Shahateet, Kaian","last_name":"Shahateet","first_name":"Kaian"},{"full_name":"De Andrés, Eva","last_name":"De Andrés","first_name":"Eva"},{"last_name":"Corcuera","full_name":"Corcuera, María I.","first_name":"María I."},{"full_name":"Letamendia, Unai","last_name":"Letamendia","first_name":"Unai"},{"first_name":"José M","id":"e1037a6d-646e-11ef-b402-e0ed9ab0901e","orcid":"0000-0002-1990-8508","full_name":"Muñoz Hermosilla, José M","last_name":"Muñoz Hermosilla"}],"publication_status":"published","scopus_import":"1","ddc":["550"],"intvolume":"        63","oa_version":"Published Version","page":"101-106","language":[{"iso":"eng"}],"OA_place":"publisher","extern":"1","das_tickbox":"1","OA_type":"gold","issue":"87-89","citation":{"ama":"Navarro F, Recio-Blitz C, Rodríguez-Cielos R, et al. Surface mass balance monitoring of the peripheral glaciers of the Antarctic Peninsula in the context of regional climate change. <i>Annals of Glaciology</i>. 2022;63(87-89):101-106. doi:<a href=\"https://doi.org/10.1017/aog.2023.18\">10.1017/aog.2023.18</a>","apa":"Navarro, F., Recio-Blitz, C., Rodríguez-Cielos, R., Otero, J., Shahateet, K., De Andrés, E., … Muñoz Hermosilla, J. M. (2022). Surface mass balance monitoring of the peripheral glaciers of the Antarctic Peninsula in the context of regional climate change. <i>Annals of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/aog.2023.18\">https://doi.org/10.1017/aog.2023.18</a>","short":"F. Navarro, C. Recio-Blitz, R. Rodríguez-Cielos, J. Otero, K. Shahateet, E. De Andrés, M.I. Corcuera, U. Letamendia, J.M. Muñoz Hermosilla, Annals of Glaciology 63 (2022) 101–106.","chicago":"Navarro, Francisco, Cayetana Recio-Blitz, Ricardo Rodríguez-Cielos, Jaime Otero, Kaian Shahateet, Eva De Andrés, María I. Corcuera, Unai Letamendia, and José M Muñoz Hermosilla. “Surface Mass Balance Monitoring of the Peripheral Glaciers of the Antarctic Peninsula in the Context of Regional Climate Change.” <i>Annals of Glaciology</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/aog.2023.18\">https://doi.org/10.1017/aog.2023.18</a>.","ieee":"F. Navarro <i>et al.</i>, “Surface mass balance monitoring of the peripheral glaciers of the Antarctic Peninsula in the context of regional climate change,” <i>Annals of Glaciology</i>, vol. 63, no. 87–89. Cambridge University Press, pp. 101–106, 2022.","mla":"Navarro, Francisco, et al. “Surface Mass Balance Monitoring of the Peripheral Glaciers of the Antarctic Peninsula in the Context of Regional Climate Change.” <i>Annals of Glaciology</i>, vol. 63, no. 87–89, Cambridge University Press, 2022, pp. 101–06, doi:<a href=\"https://doi.org/10.1017/aog.2023.18\">10.1017/aog.2023.18</a>.","ista":"Navarro F, Recio-Blitz C, Rodríguez-Cielos R, Otero J, Shahateet K, De Andrés E, Corcuera MI, Letamendia U, Muñoz Hermosilla JM. 2022. Surface mass balance monitoring of the peripheral glaciers of the Antarctic Peninsula in the context of regional climate change. Annals of Glaciology. 63(87–89), 101–106."},"has_accepted_license":"1","publication":"Annals of Glaciology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"01","article_processing_charge":"Yes","year":"2022","_id":"22126","date_published":"2022-09-01T00:00:00Z","date_created":"2026-06-22T12:19:18Z","oa":1,"article_type":"letter_note","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1017/aog.2023.18","status":"public","date_updated":"2026-07-02T07:19:18Z","DOAJ_listed":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/aog.2023.18"}],"publication_identifier":{"eissn":["1727-5644"],"issn":["0260-3055"]},"quality_controlled":"1","abstract":[{"text":"During the second half of the 20th century, the Antarctic Peninsula region has undergone a long and sustained warming period, followed by a shorter but also sustained cooling period, and then a very recent return to warming conditions. All of these have profoundly impacted the glaciers peripheral to the Antarctic Peninsula. This paper focuses on the analysis of the surface mass balance monitoring of such glaciers by the glaciological method, complemented by the analysis of mass-balance estimates by geodetic methods, as well as frontal ablation estimates. We aim to summarize the current knowledge and outline the main challenges faced by investigating the mass balance of such peripheral glaciers and their current contribution to sea-level rise.","lang":"eng"}],"PlanS_conform":"1","title":"Surface mass balance monitoring of the peripheral glaciers of the Antarctic Peninsula in the context of regional climate change","publisher":"Cambridge University Press"},{"scopus_import":"1","ddc":["500"],"intvolume":"        18","department":[{"_id":"VaKa"}],"author":[{"full_name":"Arnaud, Marie-Claude","last_name":"Arnaud","first_name":"Marie-Claude"},{"last_name":"Hofer","full_name":"Hofer, Helmut W.","first_name":"Helmut W."