scholarly journals Tracking cell lineages in 3D by incremental deep learning

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Ko Sugawara ◽  
Çağrı Çevrim ◽  
Michalis Averof
Keyword(s):  
Deep Learning ◽  
Incremental Learning ◽  
Cell Tracking ◽  
State Of The Art ◽  
Training Data ◽  
Cell Lineages ◽  
Incremental Approach ◽  
Powerful Approach ◽  
Cell Track ◽  
Bioimage Analysis

Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently lack a unified user interface. We present ELEPHANT, an interactive platform for 3D cell tracking that addresses these challenges by taking an incremental approach to deep learning. ELEPHANT provides an interface that seamlessly integrates cell track annotation, deep learning, prediction, and proofreading. This enables users to implement cycles of incremental learning starting from a few annotated nuclei. Successive prediction-validation cycles enrich the training data, leading to rapid improvements in tracking performance. We test the software’s performance against state-of-the-art methods and track lineages spanning the entire course of leg regeneration in a crustacean over 1 week (504 timepoints). ELEPHANT yields accurate, fully-validated cell lineages with a modest investment in time and effort.

scholarly journals Tracking cell lineages in 3D by incremental deep learning

2021 ◽  
Author(s):  
Ko Sugawara ◽  
Cagri Cevrim ◽  
Michalis Averof
Keyword(s):  
Deep Learning ◽  
User Interface ◽  
Incremental Learning ◽  
Cell Tracking ◽  
Cell Lineages ◽  
Powerful Approach ◽  
Bioimage Analysis

Deep learning is emerging as a powerful approach for bioimage analysis, but its wider use is limited by the scarcity of annotated data for training. We present ELEPHANT, an interactive platform for cell tracking in 4D that seamlessly integrates annotation, deep learning, and proofreading. ELEPHANT's user interface supports cycles of incremental learning starting from sparse annotations, yielding accurate, user-validated cell lineages with a modest investment in time and effort.

scholarly journals Unsupervised Deep Learning via Affinity Diffusion

2020 ◽  
Vol 34 (07) ◽  
pp. 11029-11036
Author(s):  
Jiabo Huang ◽  
Qi Dong ◽  
Shaogang Gong ◽  
Xiatian Zhu
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
General Purpose ◽  
Training Data ◽  
Learning Approach ◽  
Model Learning ◽  
Feature Representations ◽  
Discriminative Feature ◽  
Training Samples ◽  
Unsupervised Deep Learning

Convolutional neural networks (CNNs) have achieved unprecedented success in a variety of computer vision tasks. However, they usually rely on supervised model learning with the need for massive labelled training data, limiting dramatically their usability and deployability in real-world scenarios without any labelling budget. In this work, we introduce a general-purpose unsupervised deep learning approach to deriving discriminative feature representations. It is based on self-discovering semantically consistent groups of unlabelled training samples with the same class concepts through a progressive affinity diffusion process. Extensive experiments on object image classification and clustering show the performance superiority of the proposed method over the state-of-the-art unsupervised learning models using six common image recognition benchmarks including MNIST, SVHN, STL10, CIFAR10, CIFAR100 and ImageNet.

scholarly journals On the objectivity, reliability, and validity of deep learning enabled bioimage analyses

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Dennis Segebarth ◽  
Matthias Griebel ◽  
Nikolai Stein ◽  
Cora R von Collenberg ◽  
Corinna Martin ◽  
...  
Keyword(s):  
Deep Learning ◽  
Signal To Noise Ratio ◽  
Biological Effects ◽  
Reliability And Validity ◽  
Ground Truth ◽  
Training Data ◽  
Model Organisms ◽  
Data Annotation ◽  
Bioimage Analysis ◽  
Model Training

Bioimage analysis of fluorescent labels is widely used in the life sciences. Recent advances in deep learning (DL) allow automating time-consuming manual image analysis processes based on annotated training data. However, manual annotation of fluorescent features with a low signal-to-noise ratio is somewhat subjective. Training DL models on subjective annotations may be instable or yield biased models. In turn, these models may be unable to reliably detect biological effects. An analysis pipeline integrating data annotation, ground truth estimation, and model training can mitigate this risk. To evaluate this integrated process, we compared different DL-based analysis approaches. With data from two model organisms (mice, zebrafish) and five laboratories, we show that ground truth estimation from multiple human annotators helps to establish objectivity in fluorescent feature annotations. Furthermore, ensembles of multiple models trained on the estimated ground truth establish reliability and validity. Our research provides guidelines for reproducible DL-based bioimage analyses.

