SpheroScan: a user-friendly deep learning tool for spheroid image analysis. Gigascience, (12)Oxford University Press (OUP), December 2022. [PUMA: 3D image deep R-CNN; learning; high-throughput analysis; segmentation spheroids; Image screening; Mask]
Deep learning improves pancreatic cancer diagnosis using RNA-based variants. Cancers (Basel), (13)11:2654, MDPI AG, May 2021. [PUMA: cancer; pancreatitis; study transcriptome-wide deep learning; topic_lifescience association pancreatic chronic]
Deep learning identifies inflamed fat as a risk factor for lymph node metastasis in early colorectal cancer. J. Pathol., (256)3:269--281, Wiley, March 2022. [PUMA: metastasis; inflamed intelligence; deep learning; bowel predictive LNM adipose pT2 pT1 digital biomarker; cancer; artificial AI; pathology; colorectal and prediction new tissue; early]
Introduction to the BioChemical Library (BCL): An application-based open-source toolkit for integrated cheminformatics and machine learning in computer-aided drug discovery. Front. Pharmacol., (13):833099, Frontiers Media SA, February 2022. [PUMA: discovery; library; cheminformatics; deep network; neural biochemical open-source BCL; drug design; topic_lifescience QSAR;]
Leptin deficiency-caused behavioral change - A comparative analysis using EthoVision and DeepLabCut. Front. Neurosci., (17):1052079, March 2023. [PUMA: deep learning; behavioral analysis; DeepLabCut; EthoVision; obesity]
Benchmarking weakly-supervised deep learning pipelines for whole slide classification in computational pathology. Med. Image Anal., (79)102474:102474, Elsevier BV, July 2022. [PUMA: Convolutional Artificial intelligence; Multiple-Instance deep neural networks; learning Weakly-supervised Learning; transformers; pathology; Vision Computational]
Uncertainty estimation in medical image classification: Systematic review. JMIR Med. Inform., (10)8:e36427, August 2022. [PUMA: image out-of-distribution medical detection; deep learning; imaging; classification; calibration; network uncertainty estimation topic_lifescience]
A multitask deep-learning method for predicting membrane associations and secondary structures of proteins. J. Proteome Res., (20)8:4089--4100, American Chemical Society (ACS), August 2021. [PUMA: multitask convolutional prediction; memory transmembrane deep learning; neural networks; topology long short-term structure secondary topic_lifescience prediction]
Memory-efficient deep learning on a SpiNNaker 2 prototype. Front. Neurosci., (12):840, Frontiers Media SA, November 2018. [PUMA: footprint; energy parallelism; memory pruning; SpiNNaker; efficient deep hardware; sparsity rewiring;]
Predicting mutational status of driver and suppressor genes directly from histopathology with Deep Learning: A systematic study across 23 solid tumor types. Front. Genet., (12):806386, 2021. [PUMA: genetic artificail (AI); pathway; deep learning; cancer genes; pathway TCGA; intelligence]