},{"first_name":"Michael","full_name":"Hutchings, Michael","last_name":"Hutchings"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"publication_status":"published","volume":18,"month":"11","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"1735-1803","das_tickbox":"1","citation":{"mla":"Arnaud, Marie-Claude, et al. “Dynamische Systeme.” <i>Oberwolfach Reports</i>, vol. 18, no. 3, EMS Press, 2022, pp. 1735–803, doi:<a href=\"https://doi.org/10.4171/owr/2021/33\">10.4171/owr/2021/33</a>.","chicago":"Arnaud, Marie-Claude, Helmut W. Hofer, Michael Hutchings, and Vadim Kaloshin. “Dynamische Systeme.” <i>Oberwolfach Reports</i>. EMS Press, 2022. <a href=\"https://doi.org/10.4171/owr/2021/33\">https://doi.org/10.4171/owr/2021/33</a>.","ieee":"M.-C. Arnaud, H. W. Hofer, M. Hutchings, and V. Kaloshin, “Dynamische Systeme,” <i>Oberwolfach Reports</i>, vol. 18, no. 3. EMS Press, pp. 1735–1803, 2022.","ista":"Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. 2022. Dynamische Systeme. Oberwolfach Reports. 18(3), 1735–1803.","apa":"Arnaud, M.-C., Hofer, H. W., Hutchings, M., &#38; Kaloshin, V. (2022). Dynamische Systeme. <i>Oberwolfach Reports</i>. EMS Press. <a href=\"https://doi.org/10.4171/owr/2021/33\">https://doi.org/10.4171/owr/2021/33</a>","ama":"Arnaud M-C, Hofer HW, Hutchings M, Kaloshin V. Dynamische Systeme. <i>Oberwolfach Reports</i>. 2022;18(3):1735-1803. doi:<a href=\"https://doi.org/10.4171/owr/2021/33\">10.4171/owr/2021/33</a>","short":"M.-C. Arnaud, H.W. Hofer, M. Hutchings, V. Kaloshin, Oberwolfach Reports 18 (2022) 1735–1803."},"corr_author":"1","issue":"3","day":"26","article_processing_charge":"No","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Oberwolfach Reports","date_created":"2024-05-29T06:01:19Z","_id":"17063","date_published":"2022-11-26T00:00:00Z","year":"2022","status":"public","doi":"10.4171/owr/2021/33","date_updated":"2026-07-06T11:52:32Z","article_type":"original","oa":1,"title":"Dynamische Systeme","abstract":[{"lang":"eng","text":"This workshop continued a biannual series of workshops at Oberwolfach on dynamical systems that started with a meeting organized by Moser and Zehnder in 1981. Workshops in this series focus on new results and developments in dynamical systems and related areas of mathematics, with symplectic geometry playing an important role in recent years in connection with Hamiltonian dynamics. In this year special emphasis was placed on various kinds of spectra (in contact geometry, in Riemannian geometry, in dynamical systems and in symplectic topology) and their applications to dynamics."}],"quality_controlled":"1","publisher":"EMS Press","publication_identifier":{"issn":["1660-8933"],"eissn":["1660-8941"]},"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.4171/OWR/2021/33"}]},{"issue":"1","citation":{"apa":"Liu, Y., Calcabrini, M., Yu, Y., Lee, S., Chang, C., David, J., … Ibáñez, M. (2022). Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c06720\">https://doi.org/10.1021/acsnano.1c06720</a>","ama":"Liu Y, Calcabrini M, Yu Y, et al. Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. <i>ACS Nano</i>. 2022;16(1):78-88. doi:<a href=\"https://doi.org/10.1021/acsnano.1c06720\">10.1021/acsnano.1c06720</a>","short":"Y. Liu, M. Calcabrini, Y. Yu, S. Lee, C. Chang, J. David, T. Ghosh, M.C. Spadaro, C. Xie, O. Cojocaru-Mirédin, J. Arbiol, M. Ibáñez, ACS Nano 16 (2022) 78–88.","mla":"Liu, Yu, et al. “Defect Engineering in Solution-Processed Polycrystalline SnSe Leads to High Thermoelectric Performance.” <i>ACS Nano</i>, vol. 16, no. 1, American Chemical Society, 2022, pp. 78–88, doi:<a href=\"https://doi.org/10.1021/acsnano.1c06720\">10.1021/acsnano.1c06720</a>.","chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Seungho Lee, Cheng Chang, Jérémy David, Tanmoy Ghosh, et al. “Defect Engineering in Solution-Processed Polycrystalline SnSe Leads to High Thermoelectric Performance.” <i>ACS Nano</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acsnano.1c06720\">https://doi.org/10.1021/acsnano.1c06720</a>.","ieee":"Y. Liu <i>et al.</i>, “Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance,” <i>ACS Nano</i>, vol. 16, no. 1. American Chemical Society, pp. 78–88, 2022.","ista":"Liu Y, Calcabrini M, Yu Y, Lee S, Chang C, David J, Ghosh T, Spadaro MC, Xie C, Cojocaru-Mirédin O, Arbiol J, Ibáñez M. 2022. Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance. ACS Nano. 16(1), 78–88."