Dataset Information

Early Diagnosis: End-to-End CNN-LSTM Models for Mass Spectrometry Data Classification.

ABSTRACT: Liquid chromatography-mass spectrometry (LC-MS) is a powerful method for cell profiling. The use of LC-MS technology is a tool of choice for cancer research since it provides molecular fingerprints of analyzed tissues. However, the ubiquitous presence of noise, the peaks shift between acquisitions, and the huge amount of information owing to the high dimensionality of the data make rapid and accurate cancer diagnosis a challenging task. Deep learning (DL) models are not only effective classifiers but are also well suited to jointly learn feature representation and classification tasks. This is particularly relevant when applied to raw LC-MS data and hence avoid the need for costly preprocessing and complicated feature selection. In this study, we propose a new end-to-end DL methodology that addresses all of the above challenges at once, while preserving the high potential of LC-MS data. Our DL model is designed to early discriminate between tumoral and normal tissues. It is a combination of a convolutional neural network (CNN) and a long short-term memory (LSTM) Network. The CNN network allows for significantly reducing the high dimensionality of the data while learning spatially relevant features. The LSTM network enables our model to capture temporal patterns. We show that our model outperforms not only benchmark models but also state-of-the-art models developed on the same data. Our framework is a promising strategy for improving early cancer detection during a diagnostic process.

SUBMITTER: Seddiki K

PROVIDER: S-EPMC10501374 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Early Diagnosis: End-to-End CNN-LSTM Models for Mass Spectrometry Data Classification.

Seddiki Khawla K Precioso Fŕed Eric FE Sanabria Melissa M Salzet Michel M Fournier Isabelle I Droit Arnaud A

Analytical chemistry 20230825 36

Liquid chromatography-mass spectrometry (LC-MS) is a powerful method for cell profiling. The use of LC-MS technology is a tool of choice for cancer research since it provides molecular fingerprints of analyzed tissues. However, the ubiquitous presence of noise, the peaks shift between acquisitions, and the huge amount of information owing to the high dimensionality of the data make rapid and accurate cancer diagnosis a challenging task. Deep learning (DL) models are not only effective classifier ...[more]

PMID: 37624777

Similar Datasets

Project description:Differential diagnosis of left ventricular hypertrophy (LVH) is often obscure on echocardiography and requires numerous additional tests. We aimed to develop a deep learning algorithm to aid in the differentiation of common etiologies of LVH (i.e. hypertensive heart disease [HHD], hypertrophic cardiomyopathy [HCM], and light-chain cardiac amyloidosis [ALCA]) on echocardiographic images. Echocardiograms in 5 standard views (parasternal long-axis, parasternal short-axis, apical 4-chamber, apical 2-chamber, and apical 3-chamber) were obtained from 930 subjects: 112 with HHD, 191 with HCM, 81 with ALCA and 546 normal subjects. The study population was divided into training (n = 620), validation (n = 155), and test sets (n = 155). A convolutional neural network-long short-term memory (CNN-LSTM) algorithm was constructed to independently classify the 3 diagnoses on each view, and the final diagnosis was made by an aggregate network based on the simultaneously predicted probabilities of HCM, HCM, and ALCA. Diagnostic performance of the algorithm was evaluated by the area under the receiver operating characteristic curve (AUC), and accuracy was evaluated by the confusion matrix. The deep learning algorithm was trained and verified using the training and validation sets, respectively. In the test set, the average AUC across the five standard views was 0.962, 0.982 and 0.996 for HHD, HCM and CA, respectively. The overall diagnostic accuracy was significantly higher for the deep learning algorithm (92.3%) than for echocardiography specialists (80.0% and 80.6%). In the present study, we developed a deep learning algorithm for the differential diagnosis of 3 common LVH etiologies (HHD, HCM and ALCA) by applying a hybrid CNN-LSTM model and aggregate network to standard echocardiographic images. The high diagnostic performance of our deep learning algorithm suggests that the use of deep learning can improve the diagnostic process in patients with LVH.

Project description:Background Grading of cancer histopathology slides requires more pathologists and expert clinicians as well as it is time consuming to look manually into whole-slide images. Hence, an automated classification of histopathological breast cancer sub-type is useful for clinical diagnosis and therapeutic responses. Recent deep learning methods for medical image analysis suggest the utility of automated radiologic imaging classification for relating disease characteristics or diagnosis and patient stratification. Methods To develop a hybrid model using the convolutional neural network (CNN) and the long short-term memory recurrent neural network (LSTM RNN) to classify four benign and four malignant breast cancer subtypes. The proposed CNN-LSTM leveraging on ImageNet uses a transfer learning approach in classifying and predicting four subtypes of each. The proposed model was evaluated on the BreakHis dataset comprises 2480 benign and 5429 malignant cancer images acquired at magnifications of 40×, 100×, 200× and 400×. Results The proposed hybrid CNN-LSTM model was compared with the existing CNN models used for breast histopathological image classification such as VGG-16, ResNet50, and Inception models. All the models were built using three different optimizers such as adaptive moment estimator (Adam), root mean square propagation (RMSProp), and stochastic gradient descent (SGD) optimizers by varying numbers of epochs. From the results, we noticed that the Adam optimizer was the best optimizer with maximum accuracy and minimum model loss for both the training and validation sets. The proposed hybrid CNN-LSTM model showed the highest overall accuracy of 99% for binary classification of benign and malignant cancer, and, whereas, 92.5% for multi-class classifier of benign and malignant cancer subtypes, respectively. Conclusion To conclude, the proposed transfer learning approach outperformed the state-of-the-art machine and deep learning models in classifying benign and malignant cancer subtypes. The proposed method is feasible in classification of other cancers as well as diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12880-023-00964-0.

Dataset Information

Early Diagnosis: End-to-End CNN-LSTM Models for Mass Spectrometry Data Classification.

Publications

Early Diagnosis: End-to-End CNN-LSTM Models for Mass Spectrometry Data Classification.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets