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1,369 results on '"Sahin, Ugur"'

1. Expression of the tumor antigens NY-ESO-1, tyrosinase, MAGE-A3, and TPTE in pediatric and adult melanoma: a retrospective case control study

Author

Forchhammer, Stephan, Pop, Oltin Tiberiu, Hahn, Matthias, Aebischer, Valentin, Seitz, Christian M., Schroeder, Christopher, Liebmann, Alexandra, Abele, Michael, Wild, Hannah, Bien, Ewa, Kunc, Michal, Schneider, Dominik T., Cuk, Katarina, Büttel, Isabel, Flemmig, Carina, Peters, Magdalena, Laible, Mark, Brück, Patrick, Türeci, Özlem, Sahin, Ugur, Flatz, Lukas, and Brecht, Ines B.

Published
2024
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2. Enhancing Multimodal Compositional Reasoning of Visual Language Models with Generative Negative Mining

Author

Sahin, Ugur, Li, Hang, Khan, Qadeer, Cremers, Daniel, and Tresp, Volker

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Contemporary large-scale visual language models (VLMs) exhibit strong representation capacities, making them ubiquitous for enhancing image and text understanding tasks. They are often trained in a contrastive manner on a large and diverse corpus of images and corresponding text captions scraped from the internet. Despite this, VLMs often struggle with compositional reasoning tasks which require a fine-grained understanding of the complex interactions of objects and their attributes. This failure can be attributed to two main factors: 1) Contrastive approaches have traditionally focused on mining negative examples from existing datasets. However, the mined negative examples might not be difficult for the model to discriminate from the positive. An alternative to mining would be negative sample generation 2) But existing generative approaches primarily focus on generating hard negative texts associated with a given image. Mining in the other direction, i.e., generating negative image samples associated with a given text has been ignored. To overcome both these limitations, we propose a framework that not only mines in both directions but also generates challenging negative samples in both modalities, i.e., images and texts. Leveraging these generative hard negative samples, we significantly enhance VLMs' performance in tasks involving multimodal compositional reasoning. Our code and dataset are released at https://ugorsahin.github.io/enhancing-multimodal-compositional-reasoning-of-vlm.html., Comment: Accepted to WACV

Published
2023

4. Introducing Model Inversion Attacks on Automatic Speaker Recognition

Author

Pizzi, Karla, Boenisch, Franziska, Sahin, Ugur, and Böttinger, Konstantin

Subjects
Computer Science - Sound, Computer Science - Cryptography and Security, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract

Model inversion (MI) attacks allow to reconstruct average per-class representations of a machine learning (ML) model's training data. It has been shown that in scenarios where each class corresponds to a different individual, such as face classifiers, this represents a severe privacy risk. In this work, we explore a new application for MI: the extraction of speakers' voices from a speaker recognition system. We present an approach to (1) reconstruct audio samples from a trained ML model and (2) extract intermediate voice feature representations which provide valuable insights into the speakers' biometrics. Therefore, we propose an extension of MI attacks which we call sliding model inversion. Our sliding MI extends standard MI by iteratively inverting overlapping chunks of the audio samples and thereby leveraging the sequential properties of audio data for enhanced inversion performance. We show that one can use the inverted audio data to generate spoofed audio samples to impersonate a speaker, and execute voice-protected commands for highly secured systems on their behalf. To the best of our knowledge, our work is the first one extending MI attacks to audio data, and our results highlight the security risks resulting from the extraction of the biometric data in that setup., Comment: for associated pdf, see https://www.isca-speech.org/archive/pdfs/spsc_2022/pizzi22_spsc.pdf

Published
2023
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5. Image Compression With Learned Lifting-Based DWT and Learned Tree-Based Entropy Models

Author

Sahin, Ugur Berk and Kamisli, Fatih

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Multimedia
Abstract

This paper explores learned image compression based on traditional and learned discrete wavelet transform (DWT) architectures and learned entropy models for coding DWT subband coefficients. A learned DWT is obtained through the lifting scheme with learned nonlinear predict and update filters. Several learned entropy models are proposed to exploit inter and intra-DWT subband coefficient dependencies, akin to traditional EZW, SPIHT, or EBCOT algorithms. Experimental results show that when the proposed learned entropy models are combined with traditional wavelet filters, such as the CDF 9/7 filters, compression performance that far exceeds that of JPEG2000 can be achieved. When the learned entropy models are combined with the learned DWT, compression performance increases further. The computations in the learned DWT and all entropy models, except one, can be simply parallelized, and the systems provide practical encoding and decoding times on GPUs., Comment: 11 pages, 17 figures

