scholarly journals Scellseg: a style-aware cell instance segmentation tool with pre-training and contrastive fine-tuning

2021 ◽  
Author(s):  
Dejin Xun ◽  
Deheng Chen ◽  
Yitian Zhou ◽  
Volker M. Lauschke ◽  
Rui Wang ◽  
...  

Deep learning-based cell segmentation is increasingly utilized in cell biology and molecular pathology, due to massive accumulation of diverse large-scale datasets and excellent performance in cell representation. However, the development of specialized algorithms has long been hampered by a paucity of annotated training data, whereas the performance of generalist algorithm was limited without experiment-specific calibration. Here, we present a deep learning-based tool called Scellseg consisted of novel pre-trained network architecture and contrastive fine-tuning strategy. In comparison to four commonly used algorithms, Scellseg outperformed in average precision on three diverse datasets with no need for dataset-specific configuration. Interestingly, we found that eight images are sufficient for model tuning to achieve satisfied performance based on a shot data scale experiment. We also developed a graphical user interface integrated with functions of annotation, fine-tuning and inference, that allows biologists to easily specialize their own segmentation model and analyze data at the single-cell level.

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Tao Chen ◽  
Mingfen Wu ◽  
Hexi Li

Abstract The automatic extraction of meaningful relations from biomedical literature or clinical records is crucial in various biomedical applications. Most of the current deep learning approaches for medical relation extraction require large-scale training data to prevent overfitting of the training model. We propose using a pre-trained model and a fine-tuning technique to improve these approaches without additional time-consuming human labeling. Firstly, we show the architecture of Bidirectional Encoder Representations from Transformers (BERT), an approach for pre-training a model on large-scale unstructured text. We then combine BERT with a one-dimensional convolutional neural network (1d-CNN) to fine-tune the pre-trained model for relation extraction. Extensive experiments on three datasets, namely the BioCreative V chemical disease relation corpus, traditional Chinese medicine literature corpus and i2b2 2012 temporal relation challenge corpus, show that the proposed approach achieves state-of-the-art results (giving a relative improvement of 22.2, 7.77, and 38.5% in F1 score, respectively, compared with a traditional 1d-CNN classifier). The source code is available at https://github.com/chentao1999/MedicalRelationExtraction.


Author(s):  
Tony Lindeberg

AbstractThis paper presents a hybrid approach between scale-space theory and deep learning, where a deep learning architecture is constructed by coupling parameterized scale-space operations in cascade. By sharing the learnt parameters between multiple scale channels, and by using the transformation properties of the scale-space primitives under scaling transformations, the resulting network becomes provably scale covariant. By in addition performing max pooling over the multiple scale channels, or other permutation-invariant pooling over scales, a resulting network architecture for image classification also becomes provably scale invariant. We investigate the performance of such networks on the MNIST Large Scale dataset, which contains rescaled images from the original MNIST dataset over a factor of 4 concerning training data and over a factor of 16 concerning testing data. It is demonstrated that the resulting approach allows for scale generalization, enabling good performance for classifying patterns at scales not spanned by the training data.


2020 ◽  
Author(s):  
Tim Henning ◽  
Benjamin Bergner ◽  
Christoph Lippert

Instance segmentation is a common task in quantitative cell analysis. While there are many approaches doing this using machine learning, typically, the training process requires a large amount of manually annotated data. We present HistoFlow, a software for annotation-efficient training of deep learning models for cell segmentation and analysis with an interactive user interface.It provides an assisted annotation tool to quickly draw and correct cell boundaries and use biomarkers as weak annotations. It also enables the user to create artificial training data to lower the labeling effort. We employ a universal U-Net neural network architecture that allows accurate instance segmentation and the classification of phenotypes in only a single pass of the network. Transfer learning is available through the user interface to adapt trained models to new tissue types.We demonstrate HistoFlow for fluorescence breast cancer images. The models trained using only artificial data perform comparably to those trained with time-consuming manual annotations. They outperform traditional cell segmentation algorithms and match state-of-the-art machine learning approaches. A user test shows that cells can be annotated six times faster than without the assistance of our annotation tool. Extending a segmentation model for classification of epithelial cells can be done using only 50 to 1500 annotations.Our results show that, unlike previous assumptions, it is possible to interactively train a deep learning model in a matter of minutes without many manual annotations.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Laila Rasmy ◽  
Yang Xiang ◽  
Ziqian Xie ◽  
Cui Tao ◽  
Degui Zhi