},"corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"12885","status":"public"}]},"ec_funded":1,"has_accepted_license":"1","das_tickbox":"1","oa_version":"Published Version","page":"78-88","language":[{"iso":"eng"}],"month":"01","volume":16,"author":[{"orcid":"0000-0001-7313-6740","last_name":"Liu","full_name":"Liu, Yu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Calcabrini","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano"},{"first_name":"Yuan","last_name":"Yu","full_name":"Yu, Yuan"},{"last_name":"Lee","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"last_name":"David","full_name":"David, Jérémy","first_name":"Jérémy"},{"last_name":"Ghosh","full_name":"Ghosh, Tanmoy","id":"a5fc9bc3-feff-11ea-93fe-e8015a3c7e9d","first_name":"Tanmoy"},{"full_name":"Spadaro, Maria Chiara","last_name":"Spadaro","first_name":"Maria Chiara"},{"last_name":"Xie","full_name":"Xie, Chenyang","first_name":"Chenyang"},{"full_name":"Cojocaru-Mirédin, Oana","last_name":"Cojocaru-Mirédin","first_name":"Oana"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MaIb"}],"publication_status":"published","isi":1,"acknowledgement":"This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. S.L. and M.C. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. J.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 665919 (P-SPHERE) cofunded by Severo Ochoa Programme. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. M.C.S. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754510 (PROBIST) and the Severo Ochoa programme. J.D. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 665919 (P-SPHERE) cofunded by Severo Ochoa Programme. The ICN2 is funded by the CERCA Program/Generalitat de Catalunya and by the Severo Ochoa program of the Spanish Ministry of Economy, Industry, and Competitiveness (MINECO, grant no. SEV-2017-0706). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). This project received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 823717-ESTEEM3. The FIB sample preparation was conducted in the LMA-INA-Universidad de Zaragoza.","scopus_import":"1","intvolume":"        16","ddc":["540"],"publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"file":[{"success":1,"file_id":"10808","checksum":"74f9c1aa5f95c0b992a4328e8e0247b4","content_type":"application/pdf","date_updated":"2022-03-02T16:17:29Z","file_name":"2022_ACSNano_Liu.pdf","date_created":"2022-03-02T16:17:29Z","relation":"main_file","access_level":"open_access","creator":"cchlebak","file_size":9050764}],"quality_controlled":"1","title":"Defect engineering in solution-processed polycrystalline SnSe leads to high thermoelectric performance","abstract":[{"text":"SnSe has emerged as one of the most promising materials for thermoelectric energy conversion due to its extraordinary performance in its single-crystal form and its low-cost constituent elements. However, to achieve an economic impact, the polycrystalline counterpart needs to replicate the performance of the single crystal. Herein, we optimize the thermoelectric performance of polycrystalline SnSe produced by consolidating solution-processed and surface-engineered SnSe particles. In particular, the SnSe particles are coated with CdSe molecular complexes that crystallize during the sintering process, forming CdSe nanoparticles. The presence of CdSe nanoparticles inhibits SnSe grain growth during the consolidation step due to Zener pinning, yielding a material with a high density of grain boundaries. Moreover, the resulting SnSe–CdSe nanocomposites present a large number of defects at different length scales, which significantly reduce the thermal conductivity. The produced SnSe–CdSe nanocomposites exhibit thermoelectric figures of merit up to 2.2 at 786 K, which is among the highest reported for solution-processed SnSe.","lang":"eng"}],"publisher":"American Chemical Society","oa":1,"article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","date_updated":"2026-07-06T12:16:06Z","doi":"10.1021/acsnano.1c06720","keyword":["tin selenide","nanocomposite","grain growth","Zener pinning","thermoelectricity","annealing","solution processing"],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"},{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}],"file_date_updated":"2022-03-02T16:17:29Z","year":"2022","_id":"10042","external_id":{"pmid":["34549956"],"isi":["000767223400008"]},"date_published":"2022-01-25T00:00:00Z","pmid":1,"date_created":"2021-09-24T07:55:12Z","publication":"ACS Nano","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"25","article_processing_charge":"Yes (via OA deal)"},{"pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2022-02-20T23:01:31Z","_id":"10766","external_id":{"pmid":["35165179"],"isi":["000766926900009"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"date_published":"2022-02-14T00:00:00Z","year":"2022","file_date_updated":"2022-02-21T08:45:11Z","day":"14","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"journal_article","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","abstract":[{"text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact.","lang":"eng"}],"publisher":"National