[{"conference":{"start_date":"2025-09-23","location":"Daejeon, South Korea","end_date":"2025-09-23","name":"EMA4MICCAI: Efficient Medical Artificial Intelligence"},"publisher":"Springer Nature","related_material":{"link":[{"relation":"software","url":"https://github.com/jakobtroidl/niiv-miccai"}]},"date_published":"2026-01-03T00:00:00Z","date_updated":"2026-02-16T08:50:50Z","department":[{"_id":"JoDa"}],"abstract":[{"lang":"eng","text":"Three-dimensional (3D) microscopy data is often anisotropic with significantly lower resolution (up to 8x) along the z axis than along the xy axes. Computationally generating plausible isotropic resolution from anisotropic imaging data would benefit the visual analysis of large-scale volumes. This paper proposes niiv, a self-supervised method for isotropic reconstruction of 3D microscopy data that can quickly produce images at arbitrary output resolutions. The representation embeds a learned latent code within a neural field that describes the implicit higher-resolution isotropic image region. We use an attention-guided latent interpolation approach, which allows flexible information exchange over a local latent neighborhood. Under isotropic volume assumptions, we self-supervise this representation on low-/high-resolution lateral image pairs to reconstruct an isotropic volume from low-resolution axial images. We evaluate our method on simulated and real anisotropic electron (EM) and light microscopy (LM) data. Compared to diffusion-based baselines, niiv shows improved reconstruction quality (+1 dB PSNR) and is over three orders of magnitude faster (1,000x) to infer. Specifically, niiv reconstructs a 128^3 voxel volume in 2/10th of a second, renderable at varying (continuous) high resolutions for display. Our code is available at https://github.com/jakobtroidl/niiv-miccai."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"first_name":"Yiqing","last_name":"Liang","full_name":"Liang, Yiqing"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"orcid":"0000-0002-7667-6854","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Hadwiger, Markus","first_name":"Markus","last_name":"Hadwiger"},{"last_name":"Pfister","first_name":"Hanspeter","full_name":"Pfister, Hanspeter"},{"full_name":"Tompkin, James","last_name":"Tompkin","first_name":"James"}],"citation":{"apa":"Troidl, J., Liang, Y., Beyer, J., Tavakoli, M., Danzl, J. G., Hadwiger, M., … Tompkin, J. (2026). niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In 1st International Workshop on Efficient Medical Artificial Intelligence (Vol. 16318, pp. 257–267). Daejeon, South Korea: Springer Nature. https://doi.org/10.1007/978-3-032-13961-0_26","ama":"Troidl J, Liang Y, Beyer J, et al. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. In: 1st International Workshop on Efficient Medical Artificial Intelligence. Vol 16318. Springer Nature; 2026:257-267. doi:10.1007/978-3-032-13961-0_26","short":"J. Troidl, Y. Liang, J. Beyer, M. Tavakoli, J.G. Danzl, M. Hadwiger, H. Pfister, J. Tompkin, in:, 1st International Workshop on Efficient Medical Artificial Intelligence, Springer Nature, 2026, pp. 257–267.","chicago":"Troidl, Jakob, Yiqing Liang, Johanna Beyer, Mojtaba Tavakoli, Johann G Danzl, Markus Hadwiger, Hanspeter Pfister, and James Tompkin. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” In 1st International Workshop on Efficient Medical Artificial Intelligence, 16318:257–67. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-13961-0_26.","ieee":"J. Troidl et al., “niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction,” in 1st International Workshop on Efficient Medical Artificial Intelligence, Daejeon, South Korea, 2026, vol. 16318, pp. 257–267.","mla":"Troidl, Jakob, et al. “Niiv: Interactive Self-Supervised Neural Implicit Isotropic Volume Reconstruction.” 1st International Workshop on Efficient Medical Artificial Intelligence, vol. 16318, Springer Nature, 2026, pp. 257–67, doi:10.1007/978-3-032-13961-0_26.","ista":"Troidl J, Liang Y, Beyer J, Tavakoli M, Danzl JG, Hadwiger M, Pfister H, Tompkin J. 2026. niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction. 1st International Workshop on Efficient Medical Artificial Intelligence. EMA4MICCAI: Efficient Medical Artificial Intelligence, LNCS, vol. 16318, 257–267."},"language":[{"iso":"eng"}],"oa_version":"Preprint","alternative_title":["LNCS"],"quality_controlled":"1","publication_status":"published","year":"2026","type":"conference","status":"public","oa":1,"_id":"21135","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.09.07.611785"}],"doi":"10.1007/978-3-032-13961-0_26","publication_identifier":{"isbn":["9783032139603"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication":"1st International Workshop on Efficient Medical Artificial Intelligence","OA_type":"green","scopus_import":"1","OA_place":"repository","acknowledgement":"This work was supported by NIH grants 1U01NS132158 and R01HD104969. We thank the reviewers for their constructive feedback.","date_created":"2026-02-01T23:01:44Z","day":"03","month":"01","article_processing_charge":"No","volume":16318,"intvolume":" 16318","title":"niiv: Interactive Self-supervised Neural Implicit Isotropic Volume Reconstruction","page":"257-267"},{"publication":"Laboratory Animals","day":"14","scopus_import":"1","OA_type":"hybrid","acknowledgement":"We deeply acknowledge all the animal care staff and laboratory technicians who participated in this study! We acknowledge Working Groups 1 and 4 from COST Action IMPROVE (“3Rs concepts to improve the quality of biomedical science”), CA21139, supported by COST (European Cooperation in Science and Technology) for their feedback and support. We also acknowledge Aoife Milford for her comments and contributions to the final draft of the manuscript.\r\nThis publication was based on work from the COST Action IMPROVE (“3Rs concepts to improve the quality of biomedical science”), CA21139, supported by COST (European Cooperation in Science and Technology).","date_created":"2026-04-26T22:01:47Z","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","month":"04","title":"Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science","publication_status":"epub_ahead","year":"2026","type":"journal_article","status":"public","quality_controlled":"1","article_type":"original","oa":1,"_id":"21767","main_file_link":[{"url":"https://doi.org/10.1177/00236772251400976","open_access":"1"}],"doi":"10.1177/00236772251400976","publication_identifier":{"eissn":["1758-1117"],"issn":["0023-6772"]},"author":[{"full_name":"Gonzalez-Uarquin, Fernando","first_name":"Fernando","last_name":"Gonzalez-Uarquin"},{"first_name":"Paulin","last_name":"Jirkof","full_name":"Jirkof, Paulin"},{"full_name":"Bert, Bettina","last_name":"Bert","first_name":"Bettina"},{"first_name":"Penny","last_name":"Hawkins","full_name":"Hawkins, Penny"},{"first_name":"Ljupco","last_name":"Angelovski","full_name":"Angelovski, Ljupco"},{"full_name":"Baumgart, Jan","last_name":"Baumgart","first_name":"Jan"},{"full_name":"Baumgart, Nadine","last_name":"Baumgart","first_name":"Nadine"},{"last_name":"Cevik","first_name":"Özge S.","full_name":"Cevik, Özge S."},{"full_name":"Franco, Nuno H.","first_name":"Nuno H.","last_name":"Franco"},{"full_name":"Horata, Erdal","first_name":"Erdal","last_name":"Horata"},{"full_name":"Kaura, Rohish","first_name":"Rohish","last_name":"Kaura"},{"last_name":"Neuhaus","first_name":"Winfried","full_name":"Neuhaus, Winfried"},{"full_name":"Riso, Brigida","last_name":"Riso","first_name":"Brigida"},{"first_name":"Adrian J.","last_name":"Smith","full_name":"Smith, Adrian J."},{"first_name":"Athanassia","last_name":"Sotiropoulos","full_name":"Sotiropoulos, Athanassia"},{"full_name":"Vitale, Augusto","last_name":"Vitale","first_name":"Augusto"},{"id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie","last_name":"Schober","full_name":"Schober, Sophie"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"F. Gonzalez-Uarquin, P. Jirkof, B. Bert, P. Hawkins, L. Angelovski, J. Baumgart, N. Baumgart, Ö.S. Cevik, N.H. Franco, E. Horata, R. Kaura, W. Neuhaus, B. Riso, A.J. Smith, A. Sotiropoulos, A. Vitale, S. Schober, Laboratory Animals (2026).","ama":"Gonzalez-Uarquin F, Jirkof P, Bert B, et al. Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science. Laboratory Animals. 2026. doi:10.1177/00236772251400976","apa":"Gonzalez-Uarquin, F., Jirkof, P., Bert, B., Hawkins, P., Angelovski, L., Baumgart, J., … Schober, S. (2026). Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science. Laboratory Animals. SAGE Publications. https://doi.org/10.1177/00236772251400976","ieee":"F. Gonzalez-Uarquin et al., “Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science,” Laboratory Animals. SAGE Publications, 2026.","chicago":"Gonzalez-Uarquin, Fernando, Paulin Jirkof, Bettina Bert, Penny Hawkins, Ljupco Angelovski, Jan Baumgart, Nadine Baumgart, et al. “Building Bridges: Involvement of Animal Care Staff and Laboratory Technicians in Experimental Planning and Conduct of Animal Studies for Better Job Satisfaction and Science.” Laboratory Animals. SAGE Publications, 2026. https://doi.org/10.1177/00236772251400976.","ista":"Gonzalez-Uarquin F, Jirkof P, Bert B, Hawkins P, Angelovski L, Baumgart J, Baumgart N, Cevik ÖS, Franco NH, Horata E, Kaura R, Neuhaus W, Riso B, Smith AJ, Sotiropoulos A, Vitale A, Schober S. 2026. Building bridges: Involvement of animal care staff and laboratory technicians in experimental planning and conduct of animal studies for better job satisfaction and science. Laboratory Animals.","mla":"Gonzalez-Uarquin, Fernando, et al. “Building Bridges: Involvement of Animal Care Staff and Laboratory Technicians in Experimental Planning and Conduct of Animal Studies for Better Job Satisfaction and Science.” Laboratory Animals, SAGE Publications, 2026, doi:10.1177/00236772251400976."},"language":[{"iso":"eng"}],"oa_version":"Published Version","publisher":"SAGE Publications","date_published":"2026-04-14T00:00:00Z","abstract":[{"text":"The involvement of non-scientific staff in discussions about animal welfare and scientific quality is essential for biomedical research progress. In this study, we developed a survey to collect the self-perception of animal care staff (ACS) and laboratory technicians about their involvement in scientific planning and conduct. Participants were contacted to complete an anonymous online questionnaire. We obtained 850 responses, mainly from Europe: 564 from ACS and 286 from laboratory technicians. Job satisfaction was assessed as positive by ACS and laboratory technicians despite the low frequency of culture of care activities and mental health meetings. Both groups expressed their desire to be trained in research planning and conduct; however, regular training was not reported. In addition, the inability to act on animal welfare concerns owing to experimental reasons was reported by both groups. Over half of the participants felt valued and appreciated by the lead scientists or animal facility manager; however, it is not clear how they are acknowledged, as their names on the authors list or in the manuscript acknowledgments are barely included. Our results indicated that involvement of ACS and laboratory technicians in planning and conducting studies would improve their understanding of how experiments are done, and therefore communication processes, work satisfaction, animal welfare, and scientific quality. Finally, we provided recommendations to improve the engagement of ACS and laboratory technicians in discussions about animal research planning and conduct.","lang":"eng"},{"text":"La participation de personnel non-scientifique aux discussions sur le bien-être animal et la qualité scientifique est essentielle aux progrès la recherche biomédicale. Dans cette étude, nous avons développé une enquête pour recueillir l'auto-perception du personnel chargé des soins prodigués aux animaux (PCSA) et des techniciens de laboratoire (TL) sur leur implication dans la planification et la conduite scientifiques. Les participants ont été contactés pour remplir un questionnaire anonyme en ligne. Nous avons obtenu 850 réponses, principalement en Europe : 564 provenant de PCSA et 286 de TL. La satisfaction au travail a été évaluée comme positive par le PCSA et les TL malgré la faible fréquence d’activités sur la culture des soins et de réunions concernant la santé mentale. Bien que les deux groupes aient exprimé leur désir d'être formés à la planification et à la conduite de la recherche, aucune formation réelle régulière n'a été signalée. De plus, l'incapacité d'agir sur les préoccupations relatives au bien-être animal pour des raisons expérimentales a été signalée par les deux groupes. Plus de la moitié des participants se sont sentis valorisés et appréciés par les scientifiques principaux ou le gestionnaire de l’installation animale mais on ne sait pas clairement comment ils sont reconnus, car leurs noms sur la liste des auteurs ou dans les remerciements sont à peine inclus dans la documentation. Nos résultats ont indiqué que la participation du PCSA et des TL à la planification et à la conduite des études améliorerait leur compréhension de la façon dont les expériences sont effectuées et, par conséquent, les processus de communication, leur satisfaction au travail ainsi que le bien-être animal et la qualité scientifique. Enfin, nous avons formulé des recommandations pour améliorer la participation du PCSA et des TL aux discussions sur la planification et la conduite de la recherche animale.","lang":"fre"},{"text":"Die Einbeziehung von nichtwissenschaftlichem Personal in Diskussionen über Tierschutz und wissenschaftliche Qualität ist für Fortschritte in biomedizinischer Forschung von entscheidender Bedeutung. In dieser Studie haben wir eine Umfrage entwickelt, um die Selbsteinschätzung von Tierpflegern (ACS) und Labortechnikern (LT) hinsichtlich ihrer Beteiligung an der wissenschaftlichen Planung und Durchführung zu erfassen. Die Teilnehmer wurden gebeten, einen anonymen Online-Fragebogen auszufüllen. Wir erhielten 850 Rückmeldungen, hauptsächlich aus Europa: 564 von ACS und 286 von LT. Die Arbeitszufriedenheit wurde von ACS und LT trotz der geringen Häufigkeit von Pflegeaktivitäten und Treffen zum Thema psychische Gesundheit als positiv bewertet. Beide Gruppen äußerten den Wunsch, in der Forschungsplanung und -durchführung geschult zu werden, doch regelmäßig stattfindende Schulungen wurden nicht berichtet. Außerdem wurde von beiden Gruppen vermeldet, dass sie aus versuchstechnischen Gründen nicht in der Lage waren, auf Tierschutzbedenken zu reagieren. Über die Hälfte der Teilnehmer fühlte sich von den leitenden Wissenschaftlern oder dem Leiter der Tierhaltungseinrichtung geschätzt und anerkannt; es ist jedoch unklar, inwiefern sie wirklich gewürdigt werden, da ihre Namen kaum in der Autorenliste oder in den Danksagungen des Manuskripts aufgeführt sind. Unsere Ergebnisse deuteten darauf hin, dass die Einbeziehung von ACS und LT in die Planung und Durchführung von Studien ihr Verständnis für die Durchführung von Experimenten verbessern würde – und damit auch Kommunikationsprozesse, Arbeitszufriedenheit, Tierwohl und wissenschaftliche Qualität. Abschließend gaben wir Empfehlungen zur Verbesserung der Einbeziehung von ACS und LT in Diskussionen über die Planung und Durchführung von Tierversuchen.","lang":"ger"},{"lang":"spa","text":"La participación del personal no científico en los debates sobre el bienestar animal y la calidad científica es fundamental para el avance de la investigación biomédica. En este estudio, desarrollamos una encuesta para recoger la autopercepción del personal encargado del cuidado de los animales (ACS) y de los técnicos de laboratorio (LT) sobre su implicación en la planificación y la realización científicas. Se contactó con los participantes para que cumplimentaran un cuestionario anónimo en línea. Obtuvimos 850 respuestas, principalmente de Europa: 564 de ACS y 286 de LT. La satisfacción laboral fue evaluada como positiva por ACS y técnicos de laboratorio a pesar de la baja frecuencia de actividades de cultura del cuidado y reuniones sobre bienestar mental. Ambos grupos expresaron su deseo de recibir formación en planificación y realización de investigaciones, sin embargo, no se informó sobre una formación regular. Asimismo, ambos grupos señalaron la incapacidad de actuar ante las preocupaciones sobre el bienestar animal por motivos experimentales. Más de la mitad de los participantes se sintieron valorados y apreciados por los científicos principales o el responsable de las instalaciones de animales; sin embargo, no está claro cómo se les reconoce, ya que apenas se incluyen sus nombres en la lista de autores o en los agradecimientos del manuscrito. Nuestros resultados indicaron que la participación de los ACS y los LT en la planificación y realización de los estudios mejoraría su comprensión de cómo se hacen los experimentos y, por tanto, los procesos de comunicación, la satisfacción laboral, el bienestar animal y la calidad científica. Finalmente, proporcionamos recomendaciones para mejorar el compromiso de la AEC y la LT en los debates sobre la planificación y la realización de investigaciones con animales."}],"date_updated":"2026-06-18T08:33:36Z","department":[{"_id":"PreCl"}],"ddc":["570"]},{"license":"https://creativecommons.org/licenses/by/4.0/","conference":{"name":"MIDL: Medical Imaging with Deep Learning","end_date":"2026-07-10","location":"Taipei, Taiwan","start_date":"2026-07-08"},"related_material":{"link":[{"url":"https://github.com/tamirshor7/T1-PILOT","relation":"software"}]},"publisher":"ML Research Press","date_published":"2026-03-17T00:00:00Z","department":[{"_id":"AlBr"}],"date_updated":"2026-06-08T08:05:24Z","abstract":[{"text":"Cardiac T1 mapping provides critical quantitative insights into myocardial tissue composition, enabling the assessment of pathologies such as fibrosis, inflammation, and edema.\r\nHowever, the inherently dynamic nature of the heart imposes strict limits on acquisition\r\ntimes, making high-resolution T1 mapping a persistent challenge. Compressed sensing (CS)\r\napproaches have reduced scan durations by undersampling k-space and reconstructing images from partial data, and recent studies show that jointly optimizing the undersampling\r\npatterns with the reconstruction network can substantially improve performance. Still,\r\nmost current T1 mapping pipelines rely on static, hand-crafted masks that do not exploit\r\nthe full acceleration and accuracy potential. Furthermore, most existing methods do not\r\nlevarage the physical T1 decay model in optimization. In this work, we introduce T1-\r\nPILOT: an end-to-end method that explicitly incorporates the T1 signal relaxation model\r\ninto the sampling–reconstruction framework to guide the learning of non-Cartesian trajectories, cross-frame alignment, and T1 decay estimation. Through extensive experiments\r\non the CMRxRecon dataset, T1-PILOT significantly outperforms several baseline strategies (including learned single-mask and fixed radial or golden-angle sampling schemes),\r\nachieving higher T1 map fidelity at greater acceleration factors. In particular, we observe consistent gains in PSNR and VIF relative to existing methods, along with marked\r\nimprovements in delineating finer myocardial structures. Our results highlight that optimizing sampling trajectories in tandem with the physical relaxation model leads to both\r\nenhanced quantitative accuracy and reduced acquisition times. Code for reproducing all\r\nexperiments and results is available at https://github.com/tamirshor7/T1-PILOT","lang":"eng"}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Shor, Tamir","last_name":"Shor","first_name":"Tamir"},{"first_name":"Moti","last_name":"Freiman","full_name":"Freiman, Moti"},{"last_name":"Baskin","first_name":"Chaim","full_name":"Baskin, Chaim"},{"first_name":"Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"}],"corr_author":"1","citation":{"apa":"Shor, T., Freiman, M., Baskin, C., & Bronstein, A. M. (n.d.). T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration. In Medical Imaging with Deep Learning (Vol. 315, pp. 1969–1982). Taipei, Taiwan: ML Research Press.","ama":"Shor T, Freiman M, Baskin C, Bronstein AM. T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration. In: Medical Imaging with Deep Learning. Vol 315. ML Research Press; :1969-1982.","short":"T. Shor, M. Freiman, C. Baskin, A.M. Bronstein, in:, Medical Imaging with Deep Learning, ML Research Press, n.d., pp. 1969–1982.","chicago":"Shor, Tamir, Moti Freiman, Chaim Baskin, and Alex M. Bronstein. “T1-PILOT: Physics-Informed Learned Optimized Trajectories for T1 Mapping Acceleration.” In Medical Imaging with Deep Learning, 315:1969–82. ML Research Press, n.d.","ieee":"T. Shor, M. Freiman, C. Baskin, and A. M. Bronstein, “T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration,” in Medical Imaging with Deep Learning, Taipei, Taiwan, vol. 315, pp. 1969–1982.","mla":"Shor, Tamir, et al. “T1-PILOT: Physics-Informed Learned Optimized Trajectories for T1 Mapping Acceleration.” Medical Imaging with Deep Learning, vol. 315, ML Research Press, pp. 1969–82.","ista":"Shor T, Freiman M, Baskin C, Bronstein AM. T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration. Medical Imaging with Deep Learning. MIDL: Medical Imaging with Deep Learning, PMLR, vol. 315, 1969–1982."},"oa_version":"Published Version","language":[{"iso":"eng"}],"alternative_title":["PMLR"],"quality_controlled":"1","status":"public","type":"conference","year":"2026","publication_status":"accepted","has_accepted_license":"1","oa":1,"publication_identifier":{"eissn":["2640-3498"]},"_id":"21949","main_file_link":[{"url":"https://openreview.net/forum?id=nZaPtHbd6N#discussion","open_access":"1"}],"publication":"Medical Imaging with Deep Learning","OA_place":"publisher","date_created":"2026-06-07T22:01:36Z","scopus_import":"1","OA_type":"gold","day":"17","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"03","article_processing_charge":"No","volume":315,"keyword":["Cardiac T1 Mapping","Trajectory Optimization and Reconstruction","PhysicsInformed Deep-Learning"],"intvolume":" 315","title":"T1-PILOT: Physics-informed learned optimized trajectories for T1 mapping acceleration","page":"1969-1982"},{"das_tickbox":"0","supplementarymaterial":"no","quality_controlled":"1","status":"public","type":"journal_article","year":"2026","publication_status":"published","has_accepted_license":"1","article_type":"original","doi":"10.46298/afm.14253","publication_identifier":{"eissn":["3117-4604"]},"_id":"22607","article_number":"14253","publication":"Annals of Formalized Mathematics","acknowledgement":"We would like to thank David Bartl and Jasmin Blanchette for frequent consultations.