AbstractDeep learning (DL)-based predictive models from electronic health records (EHRs) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required by these models to achieve high accuracy, hindering the adoption of DL-based models in scenarios with limited training data. Recently, bidirectional encoder representations from transformers (BERT) and related models have achieved tremendous successes in the natural language processing domain. The pretraining of BERT on a very large training corpus generates contextualized embeddings that can boost the performance of models trained on smaller datasets. Inspired by BERT, we propose Med-BERT, which adapts the BERT framework originally developed for the text domain to the structured EHR domain. Med-BERT is a contextualized embedding model pretrained on a structured EHR dataset of 28,490,650 patients. Fine-tuning experiments showed that Med-BERT substantially improves the prediction accuracy, boosting the area under the receiver operating characteristics curve (AUC) by 1.21–6.14% in two disease prediction tasks from two clinical databases. In particular, pretrained Med-BERT obtains promising performances on tasks with small fine-tuning training sets and can boost the AUC by more than 20% or obtain an AUC as high as a model trained on a training set ten times larger, compared with deep learning models without Med-BERT. We believe that Med-BERT will benefit disease prediction studies with small local training datasets, reduce data collection expenses, and accelerate the pace of artificial intelligence aided healthcare.


2021 ◽  
Author(s):  
Geoffrey F. Schau ◽  
Hassan Ghani ◽  
Erik A. Burlingame ◽  
Guillaume Thibault ◽  
Joe W. Gray ◽  
...  

AbstractAccurate diagnosis of metastatic cancer is essential for prescribing optimal control strategies to halt further spread of metastasizing disease. While pathological inspection aided by immunohistochemistry staining provides a valuable gold standard for clinical diagnostics, deep learning methods have emerged as powerful tools for identifying clinically relevant features of whole slide histology relevant to a tumor’s metastatic origin. Although deep learning models require significant training data to learn effectively, transfer learning paradigms provide mechanisms to circumvent limited training data by first training a model on related data prior to fine-tuning on smaller data sets of interest. In this work we propose a transfer learning approach that trains a convolutional neural network to infer the metastatic origin of tumor tissue from whole slide images of hematoxylin and eosin (H&E) stained tissue sections and illustrate the advantages of pre-training network on whole slide images of primary tumor morphology. We further characterize statistical dissimilarity between primary and metastatic tumors of various indications on patch-level images to highlight limitations of our indication-specific transfer learning approach. Using a primary-to-metastatic transfer learning approach, we achieved mean class-specific areas under receiver operator characteristics curve (AUROC) of 0.779, which outperformed comparable models trained on only images of primary tumor (mean AUROC of 0.691) or trained on only images of metastatic tumor (mean AUROC of 0.675), supporting the use of large scale primary tumor imaging data in developing computer vision models to characterize metastatic origin of tumor lesions.


Author(s):  
Nukabathini Mary Saroj Sahithya ◽  
Manda Prathyusha ◽  
Nakkala Rachana ◽  
Perikala Priyanka ◽  
P. J. Jyothi

Product reviews are valuable for upcoming buyers in helping them make decisions. To this end, different opinion mining techniques have been proposed, where judging a review sentence�s orientation (e.g. positive or negative) is one of their key challenges. Recently, deep learning has emerged as an effective means for solving sentiment classification problems. Deep learning is a class of machine learning algorithms that learn in supervised and unsupervised manners. A neural network intrinsically learns a useful representation automatically without human efforts. However, the success of deep learning highly relies on the large-scale training data. We propose a novel deep learning framework for product review sentiment classification which employs prevalently available ratings supervision signals. The framework consists of two steps: (1) learning a high-level representation (an embedding space) which captures the general sentiment distribution of sentences through rating information; (2) adding a category layer on top of the embedding layer and use labelled sentences for supervised fine-tuning. We explore two kinds of low-level network structure for modelling review sentences, namely, convolutional function extractors and long temporary memory. Convolutional layer is the core building block of a CNN and it consists of kernels. Applications are image and video recognition, natural language processing, image classification


2019 ◽  
Vol 8 (9) ◽  
pp. 421 ◽  
Author(s):  
Hao Li ◽  
Maosheng Hu ◽  
Youxin Huang

The identification of overpass structures in road networks has great significance for multi-scale modeling of roads, congestion analysis, and vehicle navigation. The traditional vector-based methods identify overpasses by the methodologies coming from computational geometry and graph theory, and they overly rely on the artificially designed features and have poor adaptability to complex scenes. This paper presents a novel method of identifying overpasses based on a target detection model (Faster-RCNN). This method utilizes raster representation of vector data and convolutional neural networks (CNNs) to learn task adaptive features from raster data, then identifies the location of an overpass by a Region Proposal network (RPN). The contribution of this paper is: (1) An overpass labelling geodatabase (OLGDB) for the OpenStreetMap (OSM) road network data of six typical cities in China is established; (2) Three different CNNs (ZF-net, VGG-16, Inception-ResNet V2) are integrated into Faster-RCNN and evaluated by accuracy performance; (3) The optimal combination of learning rate and batchsize is determined by fine-tuning; and (4) Five geometric metrics (perimeter, area, squareness, circularity, and W/L) are synthetized into image bands to enhance the training data, and their contribution to the overpass identification task is determined. The experimental results have shown that the proposed method has good accuracy performance (around 90%), and could be improved with the expansion of OLGDB and switching to more sophisticated target detection models. The deep learning target detection model has great application potential in large-scale road network pattern recognition, it can task-adaptively learn road structure features and easily extend to other road network patterns.