Academy of Sciences","file":[{"file_name":"2022_PNAS_Slovakova.pdf","date_created":"2022-02-21T08:45:11Z","relation":"main_file","access_level":"open_access","file_size":1609678,"creator":"dernst","success":1,"checksum":"d49f83c3580613966f71768ddb9a55a5","content_type":"application/pdf","file_id":"10780","date_updated":"2022-02-21T08:45:11Z"}],"publication_identifier":{"eissn":["1091-6490"]},"status":"public","date_updated":"2026-07-06T12:45:39Z","doi":"10.1073/pnas.2122030119","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","grant_number":"187-2013","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension"}],"article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":"       119","ddc":["570"],"acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda  for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","author":[{"first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","last_name":"Slovakova"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K"},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan","full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566"},{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"isi":1,"publication_status":"published","volume":119,"month":"02","has_accepted_license":"1","related_material":{"record":[{"id":"9750","status":"public","relation":"earlier_version"}]},"ec_funded":1,"citation":{"ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>","short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. National Academy of Sciences, 2022.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119."},"article_number":"e2122030119","corr_author":"1","issue":"8"},{"doi":"10.7554/eLife.78995","status":"public","date_updated":"2026-07-06T12:48:19Z","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa":1,"article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"date_created":"2022-08-16T08:57:37Z","relation":"main_file","file_size":2057577,"creator":"cchlebak","access_level":"open_access","file_name":"2022_eLife_Tomasek.pdf","date_updated":"2022-08-16T08:57:37Z","success":1,"checksum":"002a3c7c7ea5caa9af9cfbea308f6ea4","file_id":"11861","content_type":"application/pdf"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","publisher":"eLife Sciences Publications","publication_identifier":{"eissn":["2050-084X"]},"day":"26","article_processing_charge":"Yes","publication":"eLife","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"_id":"11843","external_id":{"isi":["000838410200001"],"pmid":["35881547"]},"date_published":"2022-07-26T00:00:00Z","pmid":1,"date_created":"2022-08-14T22:01:46Z","file_date_updated":"2022-08-16T08:57:37Z","year":"2022","related_material":{"record":[{"id":"10316","status":"public","relation":"earlier_version"}]},"ec_funded":1,"has_accepted_license":"1","citation":{"ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.78995\">10.7554/eLife.78995</a>","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &#38; Sixt, M. K. (2022). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.78995\">https://doi.org/10.7554/eLife.78995</a>","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, ELife 11 (2022).","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.78995\">https://doi.org/10.7554/eLife.78995</a>.","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” <i>ELife</i>, vol. 11, e78995, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.78995\">10.7554/eLife.78995</a>.","ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. 2022. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. eLife. 11, e78995."},"corr_author":"1","article_number":"e78995","acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strains CFT073, UTI89, and 536, Frank Assen, Vlad Gavra, Maximilian Götz, Bor Kavčič, Jonna Alanko, and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp, and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to IG, the European Research Council (CoG 724373), and the Austrian Science Fund (FWF P29911) to MS.","scopus_import":"1","intvolume":"        11","ddc":["570"],"month":"07","volume":11,"department":[{"_id":"MiSi"},{"_id":"CaGu"}],"author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"orcid":"0000-0002-1073-744X","last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Glatzová, Ivana","last_name":"Glatzová","first_name":"Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d"},{"first_name":"Michael S.","last_name":"Lukesch","full_name":"Lukesch, Michael S."},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"publication_status":"published","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}]}]