\r\nWe would also like to express gratitude to Henrik Böving for a help with generalization\r\nfrom extended rationals to extended linearly ordered fields and to Andrew Yang for the\r\nproof of Finset.univ_sum_of_zero_when_not. We would also like to acknowledge Antoine\r\nChambert-Loir, Apurva Nakade, Yaël Dillies, Richard Copley, Edward van de Meent, Markus\r\nHimmel, Mario Carneiro, and Kevin Buzzard.","date_created":"2026-07-29T09:06:55Z","OA_place":"publisher","OA_type":"hybrid","day":"13","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","month":"03","volume":2,"keyword":["Farkas lemma","linear programming","extended reals","calculus of inductive constructions"],"intvolume":" 2","title":"Duality theory in linear optimization and its extensions -- formally verified","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"20071"}]},"publisher":"EPI Sciences","date_published":"2026-03-13T00:00:00Z","PlanS_conform":"1","arxiv":1,"department":[{"_id":"VlKo"},{"_id":"GradSch"}],"date_updated":"2026-07-29T10:50:17Z","abstract":[{"text":"Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\".\r\nCode: https://github.com/madvorak/duality/tree/v3.2.0","lang":"eng"}],"external_id":{"arxiv":["2409.08119"]},"ddc":["500"],"mathsc":["68V20","15A39","90C05"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","last_name":"Dvorak","first_name":"Martin"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"researchdata_availability":"no","corr_author":"1","citation":{"ama":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2026;2. doi:10.46298/afm.14253","short":"M. Dvorak, V. Kolmogorov, Annals of Formalized Mathematics 2 (2026).","apa":"Dvorak, M., & Kolmogorov, V. (2026). Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. EPI Sciences. https://doi.org/10.46298/afm.14253","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” Annals of Formalized Mathematics, vol. 2, 14253, EPI Sciences, 2026, doi:10.46298/afm.14253.","ista":"Dvorak M, Kolmogorov V. 2026. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2, 14253.","ieee":"M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” Annals of Formalized Mathematics, vol. 2. EPI Sciences, 2026.","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” Annals of Formalized Mathematics. EPI Sciences, 2026. https://doi.org/10.46298/afm.14253."},"oa_version":"Published Version","language":[{"iso":"eng"}]},{"citation":{"ama":"Borovkov M. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. 2026. doi:10.15479/AT-ISTA-22242","short":"M. Borovkov, (2026).","apa":"Borovkov, M. (2026). Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22242","ista":"Borovkov M. 2026. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22242.","mla":"Borovkov, Maksim. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22242.","ieee":"M. Borovkov, “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026.","chicago":"Borovkov, Maksim. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22242."},"contributor":[{"contributor_type":"contact_person","first_name":"Maksim","last_name":"Borovkov","id":"1fd0975f-8b61-11ed-b69e-d149334f28c5"}],"oa_version":"Published Version","author":[{"full_name":"Borovkov, Maksim","first_name":"Maksim","last_name":"Borovkov","id":"1fd0975f-8b61-11ed-b69e-d149334f28c5"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"corr_author":"1","abstract":[{"lang":"eng","text":"This deposit contains the data and analysis code accompanying the publication \"Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices\" (Borovkov et al.). The deposit includes the raw transport and current-noise measurements of three gate-defined quantum-dot devices as QCodes SQLite databases, the master table of the charge-noise (flank-method) analysis with the pointers linking every analyzed PSD trace to the raw data, the toy-model noise simulation datasets behind the supplementary figures, the archived analysis figures (PSD fits and lever-arm extractions), and the Python code reproducing the full analysis and all figures. The code is also maintained at https://github.com/ISTA-Nanoelectronics/noise_paper_public; instructions are provided in the README files."}],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_updated":"2026-08-03T11:08:38Z","doi_confirm":"1","ddc":["530"],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"22619"}],"link":[{"relation":"research_data","url":"https://github.com/ISTA-Nanoelectronics/noise_paper_public"}]},"date_published":"2026-07-04T00:00:00Z","file":[{"relation":"main_file","creator":"mborovko","file_id":"22243","checksum":"2a1ea297e01a7a202a6b144d69a46eef","date_created":"2026-07-04T17:28:49Z","access_level":"open_access","success":1,"file_name":"noise_paper_public_deposit.zip","file_size":3082596099,"content_type":"application/x-zip-compressed","date_updated":"2026-07-04T17:28:49Z"}],"month":"07","article_processing_charge":"No","title":"Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices","project":[{"grant_number":"101115315","name":"Quantum bits with Kitaev Transmons","_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","grant_number":"F8606"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"name":"Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium","grant_number":"101150858","_id":"8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3"},{"_id":"5b9e579c-ab3d-11f0-914f-88754c5b5a3f","name":"Superconducting spin qubits in planar Ge","grant_number":"PAT 7682124"}],"day":"04","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"OA_place":"repository","date_created":"2026-07-04T17:32:27Z","oa":1,"has_accepted_license":"1","doi":"10.15479/AT-ISTA-22242","_id":"22242","type":"research_data","status":"public","year":"2026","file_date_updated":"2026-07-04T17:28:49Z"},{"scopus_import":"1","OA_type":"hybrid","acknowledgement":"The authors wish to acknowledge Dr. Paweł Baster for cloning PIN1-GFP-2/pDONR221, Ms. Aline Monzer and Dr. Mingyue Li for help with CHC protein level evaluation, Dr. Michał Rychłowski for help with confocal microscopy, Prof. Ari Pekka Mähönen for sharing the p1R4-pUBQ10:XVE plasmid, and Prof. Ying Gu for sharing seeds of the sec5 mutant. M.A. would like to thank Dr. Xixi Zhang and Prof. Sebastian Bednarek for inspiring discussions. This work was supported by the Taif University Researchers Supporting Project, TURSP-HC2022/02 to JF and SA and Austrian Science Fund (FWF): I 3630-B25 to JF. Open Access funding provided by Institute of Science and Technology Austria.","OA_place":"publisher","date_created":"2026-08-04T06:48:41Z","pmid":1,"day":"20","publication":"New Phytologist","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"title":"The role of clathrin in post‐Golgi secretion in plant cells","month":"07","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","supplementarymaterial":"yes","publication_status":"epub_ahead","year":"2026","type":"journal_article","status":"public","das_tickbox":"1","_id":"22647","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.71454"}],"doi":"10.1111/nph.71454","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"article_number":"nph.71454","article_type":"original","oa":1,"corr_author":"1","researchdata_availability":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","dataavailabilitystatement":"Original data associated with this study have been deposited in Dataset S1. The accession nos. of A. thaliana genes used in this study are as follows: CHC1 (AT3G11130), CHC2 (AT3G08530), CLC2 (AT2G40060), TPLATE (AT3G01780), AP2A1 (AT5G22770), DRP1C (AT1G14830), GNOM-LIKE1 (AT5G39500), BEN3/BIG2 (AT3G60860), TMK4 (AT3G23750), PIN1 (AT1G73590), AUXILIN-LIKE1 (AT4G12780), AP1M2 (AT1G60780), ECHIDNA (AT1G09330), SEC5A (AT1G76850), SEC5B (AT1G21170), TUB2 (AT5G62690), and PP2AA3 (AT1G13320).","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"},{"last_name":"Gackowski","first_name":"Adam","full_name":"Gackowski, Adam"},{"last_name":"Matijevic","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"},{"first_name":"Saqer S.","last_name":"Alotaibi","full_name":"Alotaibi, Saqer S."},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"short":"M. Adamowski, A. Gackowski, I. Matijevic, S.S. Alotaibi, J. Friml, New Phytologist (2026).","ama":"Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. 2026. doi:10.1111/nph.71454","apa":"Adamowski, M., Gackowski, A., Matijevic, I., Alotaibi, S. S., & Friml, J. (2026). The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. Wiley. https://doi.org/10.1111/nph.71454","ieee":"M. Adamowski, A. Gackowski, I. Matijevic, S. S. Alotaibi, and J. Friml, “The role of clathrin in post‐Golgi secretion in plant cells,” New Phytologist. Wiley, 2026.","chicago":"Adamowski, Maciek, Adam Gackowski, Ivana Matijevic, Saqer S. Alotaibi, and Jiří Friml. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71454.","ista":"Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. 2026. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist., nph. 71454.","mla":"Adamowski, Maciek, et al. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist, nph. 71454, Wiley, 2026, doi:10.1111/nph.71454."},"date_published":"2026-07-20T00:00:00Z","publisher":"Wiley","external_id":{"pmid":["42477503"]},"date_updated":"2026-08-04T07:58:27Z","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"Within the plant endomembrane system, the vesicle coat protein clathrin localizes to the plasma membrane (PM) and the trans-Golgi Network/early endosome (TGN/EE). While the role of clathrin in endocytosis at the PM is well established, its function at TGN/EE, presumably in late secretion (trafficking from the TGN/EE to the cell surface) or en route to the vacuole, is debated. Similarly debated are potential homeostatic mechanisms balancing the trafficking routes, especially endocytosis and late secretion.\r\nWe address these questions in Arabidopsis thaliana using conditional silencing of CLATHRIN HEAVY CHAIN (CHC), conditional overexpression of the clathrin uncoating factor AUXILIN-LIKE1, and secretory mutants.\r\nCHC silencing interferes with trafficking of cargoes destined for the apoplast and the PM, supporting a function of clathrin in late secretion. The secretory cargoes become abnormally rerouted from the TGN/EE to the vacuole. Unlike CHC silencing, overexpression of AUXILIN-LIKE1 selectively inhibits clathrin-mediated endocytosis while secretion continues normally at early points of induction. Conversely, secretory mutants exhibit a reduced PM recruitment of clathrin, and variably, of the TPLATE endocytic component.\r\nTogether, our data show a role of clathrin in secretion and suggest secretion as a fundamental trafficking process to which endocytosis is adjusted by a weak homeostatic mechanism."}]},{"ddc":["000"],"doi":"10.5281/ZENODO.14500423","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.14500423","open_access":"1"}],"_id":"21668","oa":1,"abstract":[{"text":"This artifact allows to review and reproduce the experiments from the paper *A Revised Practitioner's Guide to MDP Model Checking Algorithms*.\r\nThe package contains all original logfiles and derived data used to generate the plots as in the paper. Furthermore, the artifact contains the model checking tools `Storm` and `mcsta` in the version exercised in the paper, the used Docker container, as well as benchmark instances and execution scripts to reproduce the experiments.\r\n\r\nSee also the artifact of the conference paper: https://zenodo.org/records/7509474","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2026-04-07T09:52:55Z","status":"public","type":"research_data_reference","year":"2025","date_published":"2025-03-07T00:00:00Z","publisher":"Zenodo","related_material":{"record":[{"relation":"used_for_analysis_in","status":"public","id":"21661"}]},"oa_version":"Published Version","title":"Benchmark data for the revised practitioner's guide to MDP model checking algorithms","citation":{"mla":"Hartmanns, Arnd, et al. Benchmark Data for the Revised Practitioner’s Guide to MDP Model Checking Algorithms. Zenodo, 2025, doi:10.5281/ZENODO.14500423.","ista":"Hartmanns A, Junges S, Quatmann T, Weininger M. 2025. Benchmark data for the revised practitioner’s guide to MDP model checking algorithms, Zenodo, 10.5281/ZENODO.14500423.","chicago":"Hartmanns, Arnd, Sebastian Junges, Tim Quatmann, and Maximilian Weininger. “Benchmark Data for the Revised Practitioner’s Guide to MDP Model Checking Algorithms.