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1680 Publications visible to you, out of a total of 1680
Enhanced sampling simulations and machine learning to address infectious diseases

Abstract

Not specified

Author: Matheus Ferraz

Date Published: 2023

Publication Type: Doctoral Thesis

Shot noise reduction in radiographic and tomographic multi-channel imaging with self-supervised deep learning

Abstract (Expand)

Shot noise is a critical issue in radiographic and tomographic imaging, especially when additional constraints lead to a significant reduction of the signal-to-noise ratio. This paper presents a method …. This paper presents a method for improving the quality of noisy multi-channel imaging datasets, such as data from time or energy-resolved imaging, by exploiting structural similarities between channels. To achieve that, we broaden the application domain of the Noise2Noise self-supervised denoising approach. The method draws pairs of samples from a data distribution with identical signals but uncorrelated noise. It is applicable to multi-channel datasets if adjacent channels provide images with similar enough information but independent noise. We demonstrate the applicability and performance of the method via three case studies, namely spectroscopic X-ray tomography, energy-dispersive neutron tomography, and in vivo X-ray cine-radiography.

Authors: Yaroslav Zharov, Evelina Ametova, Rebecca Spiecker, Tilo Baumbach, Genoveva Burca, Vincent Heuveline

Date Published: 2023

Publication Type: Journal

Regression diagnostics meets forecast evaluation: Conditional calibration, reliability diagrams, and coefficient of determination

Abstract

Not specified

Authors: Tilmann Gneiting, Johannes Resin

Date Published: 2023

Publication Type: Journal

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Abstract (Expand)

Abstract The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host …ribing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.

Authors: Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Martina Kutmon, Marc E. Gillespie, Akira Funahashi, Marcio Luis Acencio, Ahmed Hemedan, Michael Aichem, Karsten Klein, Tobias Czauderna, Felicia Burtscher, Takahiro G. Yamada, Yusuke Hiki, Noriko F. Hiroi, Finterly Hu, Nhung Pham, Friederike Ehrhart, Egon L. Willighagen, Alberto Valdeolivas, Aurelien Dugourd, Francesco Messina, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Sylvain Soliman, Sara Sadat Aghamiri, Bhanwar Lal Puniya, Aurélien Naldi, Tomáš Helikar, Vidisha Singh, Marco Fariñas Fernández, Viviam Bermudez, Eirini Tsirvouli, Arnau Montagud, Vincent Noël, Miguel Ponce de Leon, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Augustin Luna, Janet Pinero, Laura I. Furlong, Irina Balaur, Adrien Rougny, Yohan Jarosz, Rupert W. Overall, Robert Phair, Livia Perfetto, Lisa Matthews, Devasahayam Arokia Balaya Rex, Marija Orlic-Milacic, Monraz Gomez Luis Cristobal, Bertrand De Meulder, Jean Marie Ravel, Bijay Jassal, Venkata Satagopam, Guanming Wu, Martin Golebiewski, Piotr Gawron, Laurence Calzone, Jacques S. Beckmann, Chris T. Evelo, Peter D’Eustachio, Falk Schreiber, Julio Saez-Rodriguez, Joaquin Dopazo, Martin Kuiper, Alfonso Valencia, Olaf Wolkenhauer, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider

Date Published: 19th Dec 2022

Publication Type: Misc

EU-wide mapping report on good practice examples for integrating phenotype and large scale data

Abstract (Expand)

The report focusses on national and EU-case studies (good practice examples) for integrating patient derived data, such as phenotype and large scale data, for in silico modelling in personalized medicine. …Not specified

Authors: Martin Golebiewski, Marc Kirschner, Sylvia Krobitsch, EU-STANDS4PM consortium

Date Published: 15th Dec 2022

Publication Type: Tech report

Constrained density matching and modeling for cross-lingual alignment of contextualized representations

Abstract (Expand)

Multilingual representations pre-trained with monolingual data exhibit considerably unequal task performances across languages. Previous studies address this challenge with resource-intensive contextualized … alignment, which assumes the availability of large parallel data, thereby leaving under-represented language communities behind. In this work, we attribute the data hungriness of previous alignment techniques to two limitations: (i) the inability to sufficiently leverage data and (ii) these techniques are not trained properly. To address these issues, we introduce supervised and unsupervised density-based approaches named Real-NVP and GAN-Real-NVP, driven by Normalizing Flow, to perform alignment, both dissecting the alignment of multilingual subspaces into density matching and density modeling. We complement these approaches with our validation criteria in order to guide the training process. Our experiments encompass 16 alignments, including our approaches, evaluated across 6 language pairs, synthetic data and 5 NLP tasks. We demonstrate the effectiveness of our approaches in the scenarios of limited and no parallel data. First, our supervised approach trained on 20k parallel data (sentences) mostly surpasses Joint-Align and InfoXLM trained on over 100k parallel sentences. Second, parallel data can be removed without sacrificing performance when integrating our unsupervised approach in our bootstrapping procedure, which is theoretically motivated to enforce equality of multilingual subspaces. Moreover, we demonstrate the advantages of validation criteria over validation data for guiding supervised training.

Authors: Wei Zhao, Steffen Eger

Date Published: 12th Dec 2022

Publication Type: InProceedings

Computational Investigation of the Structure Kinetics Relationship of Small-Molecule Compounds Binding the Histamine-1-Receptor

Abstract

Not specified

Author: Melanie Kaeser

Date Published: 9th Dec 2022

Publication Type: Master's Thesis

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