scholarly journals Examining Deep Learning Architectures for Crime Classification and Prediction

Forecasting ◽  
2021 ◽  
Vol 3 (4) ◽  
pp. 741-762
Author(s):  
Panagiotis Stalidis ◽  
Theodoros Semertzidis ◽  
Petros Daras
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Open Data ◽  
Training Data ◽  
Crime Prediction ◽  
Crime Types ◽  
Improved Performance ◽  
Learning Architectures ◽  
And Training ◽  
Crime Classification

In this paper, a detailed study on crime classification and prediction using deep learning architectures is presented. We examine the effectiveness of deep learning algorithms in this domain and provide recommendations for designing and training deep learning systems for predicting crime areas, using open data from police reports. Having time-series of crime types per location as training data, a comparative study of 10 state-of-the-art methods against 3 different deep learning configurations is conducted. In our experiments with 5 publicly available datasets, we demonstrate that the deep learning-based methods consistently outperform the existing best-performing methods. Moreover, we evaluate the effectiveness of different parameters in the deep learning architectures and give insights for configuring them to achieve improved performance in crime classification and finally crime prediction.

scholarly journals Var-CNN: A Data-Efficient Website Fingerprinting Attack Based on Deep Learning

2019 ◽  
Vol 2019 (4) ◽  
pp. 292-310 ◽  
Author(s):  
Sanjit Bhat ◽  
David Lu ◽  
Albert Kwon ◽  
Srinivas Devadas
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
False Positive Rate ◽  
True Positive Rate ◽  
Training Data ◽  
Open World ◽  
Prior Art ◽  
Lower False Positive Rate ◽  
Positive Rate ◽  
Fingerprinting Attack

Abstract In recent years, there have been several works that use website fingerprinting techniques to enable a local adversary to determine which website a Tor user visits. While the current state-of-the-art attack, which uses deep learning, outperforms prior art with medium to large amounts of data, it attains marginal to no accuracy improvements when both use small amounts of training data. In this work, we propose Var-CNN, a website fingerprinting attack that leverages deep learning techniques along with novel insights specific to packet sequence classification. In open-world settings with large amounts of data, Var-CNN attains over 1% higher true positive rate (TPR) than state-of-the-art attacks while achieving 4× lower false positive rate (FPR). Var-CNN’s improvements are especially notable in low-data scenarios, where it reduces the FPR of prior art by 3.12% while increasing the TPR by 13%. Overall, insights used to develop Var-CNN can be applied to future deep learning based attacks, and substantially reduce the amount of training data needed to perform a successful website fingerprinting attack. This shortens the time needed for data collection and lowers the likelihood of having data staleness issues.

scholarly journals LABEL-EFFICIENT DEEP LEARNING-BASED SEMANTIC SEGMENTATION OF BUILDING POINT CLOUDS AT LOD3 LEVEL

2021 ◽  
Vol XLIII-B2-2021 ◽  
pp. 449-456
Author(s):  
Y. Cao ◽  
M. Scaioni
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Semantic Segmentation ◽  
Point Clouds ◽  
Training Data ◽  
Second Step ◽  
Dynamic Graph ◽  
Input Point ◽  
Supervised Methods ◽  
Global And Local

Abstract. In recent research, fully supervised Deep Learning (DL) techniques and large amounts of pointwise labels are employed to train a segmentation network to be applied to buildings’ point clouds. However, fine-labelled buildings’ point clouds are hard to find and manually annotating pointwise labels is time-consuming and expensive. Consequently, the application of fully supervised DL for semantic segmentation of buildings’ point clouds at LoD3 level is severely limited. To address this issue, we propose a novel label-efficient DL network that obtains per-point semantic labels of LoD3 buildings’ point clouds with limited supervision. In general, it consists of two steps. The first step (Autoencoder – AE) is composed of a Dynamic Graph Convolutional Neural Network-based encoder and a folding-based decoder, designed to extract discriminative global and local features from input point clouds by reconstructing them without any label. The second step is semantic segmentation. By supplying a small amount of task-specific supervision, a segmentation network is proposed for semantically segmenting the encoded features acquired from the pre-trained AE. Experimentally, we evaluate our approach based on the ArCH dataset. Compared to the fully supervised DL methods, we find that our model achieved state-of-the-art results on the unseen scenes, with only 10% of labelled training data from fully supervised methods as input.