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.14500423.","ieee":"A. Hartmanns, S. Junges, T. Quatmann, and M. Weininger, “Benchmark data for the revised practitioner’s guide to MDP model checking algorithms.” Zenodo, 2025.","apa":"Hartmanns, A., Junges, S., Quatmann, T., & Weininger, M. (2025). Benchmark data for the revised practitioner’s guide to MDP model checking algorithms. Zenodo. https://doi.org/10.5281/ZENODO.14500423","ama":"Hartmanns A, Junges S, Quatmann T, Weininger M. Benchmark data for the revised practitioner’s guide to MDP model checking algorithms. 2025. doi:10.5281/ZENODO.14500423","short":"A. Hartmanns, S. Junges, T. Quatmann, M. Weininger, (2025)."},"month":"03","article_processing_charge":"No","day":"07","OA_place":"repository","date_created":"2026-04-07T09:47:22Z","OA_type":"gold","author":[{"first_name":"Arnd","last_name":"Hartmanns","full_name":"Hartmanns, Arnd"},{"first_name":"Sebastian","last_name":"Junges","full_name":"Junges, Sebastian"},{"full_name":"Quatmann, Tim","last_name":"Quatmann","first_name":"Tim"},{"orcid":"0000-0002-0163-2152","full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian","id":"02ab0197-cc70-11ed-ab61-918e71f56881"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","type":"journal_article","year":"2025","publication_status":"published","quality_controlled":"1","oa":1,"article_type":"original","publication_identifier":{"issn":["0246-0203"]},"doi":"10.1214/23-AIHP1438","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01712","open_access":"1"}],"_id":"15128","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","day":"01","acknowledgement":"I would like to express my gratitude to László Erdős for suggesting the project and supervising my work. I am also thankful to Yuanyuan Xu and Oleksii Kolupaiev for many helpful discussions. Furthermore, I am grateful to Guillaume Dubach for translating the abstract into French.\r\nThe author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.","OA_place":"repository","date_created":"2024-03-20T09:41:04Z","ec_funded":1,"scopus_import":"1","OA_type":"green","volume":61,"month":"02","article_processing_charge":"No","title":"Mesoscopic eigenvalue statistics for Wigner-type matrices","page":"129-154","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"intvolume":" 61","publisher":"Institute of Mathematical Statistics","issue":"1","arxiv":1,"date_published":"2025-02-01T00:00:00Z","abstract":[{"text":"We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\\zeta)$ and a general class of related quantities involving two resolvents at nearby spectral parameters.","lang":"eng"},{"text":"On établit un théorème limite central universel pour les statistiques linéaires mésoscopiques des valeurs propres d’une matrice de type Wigner au milieu du spectre, avec des fonctions de classe \r\n et à support compact. La principale nouveauté de cette approche est qu’elle repose sur une loi locale optimale pour la fonction à deux points $T(z,\\zeta)$ , ainsi que pour une classe plus générale d’observables impliquant deux résolvantes évaluées en des paramètres proches.","lang":"fre"}],"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"date_updated":"2025-05-19T13:54:31Z","isi":1,"external_id":{"isi":["001427953600004"],"arxiv":["2301.01712"]},"author":[{"full_name":"Riabov, Volodymyr","first_name":"Volodymyr","last_name":"Riabov","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","citation":{"apa":"Riabov, V. (2025). Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AIHP1438","ama":"Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2025;61(1):129-154. doi:10.1214/23-AIHP1438","short":"V. Riabov, Annales de l’institut Henri Poincare (B) Probability and Statistics 61 (2025) 129–154.","ista":"Riabov V. 2025. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 61(1), 129–154.","mla":"Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no. 1, Institute of Mathematical Statistics, 2025, pp. 129–54, doi:10.1214/23-AIHP1438.","chicago":"Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2025. https://doi.org/10.1214/23-AIHP1438.","ieee":"V. Riabov, “Mesoscopic eigenvalue statistics for Wigner-type matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no. 1. Institute of Mathematical Statistics, pp. 129–154, 2025."},"oa_version":"Preprint","language":[{"iso":"eng"}]},{"date_published":"2025-02-05T00:00:00Z","year":"2025","status":"public","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"19024"}]},"publisher":"Fairdata","main_file_link":[{"url":"https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1","open_access":"1"}],"_id":"19033","doi":"10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1","ddc":["530"],"date_updated":"2025-09-30T10:31:44Z","has_accepted_license":"1","department":[{"_id":"RaKl"}],"abstract":[{"text":"This data set contains the simulation input files, scripts, and figures data belonging to the publication\r\n\r\nAlberto Scacchi, Carlo Rigoni, Mikko P. Haataja, Jakko V. I. Timonen, and Maria Sammalkorpi, \"A Coarse-grained Model for Aqueous Two-phase Systems: Application to Ferrofluids\", Journal of Colloids and Interface Science (2025). https://doi.org/10.1016/j.jcis.2025.01.256.","lang":"eng"}],"oa":1,"OA_place":"publisher","acknowledgement":"This work was supported by the Swiss National Science Foundation under the project no. P500PT_206916 (A.S.) and the Academy of Finland through its Centres of Excellence Programs (2022-2029, LIBER) under projects no. 346111 and 364205 (M.S.) and 346112 and 364206 (J.T.). MPH was supported by the National Science Foundation through the Princeton University (PCCM) Materials Research Science and Engineering Center DMR-2011750. A.S. warmly thanks Bob Evans for extensive scientific discussions and for his hospitality during the research visit in Bristol. Computational resources by CSC IT Centre for Finland, the Aalto Science-IT project, and RAMI -- RawMatters Finland Infrastructure are also gratefully acknowledged.","date_created":"2025-02-17T09:00:36Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Scacchi, Alberto","last_name":"Scacchi","first_name":"Alberto"}],"title":"2025_SCACCHI_JCIS","oa_version":"Published Version","month":"02","article_processing_charge":"No","contributor":[{"id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0","last_name":"Rigoni","first_name":"Carlo"},{"first_name":"Maria","last_name":"Sammalkorpi"},{"first_name":"Mikko","last_name":"Haataja"},{"last_name":"Timonen","first_name":"Jaakoo"}],"citation":{"chicago":"Scacchi, Alberto. “2025_SCACCHI_JCIS.” Fairdata, 2025. https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1.","ieee":"A. Scacchi, “2025_SCACCHI_JCIS.” Fairdata, 2025.","ista":"Scacchi A. 2025. 2025_SCACCHI_JCIS, Fairdata, 10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1.","mla":"Scacchi, Alberto. 2025_SCACCHI_JCIS. Fairdata, 2025, doi:10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1.","apa":"Scacchi, A. (2025). 2025_SCACCHI_JCIS. Fairdata. https://doi.org/10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1","short":"A. Scacchi, (2025).","ama":"Scacchi A. 2025_SCACCHI_JCIS. 2025. doi:10.23729/4fb80194-cdb2-4f49-94f4-f8a87b8e29c1"}},{"issue":"3","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publisher":"Wiley","date_published":"2025-03-18T00:00:00Z","department":[{"_id":"CaMu"}],"date_updated":"2025-09-30T11:04:38Z","abstract":[{"text":"Recently, Biagioli and Tompkins (2023, https://doi.org/10.1029/2022ms003231) used a simple stochastic model to derive a dimensionless parameter to predict convective self aggregation (SA) development, which was based on the derivation of the maximum free convective distance ($d_{clr}$) expected in the pre-aggregated, random state. Our goal is to test and further investigate this hypothesis, namely that $d_{clr}$ can predict SA occurrence, using an ensemble of twenty-four distinct combinations of horizontal mixing, planetary boundary layer (PBL), and microphysical parameterizations. We conclude that the key impact of parameterization schemes on SA is through their control of the number of convective cores and their relative spacing, $d_{clr}$, which itself is impacted by cold-pool (CP) properties and mean updraft core size. SA is more likely when the convective core count is small, while CPs modify convective spacing via suppression in their interiors and triggering by gust-front convergence and collisions. Each parameterization scheme emphasizes a different mechanism. Subgrid-scale horizontal turbulent mixing mainly affects SA through the determination of convective core size and thus spacing. The sensitivity to the microphysics is mainly through rain evaporation and the subsequent impact on CPs, while perturbations to the ice cloud microphysics have a limited effect. Non-local PBL mixing schemes promote SA primarily by increasing convective inhibition through inversion entrainment and altering low cloud amounts, leading to fewer convective cores and larger $d_{clr}$. ","lang":"eng"}],"isi":1,"external_id":{"isi":["001447023900001"]},"ddc":["550"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0002-1988-5035","full_name":"Casallas Garcia, Alejandro","first_name":"Alejandro","last_name":"Casallas Garcia","id":"92081129-2d75-11ef-a48d-b04dd7a2385a"},{"first_name":"A.M.","last_name":"Tompkins","full_name":"Tompkins, A.M."},{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"full_name":"Thompson, G.","first_name":"G.","last_name":"Thompson"}],"corr_author":"1","citation":{"apa":"Casallas Garcia, A., Tompkins, A. M., Muller, C. J., & Thompson, G. (2025). Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2024MS004791","ama":"Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. 2025;17(3). doi:10.1029/2024MS004791","short":"A. Casallas Garcia, A.M. Tompkins, C.J. Muller, G. Thompson, Journal of Advances in Modeling Earth Systems 17 (2025).","chicago":"Casallas Garcia, Alejandro, A.M. Tompkins, Caroline J Muller, and G. Thompson. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” Journal of Advances in Modeling Earth Systems. Wiley, 2025. https://doi.org/10.1029/2024MS004791.","ieee":"A. Casallas Garcia, A. M. Tompkins, C. J. Muller, and G. Thompson, “Sensitivity of self-aggregation and the key role of the free convection distance,” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3. Wiley, 2025.","ista":"Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. 2025. Sensitivity of self-aggregation and the key role of the free convection distance. Journal of Advances in Modeling Earth Systems. 17(3), e2024MS004791.","mla":"Casallas Garcia, Alejandro, et al. “Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.” Journal of Advances in Modeling Earth Systems, vol. 17, no. 3, e2024MS004791, Wiley, 2025, doi:10.1029/2024MS004791."},"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","status":"public","file_date_updated":"2025-03-19T07:58:21Z","year":"2025","publication_status":"published","has_accepted_license":"1","oa":1,"article_type":"original","doi":"10.1029/2024MS004791","publication_identifier":{"eissn":["1942-2466"]},"_id":"19416","article_number":"e2024MS004791","publication":"Journal of Advances in Modeling Earth Systems","OA_place":"publisher","ec_funded":1,"acknowledgement":"This article is based on chapter 3 of AC Ph.D. thesis. The authors thank Graziano Giuliani for his coding assistance. We also thank Daniel Hernández-Deckers, Paolina Cerlini, and especially to Giovanni Biagioli for discussions and feedback. We also thank two reviewers for their insightful comments. AC was supported by a fellowship awarded by ICTP and by the European Union Horizon 2020 Marie Skłodowska-Curie grant agreement No. 101034413. CM acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041).","date_created":"2025-03-19T07:58:38Z","scopus_import":"1","OA_type":"gold","day":"18","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"Yes","month":"03","file":[{"checksum":"bc32677e63f8abb07b330f4a08da796d","date_created":"2025-03-19T07:58:21Z","relation":"main_file","file_id":"19417","creator":"acasalla","access_level":"open_access","file_name":"Casallas_et_al_2025_dclr.pdf","date_updated":"2025-03-19T07:58:21Z","content_type":"application/pdf","file_size":18285343}],"volume":17,"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","grant_number":"805041","name":"Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"intvolume":" 17","title":"Sensitivity of self-aggregation and the key role of the free convection distance"},{"OA_place":"publisher","date_created":"2025-03-23T23:01:27Z","acknowledgement":"The IMP and D.H. are generously funded by Boehringer Ingelheim. We thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for helpful discussions.","scopus_import":"1","OA_type":"hybrid","day":"03","pmid":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Structure","intvolume":" 33","page":"820-827.e4","title":"FakET: Simulating cryo-electron tomograms with neural style transfer","month":"04","article_processing_charge":"Yes (in subscription journal)","file":[{"file_name":"2025_Structure_Harar.pdf","content_type":"application/pdf","date_updated":"2025-08-05T12:15:13Z","file_size":4367530,"date_created":"2025-08-05T12:15:13Z","checksum":"f346bc357a66a88cca3d0eb95793fb73","relation":"main_file","creator":"dernst","file_id":"20130","success":1,"access_level":"open_access"}],"volume":33,"quality_controlled":"1","type":"journal_article","status":"public","publication_status":"published","file_date_updated":"2025-08-05T12:15:13Z","year":"2025","doi":"10.1016/j.str.2025.01.020","publication_identifier":{"eissn":["1878-4186"],"issn":["0969-2126"]},"_id":"19443","has_accepted_license":"1","oa":1,"article_type":"original","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Harar, Pavol","orcid":"0000-0001-5206-1794","first_name":"Pavol","last_name":"Harar","id":"e03d953a-6e8c-11ef-99e4-f0717d385cd5"},{"full_name":"Herrmann, Lukas","last_name":"Herrmann","first_name":"Lukas"},{"full_name":"Grohs, Philipp","last_name":"Grohs","first_name":"Philipp"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron tomograms with neural style transfer,” Structure, vol. 33, no. 4. Elsevier, p. 820–827.e4, 2025.","chicago":"Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure. Elsevier, 2025. https://doi.org/10.1016/j.str.2025.01.020.","ista":"Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 33(4), 820–827.e4.","mla":"Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4, doi:10.1016/j.str.2025.01.020.","short":"P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.","ama":"Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. 2025;33(4):820-827.e4. doi:10.1016/j.str.2025.01.020","apa":"Harar, P., Herrmann, L., Grohs, P., & Haselbach, D. (2025). FakET: Simulating cryo-electron tomograms with neural style transfer. Structure. Elsevier. https://doi.org/10.1016/j.str.2025.01.020"},"date_published":"2025-04-03T00:00:00Z","PlanS_conform":"1","issue":"4","publisher":"Elsevier","related_material":{"link":[{"relation":"software","url":"https://github.com/paloha/faket/"}]},"external_id":{"isi":["001463196100001"],"pmid":["39947174"]},"isi":1,"ddc":["570"],"department":[{"_id":"AlMi"}],"date_updated":"2025-09-30T11:13:02Z","abstract":[{"lang":"eng","text":"In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often employed to produce these datasets, limits their broad applicability. We introduce FakET, a method based on neural style transfer, capable of simulating the forward operator of any cryo transmission electron microscope. It can be used to adapt a synthetic training dataset according to reference data producing high-quality simulated micrographs or tilt-series. To assess the quality of our generated data, we used it to train a state-of-the-art localization and classification architecture and compared its performance with a counterpart trained on benchmark data. Remarkably, our technique matches the performance, boosts data generation speed 750x, uses 33x less memory, and scales well to typical transmission electron microscope detector sizes. It leverages GPU acceleration and parallel processing. The source code is available at https://github.com/paloha/faket/."}]},{"abstract":[{"lang":"eng","text":"This artifact allows to review and reproduce the Isabelle proofs and practical experiments from the paper *Fixed Point Certificates for Reachability and Expected Rewards in MDPs*.\r\nThe contents are two-fold:\r\nFirst, the artifact contains a formally verified certificate checker for the certificates presented in the paper.\r\nThe formal Isabelle/HOL proofs of the background theory can be inspected, checked by Isabelle and the code extraction can be retraced.\r\n\r\nSecond, the artifact contains a modified version of the model checking tool `Storm` with support for certificate generation. Together with the provided scripts and benchmark files, this allows to reproduce the experiments from the paper.\r\nAn appropriate subset of the experiments is given to allow a review in a timely manner. In addition, original logfiles from our experiments are provided, allowing a detailed inspection.\r\n\r\nThe package includes convenient installation scripts for [the TACAS 2023 VM](https://doi.org/10.5281/zenodo.7113223) (based on Ubuntu 22.04).\r\nA native installation on Linux or macOS systems (including the newer ARM-based machines) is also possible."}],"oa":1,"date_updated":"2025-06-02T10:55:35Z","department":[{"_id":"KrCh"}],"ddc":["000"],"_id":"19771","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.14626585"}],"doi":"10.5281/ZENODO.14626585","publisher":"Zenodo","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"19743"}]},"year":"2025","type":"research_data_reference","status":"public","date_published":"2025-01-09T00:00:00Z","citation":{"ieee":"K. Chatterjee, T. Quatmann, M. Schäffeler, M. Weininger, T. Winkler, and D. Zilken, “Artifact: Fixed point certificates for reachability and expected rewards in MDPs.” Zenodo, 2025.","chicago":"Chatterjee, Krishnendu, Tim Quatmann, Maximilian Schäffeler, Maximilian Weininger, Tobias Winkler, and Daniel Zilken. “Artifact: Fixed Point Certificates for Reachability and Expected Rewards in MDPs.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.14626585.","mla":"Chatterjee, Krishnendu, et al. Artifact: Fixed Point Certificates for Reachability and Expected Rewards in MDPs. Zenodo, 2025, doi:10.5281/ZENODO.14626585.","ista":"Chatterjee K, Quatmann T, Schäffeler M, Weininger M, Winkler T, Zilken D. 2025. Artifact: Fixed point certificates for reachability and expected rewards in MDPs, Zenodo, 10.5281/ZENODO.14626585.","ama":"Chatterjee K, Quatmann T, Schäffeler M, Weininger M, Winkler T, Zilken D. Artifact: Fixed point certificates for reachability and expected rewards in MDPs. 2025. doi:10.5281/ZENODO.14626585","short":"K. Chatterjee, T. Quatmann, M. Schäffeler, M. Weininger, T. Winkler, D. Zilken, (2025).","apa":"Chatterjee, K., Quatmann, T., Schäffeler, M., Weininger, M., Winkler, T., & Zilken, D. (2025). Artifact: Fixed point certificates for reachability and expected rewards in MDPs. Zenodo. https://doi.org/10.5281/ZENODO.14626585"},"month":"01","article_processing_charge":"No","title":"Artifact: Fixed point certificates for reachability and expected rewards in MDPs","oa_version":"Published Version","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Tim","last_name":"Quatmann","full_name":"Quatmann, Tim"},{"first_name":"Maximilian","last_name":"Schäffeler","full_name":"Schäffeler, Maximilian"},{"full_name":"Weininger, Maximilian","id":"02ab0197-cc70-11ed-ab61-918e71f56881","first_name":"Maximilian","last_name":"Weininger"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"},{"full_name":"Zilken, Daniel","id":"d8ebc24a-3f98-11f0-9044-8296d4f39ab3","last_name":"Zilken","first_name":"Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"09","OA_type":"green","date_created":"2025-06-02T10:13:24Z","OA_place":"repository"},{"publication_status":"published","year":"2025","file_date_updated":"2025-06-10T07:07:45Z","type":"journal_article","status":"public","quality_controlled":"1","article_type":"original","oa":1,"has_accepted_license":"1","article_number":"btaf280","_id":"19796","publication_identifier":{"eissn":["1367-4811"]},"doi":"10.1093/bioinformatics/btaf280","publication":"Bioinformatics","pmid":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","scopus_import":"1","OA_type":"gold","DOAJ_listed":"1","ec_funded":1,"date_created":"2025-06-08T22:01:22Z","OA_place":"publisher","acknowledgement":"V.-G.T. was supported by Institut Carnot STAR, Marseille, France. K.H.P. was supported by NSF grant MCB1715826 to Réka Albert. S.P. has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. J.C.R. was supported by internal departmental funds provided by Luis M. Rocha. No funding bodies had any role in study design, analysis, decision to publish, or preparation of the article.","volume":41,"file":[{"content_type":"application/pdf","date_updated":"2025-06-10T07:07:45Z","file_size":2695801,"file_name":"2025_Bioinformatics_Trinh.pdf","success":1,"access_level":"open_access","checksum":"fa9d68aa0f5ce37598a623c9be936f09","date_created":"2025-06-10T07:07:45Z","relation":"main_file","file_id":"19801","creator":"dernst"}],"month":"05","article_processing_charge":"Yes","title":"Mapping the attractor landscape of Boolean networks with biobalm","intvolume":" 41","project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publisher":"Oxford University Press","related_material":{"record":[{"id":"19800","relation":"research_data","status":"public"}],"link":[{"url":"https://github.com/jcrozum/biobalm","relation":"software"}]},"issue":"5","date_published":"2025-05-01T00:00:00Z","abstract":[{"lang":"eng","text":"Motivation: Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram (SD) describes this interplay in a discrete analog of Waddington’s epigenetic attractor landscape that allows for fast identification of attractors and attractor control strategies. Efficient computational tools for studying SDs are essential for the understanding of Boolean attractor landscapes and connecting them to their biological functions.\r\nResults: We present a new approach to SD construction for asynchronously updated Boolean networks, implemented in the biologist’s Boolean attractor landscape mapper, biobalm. We compare biobalm to similar tools and find a substantial performance increase in SD construction, attractor identification, and attractor control. We perform the most comprehensive comparative analysis to date of the SD structure in experimentally-validated Boolean models of cell processes and random ensembles. We find that random models (including critical Kauffman networks) have relatively small SDs, indicating simple decision structures. In contrast, nonrandom models from the literature are enriched in extremely large SDs, indicating an abundance of decision points and suggesting the presence of complex Waddington landscapes in nature.