Published
2022

10. Prediction of response to neoadjuvant chemotherapy by MammaTyper® across breast cancer subtypes: A retrospective cross-sectional study

Author

Schettini, Francesco, Saracchini, Silvana, Bassini, Anna, Marus, Wally, Corsetti, Serena, Specogna, Ilaria, Bertola, Manuela, Micheli, Elvia, Wirtz, Ralph M., Laible, Mark, Şahin, Uğur, Strina, Carla, Milani, Manuela, Aguggini, Sergio, Tancredi, Richard, Fiorio, Elena, Sulfaro, Sandro, and Generali, Daniele

Published
2024
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12. More than a Virus: How COVID 19 Infected Education in Turkey?

Author

Akbulut, Melisa, Sahin, Ugur, and Esen, Ali Can

Abstract

Purpose: We aim with this report to provide information on how the Covid-19 pandemic affected education and citizenship education in Turkey. Design: The report is based on literature review, the analysis of social media, and the observations of the authors. We provide a general framework of Turkish education after the pandemic using sources such as official statements from government offices; social media entries were analyzed to provide different perspectives. Finally, observations of the authors based on their experiences with distance learning were included in the report. Findings: We argue that despite the efforts of the state, there are still problems in the distance learning process, mainly relating to the access to online classes and the very limited room given to Covid-19 as a topic in social studies courses. In addition, we find that social media have played a significant role in increasing citizen participation as a consequence of the pandemic.

Published
2020

14. Expression of the membrane tetraspanin claudin 18 on cancer cells promotes T lymphocyte infiltration and antitumor immunity in pancreatic cancer

Author

De Sanctis, Francesco, Dusi, Silvia, Caligola, Simone, Anselmi, Cristina, Petrova, Varvara, Rossi, Barbara, Angelini, Gabriele, Erdeljan, Michael, Wöll, Stefan, Schlitter, Anna Melissa, Metzler, Thomas, Steiger, Katja, Borok, Zea, Bailey, Peter, Bauer, Aline, Halin, Cornelia, Boschi, Federico, Giugno, Rosalba, Canè, Stefania, Lawlor, Rita, Corbo, Vincenzo, Scarpa, Aldo, Constantin, Gabriela, Ugel, Stefano, Vascotto, Fulvia, Sahin, Ugur, Türeci, Özlem, and Bronte, Vincenzo

Published
2024
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16. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

Author

Rojas, Luis A., Sethna, Zachary, Soares, Kevin C., Olcese, Cristina, Pang, Nan, Patterson, Erin, Lihm, Jayon, Ceglia, Nicholas, Guasp, Pablo, Chu, Alexander, Yu, Rebecca, Chandra, Adrienne Kaya, Waters, Theresa, Ruan, Jennifer, Amisaki, Masataka, Zebboudj, Abderezak, Odgerel, Zagaa, Payne, George, Derhovanessian, Evelyna, Müller, Felicitas, Rhee, Ina, Yadav, Mahesh, Dobrin, Anton, Sadelain, Michel, Łuksza, Marta, Cohen, Noah, Tang, Laura, Basturk, Olca, Gönen, Mithat, Katz, Seth, Do, Richard Kinh, Epstein, Andrew S., Momtaz, Parisa, Park, Wungki, Sugarman, Ryan, Varghese, Anna M., Won, Elizabeth, Desai, Avni, Wei, Alice C., D’Angelica, Michael I., Kingham, T. Peter, Mellman, Ira, Merghoub, Taha, Wolchok, Jedd D., Sahin, Ugur, Türeci, Özlem, Greenbaum, Benjamin D., Jarnagin, William R., Drebin, Jeffrey, O’Reilly, Eileen M., and Balachandran, Vinod P.

Published
2023
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20. Designing a Prospective COVID-19 Therapeutic with Reinforcement Learning

Author

Skwark, Marcin J., Carranza, Nicolás López, Pierrot, Thomas, Phillips, Joe, Said, Slim, Laterre, Alexandre, Kerkeni, Amine, Şahin, Uğur, and Beguir, Karim

Subjects
Quantitative Biology - Biomolecules, Computer Science - Machine Learning
Abstract

The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from human cells. Here we formulate a novel protein design framework as a reinforcement learning problem. We generate new designs efficiently through the combination of a fast, biologically-grounded reward function and sequential action-space formulation. The use of Policy Gradients reduces the compute budget needed to reach consistent, high-quality designs by at least an order of magnitude compared to standard methods. Complexes designed by this method have been validated by molecular dynamics simulations, confirming their increased stability. This suggests that combining leading protein design methods with modern deep reinforcement learning is a viable path for discovering a Covid-19 cure and may accelerate design of peptide-based therapeutics for other diseases.

Published
2020

24. Progressive loss of conserved spike protein neutralizing antibody sites in Omicron sublineages is balanced by preserved T cell immunity

Author

Muik, Alexander, Lui, Bonny Gaby, Quandt, Jasmin, Diao, Huitian, Fu, Yunguan, Bacher, Maren, Gordon, Jessica, Toker, Aras, Grosser, Jessica, Ozhelvaci, Orkun, Grikscheit, Katharina, Hoehl, Sebastian, Kohmer, Niko, Lustig, Yaniv, Regev-Yochay, Gili, Ciesek, Sandra, Beguir, Karim, Poran, Asaf, Vogler, Isabel, Türeci, Özlem, and Sahin, Ugur

Published
2023
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26. The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection

Author

Arieta, Christina M., Xie, Yushu Joy, Rothenberg, Daniel A., Diao, Huitian, Harjanto, Dewi, Meda, Shirisha, Marquart, Krisann, Koenitzer, Byron, Sciuto, Tracey E., Lobo, Alexander, Zuiani, Adam, Krumm, Stefanie A., Cadima Couto, Carla Iris, Hein, Stephanie, Heinen, André P., Ziegenhals, Thomas, Liu-Lupo, Yunpeng, Vogel, Annette B., Srouji, John R., Fesser, Stephanie, Thanki, Kaushik, Walzer, Kerstin, Addona, Theresa A., Türeci, Özlem, Şahin, Uğur, Gaynor, Richard B., and Poran, Asaf

Published
2023
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31. Hybrid core-shell particles for mRNA systemic delivery

Author

Andretto, Valentina, Repellin, Mathieu, Pujol, Marine, Almouazen, Eyad, Sidi-Boumedine, Jacqueline, Granjon, Thierry, Zhang, Heyang, Remaut, Katrien, Jordheim, Lars Petter, Briançon, Stéphanie, Keil, Isabell Sofia, Vascotto, Fulvia, Walzer, Kerstin C., Sahin, Ugur, Haas, Heinrich, Kryza, David, and Lollo, Giovanna

Published
2023
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34. Preliminary results correlating post-operative ctDNA status with disease-free survival in patients with stage II (high risk)/III colorectal cancer in the BNT000-001 epidemiology study.

Author

Reinacher-Schick, Anke C., primary, Reboredo Lopez, Margarita, additional, Alonso-Orduña, Vicente, additional, Páez Lopez-Bravo, David, additional, Vergauwe, Philippe, additional, Tannapfel, Andrea, additional, Bortolini Silveira, Amanda, additional, Schlombs, Kornelia, additional, Young, Philip, additional, He, Ying, additional, Henn, Hilja, additional, Manning, Luisa, additional, Preußner, Liane, additional, Mueller, Felicitas, additional, Sahin, Ugur, additional, and Türeci, Özlem, additional

Published
2024
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35. Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates

Author

Lang, Franziska, primary, Sorn, Patrick, additional, Suchan, Martin, additional, Henrich, Alina, additional, Albrecht, Christian, additional, Köhl, Nina, additional, Beicht, Aline, additional, Riesgo-Ferreiro, Pablo, additional, Holtsträter, Christoph, additional, Schrörs, Barbara, additional, Weber, David, additional, Löwer, Martin, additional, Sahin, Ugur, additional, and Ibn-Salem, Jonas, additional

Published
2024
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36. Immunogenicity and safety of BNT162b2 mRNA vaccine in Chinese adults: A phase 2 randomised clinical trial

Author

Hui, Ai-Min, Li, Jingxin, Zhu, Li, Tang, Rong, Ye, Huayue, Lin, Mei, Ge, Lei, Wang, Xiyuan, Peng, Fuzhong, Wu, Zhenggang, Guo, Xiling, Shi, Yunfeng, Pan, Hongxing, Zhu, Jiahong, Song, Zhizhou, Qiu, Jingjun, Wang, Wei, Zheng, Jianfei, Ozhelvaci, Orkun, Shpyro, Svetlana, Bushway, Meghan, Derhovanessian, Evelyna, Kühnle, Marie-Cristine, Luxemburger, Ulrich, Muik, Alexander, Shishkova, Yoana, Khondker, Zakaria, Hu, Simin, Lagkadinou, Eleni, Şahin, Uğur, Türeci, Özlem, and Zhu, Fengcai

Published
2022
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37. Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma* [S]

Author

Shraibman, Bracha, Barnea, Eilon, Kadosh, Dganit Melamed, Haimovich, Yael, Slobodin, Gleb, Rosner, Itzhak, López-Larrea, Carlos, Hilf, Norbert, Kuttruff, Sabrina, Song, Colette, Britten, Cedrik, Castle, John, Kreiter, Sebastian, Frenzel, Katrin, Tatagiba, Marcos, Tabatabai, Ghazaleh, Dietrich, Pierre-Yves, Dutoit, Valérie, Wick, Wolfgang, Platten, Michael, Winkler, Frank, von Deimling, Andreas, Kroep, Judith, Sahuquillo, Juan, Martinez-Ricarte, Francisco, Rodon, Jordi, Lassen, Ulrik, Ottensmeier, Christian, van der Burg, Sjoerd H, Thor Straten, Per, Poulsen, Hans Skovgaard, Ponsati, Berta, Okada, Hideho, Rammensee, Hans-Georg, Sahin, Ugur, Singh, Harpreet, and Admon, Arie

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Clinical Research, Rare Diseases, Brain Disorders, Neurosciences, Brain Cancer, Cancer, Good Health and Well Being, Alleles, Antigens, Neoplasm, Biomarkers, Tumor, Brain Neoplasms, Glioblastoma, Histocompatibility Antigens Class I, Humans, Peptides, Proteome, CTA, Cancer Biomarker(s), Cancer Therapeutics, HLA, Immunoaffinity, Immunotherapy, MHC, Peptidomics, Plasma or Serum Analysis, Biochemistry & Molecular Biology
Abstract

Glioblastoma multiforme (GBM) is the most aggressive brain tumor with poor prognosis to most patients. Immunotherapy of GBM is a potentially beneficial treatment option, whose optimal implementation may depend on familiarity with tumor specific antigens, presented as HLA peptides by the GBM cells. Further, early detection of GBM, such as by a routine blood test, may improve survival, even with the current treatment modalities. This study includes large-scale analyses of the HLA peptidome (immunopeptidome) of the plasma-soluble HLA molecules (sHLA) of 142 plasma samples, and the membranal HLA of GBM tumors of 10 of these patients' tumor samples. Tumor samples were fresh-frozen immediately after surgery and the plasma samples were collected before, and at multiple visits after surgery. In total, this HLA peptidome analysis involved 52 different HLA allotypes and resulted in the identification of more than 35,000 different HLA peptides. Strong correlations were observed in the signal intensities and in the repertoires of identified peptides between the tumors and plasma-soluble HLA peptidomes of the individual patients, whereas low correlations were observed between these HLA peptidomes and the tumors' proteomes. HLA peptides derived from Cancer/Testis Antigens (CTAs) were selected based on their presence among the HLA peptidomes of the patients and absence of expression of their source genes from any healthy and essential human tissues, except from immune-privileged sites. Additionally, peptides were selected as potential biomarkers if their levels in the plasma-sHLA peptidome were significantly reduced after the removal of tumor mass. The CTAs identified among the analyzed HLA peptidomes provide new opportunities for personalized immunotherapy and for early diagnosis of GBM.

