no code implementations • 10 Aug 2023 • Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Haofeng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F. Greenwald, David Van Valen, Erin Weisbart, Beth A. Cimini, Trevor Cheung, Oscar Brück, Gary D. Bader, Bo wang
This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.
1 code implementation • 2 Jun 2023 • Ronald Xie, Kuan Pang, Sai W. Chung, Catia T. Perciani, Sonya A. MacParland, Bo wang, Gary D. Bader
Our results demonstrate the potential of BLEEP to provide insights into the molecular mechanisms underlying tissue architecture, with important implications in diagnosis and research of various diseases.
no code implementations • 24 May 2023 • Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D. Bader, Sylvie Baier, David B. Blumenthal, Jing Chen, Maria L. Elkjaer, Carlos Garcia-Hernandez, Mohamed Helmy, Markus Hoffmann, Igor Jurisica, Max Kotlyar, Olga Lazareva, Hagai Levi, Markus List, Sebastian Lobentanzer, Joseph Loscalzo, Noel Malod-Dognin, Quirin Manz, Julian Matschinske, Miles Mee, Mhaned Oubounyt, Alexander R. Pico, Rudolf T. Pillich, Julian M. Poschenrieder, Dexter Pratt, Nataša Pržulj, Sepideh Sadegh, Julio Saez-Rodriguez, Suryadipto Sarkar, Gideon Shaked, Ron Shamir, Nico Trummer, Ugur Turhan, Ruisheng Wang, Olga Zolotareva, Jan Baumbach
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood.
1 code implementation • CVPR 2023 • Ronald Xie, Kuan Pang, Gary D. Bader, Bo wang
Complete manual segmentation is unfeasible for large datasets, and while supervised methods have been proposed to automate segmentation, they often rely on manually generated ground truths which are especially challenging and time consuming to generate in biology due to the requirement of domain expertise.
2 code implementations • BioNLP (ACL) 2022 • John Giorgi, Gary D. Bader, Bo wang
In this paper, we develop a sequence-to-sequence approach, seq2rel, that can learn the subtasks of DocRE (entity extraction, coreference resolution and relation extraction) end-to-end, replacing a pipeline of task-specific components.
Ranked #1 on Joint Entity and Relation Extraction on CDR
coreference-resolution Document-level Relation Extraction +3
1 code implementation • 20 Dec 2019 • John Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo wang
In this paper, we propose a neural, end-to-end model for jointly extracting entities and their relations which does not rely on external NLP tools and which integrates a large, pre-trained language model.