\r\nAvailability and implementation: The tool biobalm is available online at https://github.com/jcrozum/biobalm. Further data, scripts for testing, analysis, and figure generation are available online at https://github.com/jcrozum/biobalm-analysis and in the reproducibility artefact at https://doi.org/10.5281/zenodo.13854760."}],"date_updated":"2025-09-30T12:46:33Z","department":[{"_id":"ToHe"}],"ddc":["000"],"isi":1,"external_id":{"pmid":["40327535"],"isi":["001493400600001"]},"author":[{"full_name":"Trinh, Van Giang","last_name":"Trinh","first_name":"Van Giang"},{"full_name":"Park, Kyu Hyong","first_name":"Kyu Hyong","last_name":"Park"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","first_name":"Samuel","full_name":"Pastva, Samuel","orcid":"0000-0003-1993-0331"},{"first_name":"Jordan C.","last_name":"Rozum","full_name":"Rozum, Jordan C."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","citation":{"apa":"Trinh, V. G., Park, K. H., Pastva, S., & Rozum, J. C. (2025). Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaf280","ama":"Trinh VG, Park KH, Pastva S, Rozum JC. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 2025;41(5). doi:10.1093/bioinformatics/btaf280","short":"V.G. Trinh, K.H. Park, S. Pastva, J.C. Rozum, Bioinformatics 41 (2025).","chicago":"Trinh, Van Giang, Kyu Hyong Park, Samuel Pastva, and Jordan C. Rozum. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics. Oxford University Press, 2025. https://doi.org/10.1093/bioinformatics/btaf280.","ieee":"V. G. Trinh, K. H. Park, S. Pastva, and J. C. Rozum, “Mapping the attractor landscape of Boolean networks with biobalm,” Bioinformatics, vol. 41, no. 5. Oxford University Press, 2025.","ista":"Trinh VG, Park KH, Pastva S, Rozum JC. 2025. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 41(5), btaf280.","mla":"Trinh, Van Giang, et al. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics, vol. 41, no. 5, btaf280, Oxford University Press, 2025, doi:10.1093/bioinformatics/btaf280."},"language":[{"iso":"eng"}],"oa_version":"Published Version"},{"file_date_updated":"2025-07-22T07:58:22Z","publication_status":"published","year":"2025","type":"conference","status":"public","quality_controlled":"1","oa":1,"has_accepted_license":"1","_id":"20032","publication_identifier":{"isbn":["9798331320850"]},"publication":"13th International Conference on Learning Representations","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","scopus_import":"1","OA_type":"diamond","OA_place":"publisher","date_created":"2025-07-20T22:02:01Z","file":[{"file_name":"2025_ICLR_Chen.pdf","file_size":732745,"content_type":"application/pdf","date_updated":"2025-07-22T07:58:22Z","relation":"main_file","creator":"dernst","file_id":"20065","date_created":"2025-07-22T07:58:22Z","checksum":"64cfdb12ae3e4e8ba57b1403e1066776","access_level":"open_access","success":1}],"month":"04","article_processing_charge":"No","title":"Scalable mechanistic neural networks","page":"63716-63737","publisher":"ICLR","related_material":{"link":[{"url":"https://github.com/IST-DASLab/ScalableMNN","relation":"software"}]},"conference":{"start_date":"2025-04-24","location":"Singapore, Singapore","end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations"},"arxiv":1,"date_published":"2025-04-01T00:00:00Z","abstract":[{"text":"We propose Scalable Mechanistic Neural Network (S-MNN), an enhanced neural network framework designed for scientific machine learning applications involving long temporal sequences. By reformulating the original Mechanistic Neural Network (MNN) (Pervez et al., 2024), we reduce the computational time and space complexities from cubic and quadratic with respect to the sequence length, respectively, to linear. This significant improvement enables efficient modeling of long-term dynamics without sacrificing accuracy or interpretability. Extensive experiments demonstrate that S-MNN matches the original MNN in precision while substantially reducing computational resources. Consequently, S-MNN can drop-in replace the original MNN in applications, providing a practical and efficient tool for integrating mechanistic bottlenecks into neural network models of complex dynamical systems. Source code is available at https://github.com/IST-DASLab/ScalableMNN.","lang":"eng"}],"date_updated":"2025-08-04T08:03:11Z","department":[{"_id":"DaAl"},{"_id":"FrLo"}],"ddc":["000"],"external_id":{"arxiv":["2410.06074"]},"author":[{"orcid":"0000-0001-5337-5875","full_name":"Chen, Jiale","last_name":"Chen","first_name":"Jiale","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785"},{"full_name":"Yao, Dingling","id":"d3e02e50-48a8-11ee-8f62-c108061797fa","first_name":"Dingling","last_name":"Yao"},{"first_name":"Adeel A","last_name":"Pervez","id":"fca6d90c-d47f-11ee-bc87-93ff51604981","full_name":"Pervez, Adeel A"},{"last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","citation":{"short":"J. Chen, D. Yao, A.A. Pervez, D.-A. Alistarh, F. Locatello, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 63716–63737.","ama":"Chen J, Yao D, Pervez AA, Alistarh D-A, Locatello F. Scalable mechanistic neural networks. In: 13th International Conference on Learning Representations. ICLR; 2025:63716-63737.","apa":"Chen, J., Yao, D., Pervez, A. A., Alistarh, D.-A., & Locatello, F. (2025). Scalable mechanistic neural networks. In 13th International Conference on Learning Representations (pp. 63716–63737). Singapore, Singapore: ICLR.","ieee":"J. Chen, D. Yao, A. A. Pervez, D.-A. Alistarh, and F. Locatello, “Scalable mechanistic neural networks,” in 13th International Conference on Learning Representations, Singapore, Singapore, 2025, pp. 63716–63737.","chicago":"Chen, Jiale, Dingling Yao, Adeel A Pervez, Dan-Adrian Alistarh, and Francesco Locatello. “Scalable Mechanistic Neural Networks.” In 13th International Conference on Learning Representations, 63716–37. ICLR, 2025.","ista":"Chen J, Yao D, Pervez AA, Alistarh D-A, Locatello F. 2025. Scalable mechanistic neural networks. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 63716–63737.","mla":"Chen, Jiale, et al. “Scalable Mechanistic Neural Networks.” 13th International Conference on Learning Representations, ICLR, 2025, pp. 63716–37."},"language":[{"iso":"eng"}],"oa_version":"Published Version"},{"publication_identifier":{"issn":["1866-3516"]},"doi":"10.5194/essd-17-4213-2025","_id":"20546","has_accepted_license":"1","oa":1,"article_type":"original","quality_controlled":"1","status":"public","type":"journal_article","publication_status":"published","year":"2025","file_date_updated":"2025-10-27T08:38:40Z","intvolume":" 17","title":"DebDaB: A database of supraglacial debris thickness and physical properties","page":"4213-4234","article_processing_charge":"Yes","month":"08","file":[{"content_type":"application/pdf","date_updated":"2025-10-27T08:38:40Z","file_size":3842196,"file_name":"2025_EarthSystemScienceData_FontrodonaBach.pdf","success":1,"access_level":"open_access","checksum":"f77ebb9825f374134a89e0e6311fe188","date_created":"2025-10-27T08:38:40Z","creator":"dernst","file_id":"20548","relation":"main_file"}],"volume":17,"date_created":"2025-10-27T08:21:22Z","acknowledgement":"This work was supported by SNF project RENOIR (“Resolving the thickness of debris on Earth’s glaciers and its rate of change”; grant no. 204322). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and\r\ninnovation programme (grant no. 772751; RAVEN: “Rapid mass losses of debris covered glaciers in High Mountain Asia”). The authors acknowledge DCGWG of IACS for setting the stage and bringing together the debris-covered glacier community to focus on broader needs transcending a specific research topic and for starting the Zenodo community on debris-covered glaciers, where this database is hosted. The authors thank Achim A. Beylich (topical editor), Ken\r\nMankoff (chief editor), Morgan Jones (reviewer), and an anonymous reviewer for their constructive feedback, comments, and discussions on the database and paper.","OA_place":"publisher","OA_type":"gold","scopus_import":"1","DOAJ_listed":"1","day":"29","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Earth System Science Data","isi":1,"external_id":{"isi":["001560847000001"]},"ddc":["550"],"department":[{"_id":"FrPe"}],"date_updated":"2025-12-01T15:05:58Z","abstract":[{"lang":"eng","text":"Rocky debris covers around 7.3 % of the global glacier area, influencing ice melt rates and the surface mass balance of glaciers, making the dynamics and hydrology of debris-covered glaciers distinct from those of clean-ice glaciers. Accurate representation of debris in models is challenging, as measurements of the physical properties and thickness of the supraglacial debris layer are scarce. Here, we compile a database of measured and reported bulk physical properties and layer thicknesses of supraglacial debris that we call the supraglacial Debris Database (DebDaB) and that is open to community submissions. The majority of the database (90 %) is compiled from 172 sources in the literature, and the remaining 10 % was previously unpublished. DebDaB contains 8741 data entries for supraglacial debris layer thickness, of which 1770 entries also include sub-debris ablation rates, 179 thermal conductivity of debris, 160 aerodynamic surface roughness length, 79 debris albedo, 59 debris emissivity, and 37 debris porosity. The data are distributed over 84 glaciers in 13 regions in the Global Terrestrial Network for Glaciers. We show regional differences in the distribution of debris thickness measurements in DebDaB and fit simplified Østrem curves to 19 glaciers with sufficient debris thickness and ablation data. The data in DebDaB can be used for energy balance, melt, and surface mass balance studies by incorporating site-specific debris properties or for evaluation of remote sensing estimates of debris thickness and surface roughness. They can also help future field campaigns on debris-covered glaciers by identifying observation gaps. DebDaB's uneven spatial coverage points to sampling biases in community efforts to observe debris-covered glaciers, with some regions (e.g. central Europe and South Asia) well-sampled but others having gaps with prevalent debris (e.g. the Andes and Alaska). Debris thickness measurements are mostly concentrated at lower elevations, leaving higher-elevation debris-covered areas undersampled and suggesting that our knowledge of debris properties might not be representative of all elevations. The aims of DebDaB, as an openly available dataset, are to evolve over time, to be updated, and to add to community submissions as new data on supraglacial properties become available. The data described in this paper can be accessed from Zenodo at https://doi.org/10.5281/zenodo.14224835 (Groeneveld et al., 2025)."