Published
2019

45. SegmentNT: annotating the genome at single-nucleotide resolution with DNA foundation models

Author

de Almeida, Bernardo P, primary, Dalla-Torre, Hugo, additional, Richard, Guillaume, additional, Blum, Christopher, additional, Hexemer, Lorenz, additional, Gelard, Maxence, additional, Mendoza-Revilla, Javier, additional, Pandey, Priyanka, additional, Laurent, Stefan, additional, Lopez, Marie, additional, Laterre, Alexandre, additional, Lang, Maren, additional, Sahin, Ugur, additional, Beguir, Karim, additional, and Pierrot, Thomas, additional

Published
2024
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47. BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans

Author

Sahin, Ugur, Muik, Alexander, Vogler, Isabel, Derhovanessian, Evelyna, Kranz, Lena M., Vormehr, Mathias, Quandt, Jasmin, Bidmon, Nicole, Ulges, Alexander, Baum, Alina, Pascal, Kristen E., Maurus, Daniel, Brachtendorf, Sebastian, Lorks, Verena, Sikorski, Julian, Koch, Peter, and Hilker, Rolf

Subjects
T cells -- Health aspects, Viral antibodies -- Health aspects, Antibodies -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

BNT162b2, a nucleoside-modified mRNA formulated in lipid nanoparticles that encodes the SARS-CoV-2 spike glycoprotein (S) stabilized in its prefusion conformation, has demonstrated 95% efficacy in preventing COVID-19.sup.1. Here we extend a previous phase-I/II trial report.sup.2 by presenting data on the immune response induced by BNT162b2 prime-boost vaccination from an additional phase-I/II trial in healthy adults (18-55 years old). BNT162b2 elicited strong antibody responses: at one week after the boost, SARS-CoV-2 serum geometric mean 50% neutralizing titres were up to 3.3-fold above those observed in samples from individuals who had recovered from COVID-19. Sera elicited by BNT162b2 neutralized 22 pseudoviruses bearing the S of different SARS-CoV-2 variants. Most participants had a strong response of IFN[gamma].sup.+ or IL-2.sup.+ CD8.sup.+ and CD4.sup.+ T helper type 1 cells, which was detectable throughout the full observation period of nine weeks following the boost. Using peptide-MHC multimer technology, we identified several BNT162b2-induced epitopes that were presented by frequent MHC alleles and conserved in mutant strains. One week after the boost, epitope-specific CD8.sup.+ T cells of the early-differentiated effector-memory phenotype comprised 0.02-2.92% of total circulating CD8.sup.+ T cells and were detectable (0.01-0.28%) eight weeks later. In summary, BNT162b2 elicits an adaptive humoral and poly-specific cellular immune response against epitopes that are conserved in a broad range of variants, at well-tolerated doses. In a phase-I/II trial in healthy adults, the BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells against SARS-CoV-2 epitopes that are conserved in a wide range of currently circulating variants., Author(s): Ugur Sahin [sup.1] [sup.2] , Alexander Muik [sup.1] , Isabel Vogler [sup.1] , Evelyna Derhovanessian [sup.1] , Lena M. Kranz [sup.1] , Mathias Vormehr [sup.1] , Jasmin Quandt [sup.1] [...]

Published
2021
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48. Medicine, Technology and the End of Cancer

Author

Sahin, Ugur and Türeci, ÈûZlem

Subjects
Cancer, Cancer vaccines, General interest
Abstract

Byline: Ugur Sahin and Èûzlem Türeci Artificial intelligence may be the key to unlocking personalized cancer vaccines. This personal reflection is part of a series called Turning Points, in which [...]

Published
2024

49. Medicine, Technology and the End of Cancer

Author

Sahin, Ugur and Türeci, Özlem

Subjects
Cancer -- Care and treatment, Cancer vaccines, News, opinion and commentary
Abstract

Artificial intelligence may be the key to unlocking personalized cancer vaccines. https://www.nytimes.com/column/turning-points-2024 https://www.nytimes.com/column/turning-points-2024 Turning Point:https://www.nytimes.com/2023/07/06/health/alzheimers-leqembi-medicare.html Decades ago, as rookie physicians in the cancer ward of a German university hospital, we [...]

Published
2023

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