2021 ◽  
Author(s):  
Daniel Cai ◽  
Abbas Roayaei Ardakany ◽  
Ferhat Ay

Autoimmune blistering diseases (AIBDs) are rare, chronic disorders of the skin and mucous membranes, with a broad spectrum of clinical manifestations and morphological lesions. Considering that 1) diagnosis of AIBDs is a challenging task, owing to their rarity and heterogeneous clinical features, and 2) misdiagnoses are common, and the resulting diagnostic delay is a major factor in their high mortality rate, patient prognosis stands to benefit greatly from the development of a computer-aided diagnostic (CAD) tool for AIBDs. Artificial intelligence (AI) research into rare skin diseases like AIBDs is severely underrepresented, due to a variety of factors, foremost a lack of large-scale, uniformly curated imaging data. A study by Julia S. et al. finds that, as of 2020, there exists no machine learning studies on rare skin diseases [1], despite the demonstrated success of AI in the field of dermatology. Whereas previous research has primarily looked to improve performance through extensive data collection and preprocessing, this approach remains tedious and impractical for rarer, under-documented skin diseases. This study proposes a novel approach in the development of a deep learning based diagnostic aid for AIBDs. Leveraging the visual similarities between our imaging data with pre-existing repositories, we demonstrate automated classification of AIBDs using techniques such as transfer learning and data augmentation over a convolutional neural network (CNN). A three-loop process for training is used, combining feature extraction and fine-tuning to improve performance on our classification task. Our final model retains an accuracy nearly on par with dermatologists' diagnostic accuracy on more common skin cancers. Given the efficacy of our predictive model despite low amounts of training data, this approach holds the potential to benefit clinical diagnoses of AIBDs. Furthermore, our approach can be extrapolated to the diagnosis of other clinically similar rare diseases.


Author(s):  
Yi-Quan Li ◽  
Hao-Sen Chang ◽  
Daw-Tung Lin

In the field of computer vision, large-scale image classification tasks are both important and highly challenging. With the ongoing advances in deep learning and optical character recognition (OCR) technologies, neural networks designed to perform large-scale classification play an essential role in facilitating OCR systems. In this study, we developed an automatic OCR system designed to identify up to 13,070 large-scale printed Chinese characters by using deep learning neural networks and fine-tuning techniques. The proposed framework comprises four components, including training dataset synthesis and background simulation, image preprocessing and data augmentation, the process of training the model, and transfer learning. The training data synthesis procedure is composed of a character font generation step and a background simulation process. Three background models are proposed to simulate the factors of the background noise and anti-counterfeiting patterns on ID cards. To expand the diversity of the synthesized training dataset, rotation and zooming data augmentation are applied. A massive dataset comprising more than 19.6 million images was thus created to accommodate the variations in the input images and improve the learning capacity of the CNN model. Subsequently, we modified the GoogLeNet neural architecture by replacing the FC layer with a global average pooling layer to avoid overfitting caused by a massive amount of training data. Consequently, the number of model parameters was reduced. Finally, we employed the transfer learning technique to further refine the CNN model using a small number of real data samples. Experimental results show that the overall recognition performance of the proposed approach is significantly better than that of prior methods and thus demonstrate the effectiveness of proposed framework, which exhibited a recognition accuracy as high as 99.39% on the constructed real ID card dataset.


Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1052
Author(s):  
Leang Sim Nguon ◽  
Kangwon Seo ◽  
Jung-Hyun Lim ◽  
Tae-Jun Song ◽  
Sung-Hyun Cho ◽  
...  

Mucinous cystic neoplasms (MCN) and serous cystic neoplasms (SCN) account for a large portion of solitary pancreatic cystic neoplasms (PCN). In this study we implemented a convolutional neural network (CNN) model using ResNet50 to differentiate between MCN and SCN. The training data were collected retrospectively from 59 MCN and 49 SCN patients from two different hospitals. Data augmentation was used to enhance the size and quality of training datasets. Fine-tuning training approaches were utilized by adopting the pre-trained model from transfer learning while training selected layers. Testing of the network was conducted by varying the endoscopic ultrasonography (EUS) image sizes and positions to evaluate the network performance for differentiation. The proposed network model achieved up to 82.75% accuracy and a 0.88 (95% CI: 0.817–0.930) area under curve (AUC) score. The performance of the implemented deep learning networks in decision-making using only EUS images is comparable to that of traditional manual decision-making using EUS images along with supporting clinical information. Gradient-weighted class activation mapping (Grad-CAM) confirmed that the network model learned the features from the cyst region accurately. This study proves the feasibility of diagnosing MCN and SCN using a deep learning network model. Further improvement using more datasets is needed.


Sign in / Sign up

Export Citation Format

Share Document