}],"date_published":"2025-08-29T00:00:00Z","PlanS_conform":"1","issue":"8","publisher":"Copernicus Publications","related_material":{"record":[{"status":"public","relation":"research_data","id":"20547"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"apa":"Fontrodona-Bach, A., Groeneveld, L., Miles, E., McCarthy, M., Shaw, T., Melo Velasco, J. V., & Pellicciotti, F. (2025). DebDaB: A database of supraglacial debris thickness and physical properties. Earth System Science Data. Copernicus Publications. https://doi.org/10.5194/essd-17-4213-2025","ama":"Fontrodona-Bach A, Groeneveld L, Miles E, et al. DebDaB: A database of supraglacial debris thickness and physical properties. Earth System Science Data. 2025;17(8):4213-4234. doi:10.5194/essd-17-4213-2025","short":"A. Fontrodona-Bach, L. Groeneveld, E. Miles, M. McCarthy, T. Shaw, J.V. Melo Velasco, F. Pellicciotti, Earth System Science Data 17 (2025) 4213–4234.","chicago":"Fontrodona-Bach, Adrià, Lars Groeneveld, Evan Miles, Michael McCarthy, Thomas Shaw, Juan Vicente Melo Velasco, and Francesca Pellicciotti. “DebDaB: A Database of Supraglacial Debris Thickness and Physical Properties.” Earth System Science Data. Copernicus Publications, 2025. https://doi.org/10.5194/essd-17-4213-2025.","ieee":"A. Fontrodona-Bach et al., “DebDaB: A database of supraglacial debris thickness and physical properties,” Earth System Science Data, vol. 17, no. 8. Copernicus Publications, pp. 4213–4234, 2025.","mla":"Fontrodona-Bach, Adrià, et al. “DebDaB: A Database of Supraglacial Debris Thickness and Physical Properties.” Earth System Science Data, vol. 17, no. 8, Copernicus Publications, 2025, pp. 4213–34, doi:10.5194/essd-17-4213-2025.","ista":"Fontrodona-Bach A, Groeneveld L, Miles E, McCarthy M, Shaw T, Melo Velasco JV, Pellicciotti F. 2025. DebDaB: A database of supraglacial debris thickness and physical properties. Earth System Science Data. 17(8), 4213–4234."},"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"f06891fd-9f42-11ee-8632-a20971c43046","last_name":"Fontrodona-Bach","first_name":"Adrià","full_name":"Fontrodona-Bach, Adrià"},{"last_name":"Groeneveld","first_name":"Lars","full_name":"Groeneveld, Lars"},{"full_name":"Miles, Evan","last_name":"Miles","first_name":"Evan"},{"full_name":"McCarthy, Michael","first_name":"Michael","last_name":"McCarthy","id":"22a2674a-61ce-11ee-94b5-d18813baf16f"},{"id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","last_name":"Shaw","first_name":"Thomas","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas"},{"id":"2611dec0-b9c6-11ed-9bea-a81c2b17a549","first_name":"Juan Vicente","last_name":"Melo Velasco","full_name":"Melo Velasco, Juan Vicente"},{"orcid":"0000-0002-5554-8087","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}]},{"date_published":"2025-01-01T00:00:00Z","PlanS_conform":"1","publisher":"Springer Nature","related_material":{"record":[{"id":"18135","status":"public","relation":"dissertation_contains"}]},"external_id":{"isi":["001261197700002"],"pmid":["39926012"]},"isi":1,"ddc":["510"],"department":[{"_id":"RoSe"}],"date_updated":"2026-04-07T13:01:40Z","abstract":[{"lang":"eng","text":"We prove an upper bound on the energy density of the dilute spin-\\(\\frac {1}{2}\\) Fermi gas capturing the leading correction to the kinetic energy\\(8\\pi a\\rho _\\uparrow\\rho _\\downarrow\\) with an error of size smaller than\\(a\\rho^{2}(a^ 3\\rho)^{1/3-\\varepsilon}\\) for any\\(\\varepsilon> 0\\), where a denotes the scattering length of the interaction. The result is valid for a large class of interactions including interactions with a hard core. A central ingredient in the proof is a rigorous version of a fermionic cluster expansion adapted from the formal expansion of Gaudin et al. (Nucl Phys A 176(2):237–260, 1971. https://doi.org/10.1016/0375-9474(71)90267-3)."}],"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"A. B. Lauritsen, “Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion,” Annales Henri Poincare, vol. 26. Springer Nature, pp. 203–243, 2025.","chicago":"Lauritsen, Asbjørn Bækgaard. “Almost Optimal Upper Bound for the Ground State Energy of a Dilute Fermi Gas via Cluster Expansion.” Annales Henri Poincare. Springer Nature, 2025. https://doi.org/10.1007/s00023-024-01450-1.","ista":"Lauritsen AB. 2025. Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. 26, 203–243.","mla":"Lauritsen, Asbjørn Bækgaard. “Almost Optimal Upper Bound for the Ground State Energy of a Dilute Fermi Gas via Cluster Expansion.” Annales Henri Poincare, vol. 26, Springer Nature, 2025, pp. 203–43, doi:10.1007/s00023-024-01450-1.","short":"A.B. Lauritsen, Annales Henri Poincare 26 (2025) 203–243.","ama":"Lauritsen AB. Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. 2025;26:203-243. doi:10.1007/s00023-024-01450-1","apa":"Lauritsen, A. B. (2025). Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-024-01450-1"},"quality_controlled":"1","type":"journal_article","status":"public","file_date_updated":"2025-08-05T11:42:27Z","year":"2025","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"doi":"10.1007/s00023-024-01450-1","_id":"17240","has_accepted_license":"1","oa":1,"article_type":"original","date_created":"2024-07-14T22:01:12Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nWe thank Alessandro Giuliani and Robert Seiringer for helpful discussions and Robert Seiringer for his comments on the manuscript. Financial support by the Austrian Science Fund (FWF) through Grant https://doi.org/10.55776/I6427 (as part of the SFB/TRR 352) is gratefully acknowledged.","OA_place":"publisher","scopus_import":"1","OA_type":"hybrid","day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"publication":"Annales Henri Poincare","project":[{"grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"intvolume":" 26","title":"Almost optimal upper bound for the ground state energy of a dilute Fermi gas via cluster expansion","page":"203-243","article_processing_charge":"Yes (via OA deal)","month":"01","file":[{"file_name":"2025_AnnalesHenriPoincare_Lauritsen.pdf","content_type":"application/pdf","date_updated":"2025-08-05T11:42:27Z","file_size":797241,"date_created":"2025-08-05T11:42:27Z","checksum":"01b6572f55f721e97498522c85072ed2","relation":"main_file","file_id":"20125","creator":"dernst","success":1,"access_level":"open_access"}],"volume":26},{"arxiv":1,"date_published":"2025-11-27T00:00:00Z","publisher":"Université de Bordeaux","issue":"3","license":"https://creativecommons.org/licenses/by-nd/4.0/","external_id":{"arxiv":["2408.03774"]},"ddc":["510"],"abstract":[{"text":"We provide an estimate for the number of nontrivial integer points on the Pellian surface t^2 - du^2 = 1 in a bounded region. We give a lower bound on the size of fundamental solutions for almost all d in a certain class, based on a recent conjecture of Browning and Wilsch about integer points on log K3 surfaces. We also obtain an upper bound on the average of class number in this class, assuming the same conjecture.","lang":"eng"},{"lang":"fre","text":"Nous donnons une estimation du nombre de points entiers non triviaux sur la surface pellienne \r\nt^2 - du^2 = 1 dans une région bornée. Nous établissons une borne inférieure pour la taille des solutions fondamentales pour presque tout d appartenant à une certaine classe, en nous fondant sur une conjecture récente de Browning et Wilsch concernant les points entiers sur les surfaces log K3. Nous obtenons également une borne supérieure pour la moyenne du nombre de classes dans cette classe, sous la même hypothèse conjecturale."}],"department":[{"_id":"TiBr"}],"date_updated":"2026-07-16T08:45:12Z","researchdata_availability":"no","corr_author":"1","author":[{"id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","first_name":"Yijie","last_name":"Diao","orcid":"0000-0002-4989-5330","full_name":"Diao, Yijie"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"short":"Y. Diao, Journal de Theorie Des Nombres de Bordeaux 37 (2025) 973–988.","ama":"Diao Y. Class numbers and integer points on some Pellian surfaces. Journal de theorie des nombres de Bordeaux. 2025;37(3):973-988. doi:10.5802/jtnb.1348","apa":"Diao, Y. (2025). Class numbers and integer points on some Pellian surfaces. Journal de Theorie Des Nombres de Bordeaux. Université de Bordeaux. https://doi.org/10.5802/jtnb.1348","mla":"Diao, Yijie. “Class Numbers and Integer Points on Some Pellian Surfaces.” Journal de Theorie Des Nombres de Bordeaux, vol. 37, no. 3, Université de Bordeaux, 2025, pp. 973–88, doi:10.5802/jtnb.1348.","ista":"Diao Y. 2025. Class numbers and integer points on some Pellian surfaces. Journal de theorie des nombres de Bordeaux. 37(3), 973–988.","ieee":"Y. Diao, “Class numbers and integer points on some Pellian surfaces,” Journal de theorie des nombres de Bordeaux, vol. 37, no. 3. Université de Bordeaux, pp. 973–988, 2025.","chicago":"Diao, Yijie. “Class Numbers and Integer Points on Some Pellian Surfaces.” Journal de Theorie Des Nombres de Bordeaux. Université de Bordeaux, 2025. https://doi.org/10.5802/jtnb.1348."},"status":"public","type":"journal_article","publication_status":"published","year":"2025","file_date_updated":"2025-12-29T10:05:22Z","supplementarymaterial":"no","quality_controlled":"1","das_tickbox":"0","publication_identifier":{"issn":["1246-7405"],"eissn":["2118-8572"]},"doi":"10.5802/jtnb.1348","_id":"20850","oa":1,"article_type":"original","has_accepted_license":"1","day":"27","tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"date_created":"2025-12-21T23:01:35Z","OA_place":"publisher","acknowledgement":"The author would like to thank his supervisor Tim Browning for suggesting this project and many helpful conversations and useful comments. Moreover, he is grateful to Jakob Glas, Damaris Schindler, Igor Shparlinski, Matteo Verzobio, Victor Wang, Florian Wilsch and Shuntaro Yamagishi for taking their time to answer his questions and their valuable suggestions.","OA_type":"hybrid","scopus_import":"1","publication":"Journal de theorie des nombres de Bordeaux","title":"Class numbers and integer points on some Pellian surfaces","page":"973-988","intvolume":" 37","file":[{"success":1,"access_level":"open_access","checksum":"67aa0afbc0b5bcbff5341f4d25e6ba20","date_created":"2025-12-29T10:05:22Z","file_id":"20861","creator":"dernst","relation":"main_file","date_updated":"2025-12-29T10:05:22Z","content_type":"application/pdf","file_size":766196,"file_name":"2025_JTNB_Diao.pdf"}],"volume":37,"article_processing_charge":"Yes (in subscription journal)","month":"11"},{"alternative_title":["Advances in Neural Information Processing Systems"],"das_tickbox":"1","type":"conference","status":"public","year":"2025","publication_status":"published","quality_controlled":"1","oa":1,"has_accepted_license":"1","publication_identifier":{"issn":["1049-5258"]},"_id":"21068","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2505.17708","open_access":"1"}],"publication":"39th Annual Conference on Neural Information Processing Systems","day":"15","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-01-29T14:24:56Z","OA_place":"repository","acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/COE12. For open access purposes, the author has applied a CC BY public copyright license to any accepted manuscript version arising from this submission.