Search Results for author: Gary D. Bader

Found 6 papers, 4 papers with code

Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning

1 code implementation2 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.

Benchmarking Contrastive Learning +1

MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition

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.

Representation Learning Segmentation

A sequence-to-sequence approach for document-level relation extraction

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.

coreference-resolution Document-level Relation Extraction +3

End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models

1 code implementation20 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.

Language Modelling named-entity-recognition +5

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