Deep industrial transfer learning at runtime for image recognition

2021 ◽  
Vol 69 (3) ◽  
pp. 211-220
Author(s):  
Benjamin Maschler ◽  
Simon Kamm ◽  
Michael Weyrich
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
State Of The Art ◽  
Training Data ◽  
Use Case ◽  
Industrial Transfer ◽  
Distributed Training ◽  
Two Factors ◽  
Changes Over Time ◽  
Over Time

Abstract The utilization of deep learning in the field of industrial automation is hindered by two factors: The amount and diversity of training data needed as well as the need to continuously retrain as the use case changes over time. Both problems can be addressed by industrial deep transfer learning allowing for the performant, continuous and potentially distributed training on small, dispersed datasets. As a specific example, a dual memory algorithm for computer vision problems is developed and evaluated. It shows the potential for state-of-the-art performance while being trained only on fractions of the complete ImageNet dataset at multiple locations at once.

scholarly journals Automatic extraction of 12 cardiovascular concepts from German discharge letters using pre-trained language models

2021 ◽  
Vol 7 ◽  
pp. 205520762110576
Author(s):  
Phillip Richter-Pechanski ◽  
Nicolas A Geis ◽  
Christina Kiriakou ◽  
Dominic M Schwab ◽  
Christoph Dieterich
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Training Data ◽  
Language Models ◽  
University Hospital ◽  
Data Driven ◽  
Learning Methods ◽  
Concept Extraction ◽  
Automated Method ◽  
Learning Projects

Objective A vast amount of medical data is still stored in unstructured text documents. We present an automated method of information extraction from German unstructured clinical routine data from the cardiology domain enabling their usage in state-of-the-art data-driven deep learning projects. Methods We evaluated pre-trained language models to extract a set of 12 cardiovascular concepts in German discharge letters. We compared three bidirectional encoder representations from transformers pre-trained on different corpora and fine-tuned them on the task of cardiovascular concept extraction using 204 discharge letters manually annotated by cardiologists at the University Hospital Heidelberg. We compared our results with traditional machine learning methods based on a long short-term memory network and a conditional random field. Results Our best performing model, based on publicly available German pre-trained bidirectional encoder representations from the transformer model, achieved a token-wise micro-average F1-score of 86% and outperformed the baseline by at least 6%. Moreover, this approach achieved the best trade-off between precision (positive predictive value) and recall (sensitivity). Conclusion Our results show the applicability of state-of-the-art deep learning methods using pre-trained language models for the task of cardiovascular concept extraction using limited training data. This minimizes annotation efforts, which are currently the bottleneck of any application of data-driven deep learning projects in the clinical domain for German and many other European languages.

scholarly journals Transfer Learning for Named Entity Recognition in Financial and Biomedical Documents

Information ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 248 ◽  
Author(s):  
Sumam Francis ◽  
Jordy Van Landeghem ◽  
Marie-Francine Moens
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Language Models ◽  
Reasonable Assumption ◽  
Target Domain ◽  
Named Entity

Recent deep learning approaches have shown promising results for named entity recognition (NER). A reasonable assumption for training robust deep learning models is that a sufficient amount of high-quality annotated training data is available. However, in many real-world scenarios, labeled training data is scarcely present. In this paper we consider two use cases: generic entity extraction from financial and from biomedical documents. First, we have developed a character based model for NER in financial documents and a word and character based model with attention for NER in biomedical documents. Further, we have analyzed how transfer learning addresses the problem of limited training data in a target domain. We demonstrate through experiments that NER models trained on labeled data from a source domain can be used as base models and then be fine-tuned with few labeled data for recognition of different named entity classes in a target domain. We also witness an interest in language models to improve NER as a way of coping with limited labeled data. The current most successful language model is BERT. Because of its success in state-of-the-art models we integrate representations based on BERT in our biomedical NER model along with word and character information. The results are compared with a state-of-the-art model applied on a benchmarking biomedical corpus.

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