\r\n","OA_type":"green","volume":38,"article_processing_charge":"No","month":"12","title":"The third pillar of causal analysis? A measurement perspective on causal representations","intvolume":" 38","related_material":{"link":[{"url":"https://github.com/shimenghuang/a-measurement-perspective-of-crl","relation":"software"}]},"publisher":"Neural Information Processing Systems Foundation","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2025-12-07","start_date":"2025-12-02","location":"San Diego, CA, United States"},"arxiv":1,"date_published":"2025-12-15T00:00:00Z","abstract":[{"text":"Causal reasoning and discovery, two fundamental tasks of causal analysis,\r\noften face challenges in applications due to the complexity, noisiness, and highdimensionality of real-world data. Despite recent progress in identifying latent\r\ncausal structures using causal representation learning (CRL), what makes learned\r\nrepresentations useful for causal downstream tasks and how to evaluate them are\r\nstill not well understood. In this paper, we reinterpret CRL using a measurement\r\nmodel framework, where the learned representations are viewed as proxy measurements of the latent causal variables. Our approach clarifies the conditions under\r\nwhich learned representations support downstream causal reasoning and provides\r\na principled basis for quantitatively assessing the quality of representations using\r\na new Test-based Measurement EXclusivity (T-MEX) score. We validate T-MEX\r\nacross diverse causal inference scenarios, including numerical simulations and\r\nreal-world ecological video analysis, demonstrating that the proposed framework\r\nand corresponding score effectively assess the identification of learned representations and their usefulness for causal downstream tasks. Reproducible code can\r\nbe found at https://github.com/shimenghuang/a-measurement-perspective-of-crl.","lang":"eng"}],"department":[{"_id":"FrLo"}],"date_updated":"2026-07-28T07:14:27Z","external_id":{"arxiv":["2505.17708"]},"ddc":["000"],"author":[{"id":"d3e02e50-48a8-11ee-8f62-c108061797fa","first_name":"Dingling","last_name":"Yao","full_name":"Yao, Dingling"},{"id":"989c2a06-fb4e-11ef-a992-ab766442255b","last_name":"Huang","first_name":"Shimeng","orcid":"0000-0001-6919-821X","full_name":"Huang, Shimeng"},{"full_name":"Cadei, Riccardo","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b","last_name":"Cadei","first_name":"Riccardo"},{"last_name":"Zhang","first_name":"Kun","full_name":"Zhang, Kun"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","citation":{"ama":"Yao D, Huang S, Cadei R, Zhang K, Locatello F. The third pillar of causal analysis? A measurement perspective on causal representations. In: 39th Annual Conference on Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025.","short":"D. Yao, S. Huang, R. Cadei, K. Zhang, F. Locatello, in:, 39th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025.","apa":"Yao, D., Huang, S., Cadei, R., Zhang, K., & Locatello, F. (2025). The third pillar of causal analysis? A measurement perspective on causal representations. In 39th Annual Conference on Neural Information Processing Systems (Vol. 38). San Diego, CA, United States: Neural Information Processing Systems Foundation.","mla":"Yao, Dingling, et al. “The Third Pillar of Causal Analysis? A Measurement Perspective on Causal Representations.” 39th Annual Conference on Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025.","ista":"Yao D, Huang S, Cadei R, Zhang K, Locatello F. 2025. The third pillar of causal analysis? A measurement perspective on causal representations. 39th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38.","ieee":"D. Yao, S. Huang, R. Cadei, K. Zhang, and F. Locatello, “The third pillar of causal analysis? A measurement perspective on causal representations,” in 39th Annual Conference on Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38.","chicago":"Yao, Dingling, Shimeng Huang, Riccardo Cadei, Kun Zhang, and Francesco Locatello. “The Third Pillar of Causal Analysis? A Measurement Perspective on Causal Representations.” In 39th Annual Conference on Neural Information Processing Systems, Vol. 38. Neural Information Processing Systems Foundation, 2025."},"oa_version":"Preprint","language":[{"iso":"eng"}]},{"isi":1,"external_id":{"pmid":["41172130"],"isi":["001605927900001"]},"abstract":[{"text":"Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES.","lang":"eng"}],"department":[{"_id":"BiCh"},{"_id":"DaAl"}],"date_updated":"2026-08-07T10:29:06Z","date_published":"2025-10-31T00:00:00Z","publisher":"American Chemical Society","related_material":{"link":[{"url":"https://github.com/tuoping/alchemicalFES","relation":"software"}]},"issue":"22","oa_version":"None","language":[{"iso":"eng"}],"citation":{"short":"P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435.","ama":"Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 2025;21(22):11427-11435. doi:10.1021/acs.jctc.5c01248","apa":"Tuo, P., Zeng, Z., Chen, J., & Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01248","ieee":"P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” Journal of Chemical Theory and Computation, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025.","chicago":"Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01248.","mla":"Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:10.1021/acs.jctc.5c01248.","ista":"Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435."},"acknowledged_ssus":[{"_id":"ScienComp"}],"researchdata_availability":"no","corr_author":"1","author":[{"full_name":"Tuo, Ping","id":"6e5644c0-c180-11ed-a2da-facc4c9f4f09","last_name":"Tuo","first_name":"Ping"},{"id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng","full_name":"Zeng, Zezhu","orcid":"0000-0001-5126-4928"},{"id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","last_name":"Chen","first_name":"Jiale","full_name":"Chen, Jiale","orcid":"0000-0001-5337-5875"},{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1021/acs.jctc.5c01248","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"_id":"20704","article_type":"original","status":"public","type":"journal_article","publication_status":"published","year":"2025","supplementarymaterial":"no","quality_controlled":"1","das_tickbox":"0","page":"11427-11435","title":"Scalable multitemperature free energy sampling of classical Ising spin states","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"intvolume":" 21","volume":21,"month":"10","article_processing_charge":"No","day":"31","pmid":1,"date_created":"2025-11-30T23:02:06Z","acknowledgement":"P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai.","ec_funded":1,"scopus_import":"1","OA_type":"closed access","publication":"Journal of Chemical Theory and Computation"},{"publisher":"Copernicus Publications","issue":"6","date_published":"2025-06-17T00:00:00Z","abstract":[{"lang":"eng","text":"The recent surge in reservoir construction has increased global surface water storage, with Mainland\r\nSoutheast Asia (MSEA) being a significant hotspot. Such infrastructural evolution demands updates in water\r\nmanagement strategies and hydrological models. However, information on actual reservoir storage is hard to\r\nacquire, especially for transboundary river basins. To date, no high-resolution spatiotemporal dataset on absolute\r\nstorage time series is available for reservoirs in MSEA. To address this gap, we present (1) a comprehensive openaccess database of absolute storage time series (sub-monthly) for 186 reservoirs (larger than 0.1 km3) in MSEA\r\nspanning the period 1985–2023 and (2) an analysis of the reservoir storage dynamics. This dataset is derived\r\nfrom remote sensing observations, integrating satellite-based water surface area extraction from high-resolution\r\n(30 m) images and area–elevation–storage (A–E–S) relationships to estimate reservoir level and storage dynamics. The MSEA database includes static (area–elevation–storage curves, water frequency, and reservoir extent)\r\nand dynamic (area, water level, and absolute storage time series) components for each reservoir. The 186 reservoirs collectively store around 175 km3 of water, with a minimum of 140 km3 and a maximum of 210 km3. They\r\ncover an average area of 8700 km2, ranging from a minimum of 6500 km2 to a maximum of 10 000 km2. We show that the combined average reservoir storage increased from 70 to 160 km3 (+130 %) from 2008 to 2017, primarily contributed by reservoirs in the Irrawaddy, Red, Upper Mekong, and Lower Mekong basins. Our in situ validation provides a good match between estimated storage and in situ observations, with 50 % of the validation sites (10 out of 20) showing an R2 > 0.7 and an average nRMSE < 14 %. The indirect validation (based on altimetry-converted storage) shows even better results, with an R2 > 0.7 and an average nRMSE < 12 % for 70 % (14 out of 20) of the reservoirs. Furthermore, the analysis of the 2019–2020 drought event in the MSEA region reveals that nearly 30 %–40 % of the region experienced more than 5 months of drought, with the most significant impact on reservoirs in Cambodia and Thailand. As a result, storage departures ranged by up to −40 % in some reservoirs, highlighting significant impacts on water availability. Overall, this analysis demonstrates the potential of the inferred storage time series for assessing real-life water-related problems in Mainland Southeast Asia, with the possibility of applying the method to estimate reservoir storage time series in other parts of the world. The reservoir storage database in Mainland Southeast Asia (MSEA-Res database) and the associated Python code are publicly available on Zenodo at https://doi.org/10.5281/zenodo.14844580 (Mahto et al., 2025)."}],"date_updated":"2026-08-07T10:54:05Z","author":[{"last_name":"Mahto","first_name":"Shanti Shwarup","full_name":"Mahto, Shanti Shwarup"},{"full_name":"Fatichi, Simone","first_name":"Simone","last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6"},{"full_name":"Galelli, Stefano","last_name":"Galelli","first_name":"Stefano"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","extern":"1","citation":{"apa":"Mahto, S. S., Fatichi, S., & Galelli, S. (2025). A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science Data. Copernicus Publications. https://doi.org/10.5194/essd-17-2693-2025","ama":"Mahto SS, Fatichi S, Galelli S. A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science Data. 2025;17(6):2693-2712. doi:10.5194/essd-17-2693-2025","short":"S.S. Mahto, S. Fatichi, S. Galelli, Earth System Science Data 17 (2025) 2693–2712.","chicago":"Mahto, Shanti Shwarup, Simone Fatichi, and Stefano Galelli. “A 1985–2023 Time Series Dataset of Absolute Reservoir Storage in Mainland Southeast Asia (MSEA-Res).” Earth System Science Data. Copernicus Publications, 2025. https://doi.org/10.5194/essd-17-2693-2025.","ieee":"S. S. Mahto, S. Fatichi, and S. Galelli, “A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res),” Earth System Science Data, vol. 17, no. 6. Copernicus Publications, pp. 2693–2712, 2025.","mla":"Mahto, Shanti Shwarup, et al. “A 1985–2023 Time Series Dataset of Absolute Reservoir Storage in Mainland Southeast Asia (MSEA-Res).” Earth System Science Data, vol. 17, no. 6, Copernicus Publications, 2025, pp. 2693–712, doi:10.5194/essd-17-2693-2025.","ista":"Mahto SS, Fatichi S, Galelli S. 2025. A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res). Earth System Science Data. 17(6), 2693–2712."},"oa_version":"Published Version","language":[{"iso":"eng"}],"das_tickbox":"1","type":"journal_article","status":"public","year":"2025","publication_status":"published","quality_controlled":"1","oa":1,"article_type":"original","publication_identifier":{"eissn":["1866-3516"],"issn":["1866-3508"]},"doi":"10.5194/essd-17-2693-2025","_id":"22568","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/essd-17-2693-2025"}],"publication":"Earth System Science Data","day":"17","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-07-27T12:30:24Z","OA_place":"publisher","scopus_import":"1","DOAJ_listed":"1","OA_type":"gold","volume":17,"month":"06","article_processing_charge":"No","page":"2693-2712","title":"A 1985–2023 time series dataset of absolute reservoir storage in Mainland Southeast Asia (MSEA-Res)","intvolume":" 17"}]