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Surgery Surgery

Automated cephalometric landmark detection with confidence regions using Bayesian convolutional neural networks.

In BMC oral health ; h5-index 40.0

BACKGROUND : Despite the integral role of cephalometric analysis in orthodontics, there have been limitations regarding the reliability, accuracy, etc. of cephalometric landmarks tracing. Attempts on developing automatic plotting systems have continuously been made but they are insufficient for clinical applications due to low reliability of specific landmarks. In this study, we aimed to develop a novel framework for locating cephalometric landmarks with confidence regions using Bayesian Convolutional Neural Networks (BCNN).

METHODS : We have trained our model with the dataset from the ISBI 2015 grand challenge in dental X-ray image analysis. The overall algorithm consisted of a region of interest (ROI) extraction of landmarks and landmarks estimation considering uncertainty. Prediction data produced from the Bayesian model has been dealt with post-processing methods with respect to pixel probabilities and uncertainties.

RESULTS : Our framework showed a mean landmark error (LE) of 1.53 ± 1.74 mm and achieved a successful detection rate (SDR) of 82.11, 92.28 and 95.95%, respectively, in the 2, 3, and 4 mm range. Especially, the most erroneous point in preceding studies, Gonion, reduced nearly halves of its error compared to the others. Additionally, our results demonstrated significantly higher performance in identifying anatomical abnormalities. By providing confidence regions (95%) that consider uncertainty, our framework can provide clinical convenience and contribute to making better decisions.

CONCLUSION : Our framework provides cephalometric landmarks and their confidence regions, which could be used as a computer-aided diagnosis tool and education.

Lee Jeong-Hoon, Yu Hee-Jin, Kim Min-Ji, Kim Jin-Woo, Choi Jongeun


Artificial intelligence, Artificial neural networks, Bayesian method, Cephalometry, Deep learning, Dental anatomy, Machine vision, Oral & maxillofacial surgery, Orthodontic(s), Orthodontics, Orthognathic/orthognathic surgery, Radiography

General General

MSpectraAI: a powerful platform for deciphering proteome profiling of multi-tumor mass spectrometry data by using deep neural networks.

In BMC bioinformatics

BACKGROUND : Mass spectrometry (MS) has become a promising analytical technique to acquire proteomics information for the characterization of biological samples. Nevertheless, most studies focus on the final proteins identified through a suite of algorithms by using partial MS spectra to compare with the sequence database, while the pattern recognition and classification of raw mass-spectrometric data remain unresolved.

RESULTS : We developed an open-source and comprehensive platform, named MSpectraAI, for analyzing large-scale MS data through deep neural networks (DNNs); this system involves spectral-feature swath extraction, classification, and visualization. Moreover, this platform allows users to create their own DNN model by using Keras. To evaluate this tool, we collected the publicly available proteomics datasets of six tumor types (a total of 7,997,805 mass spectra) from the ProteomeXchange consortium and classified the samples based on the spectra profiling. The results suggest that MSpectraAI can distinguish different types of samples based on the fingerprint spectrum and achieve better prediction accuracy in MS1 level (average 0.967).

CONCLUSION : This study deciphers proteome profiling of raw mass spectrometry data and broadens the promising application of the classification and prediction of proteomics data from multi-tumor samples using deep learning methods. MSpectraAI also shows a better performance compared to the other classical machine learning approaches.

Wang Shisheng, Zhu Hongwen, Zhou Hu, Cheng Jingqiu, Yang Hao


Deep neural networks, Feature swath extraction, Leave-one-out cross prediction strategy, Multi-tumor types, Proteome profiling, Raw mass spectrometry data

General General

Gini in a Bottleneck: Gotta Train Me the Right Way

ArXiv Preprint

Due to the nature of deep learning approaches, it is inherently difficult to understand which aspects of a molecular graph drive the predictions of the network. As a mitigation strategy, we constrain certain weights in a multi-task graph convolutional neural network according to the Gini index to maximize the "inequality" of the learned representations. We show that this constraint does not degrade evaluation metrics for some targets, and allows us to combine the outputs of the graph convolutional operation in a visually interpretable way. We then perform a proof-of-concept experiment on quantum chemistry targets on the public QM9 dataset, and a larger experiment on ADMET targets on proprietary drug-like molecules. Since a benchmark of explainability in the latter case is difficult, we informally surveyed medicinal chemists within our organization to check for agreement between regions of the molecule they and the model identified as relevant to the properties in question.

Ryan Henderson, Djork-Arné Clevert, Floriane Montanari


General General

Correntropy induced loss based sparse robust graph regularized extreme learning machine for cancer classification.

In BMC bioinformatics

BACKGROUND : As a machine learning method with high performance and excellent generalization ability, extreme learning machine (ELM) is gaining popularity in various studies. Various ELM-based methods for different fields have been proposed. However, the robustness to noise and outliers is always the main problem affecting the performance of ELM.

RESULTS : In this paper, an integrated method named correntropy induced loss based sparse robust graph regularized extreme learning machine (CSRGELM) is proposed. The introduction of correntropy induced loss improves the robustness of ELM and weakens the negative effects of noise and outliers. By using the L2,1-norm to constrain the output weight matrix, we tend to obtain a sparse output weight matrix to construct a simpler single hidden layer feedforward neural network model. By introducing the graph regularization to preserve the local structural information of the data, the classification performance of the new method is further improved. Besides, we design an iterative optimization method based on the idea of half quadratic optimization to solve the non-convex problem of CSRGELM.

CONCLUSIONS : The classification results on the benchmark dataset show that CSRGELM can obtain better classification results compared with other methods. More importantly, we also apply the new method to the classification problems of cancer samples and get a good classification effect.

Ren Liang-Rui, Gao Ying-Lian, Liu Jin-Xing, Shang Junliang, Zheng Chun-Hou


Bioinformatics, Correntropy induced loss, Extreme learning machine, Supervised learning

General General

Sickle-cell disease diagnosis support selecting the most appropriate machinelearning method: Towards a general and interpretable approach for cellmorphology analysis from microscopy images

Computers in Biology and Medicine, 2020, pending publication

In this work we propose an approach to select the classification method and features, based on the state-of-the-art, with best performance for diagnostic support through peripheral blood smear images of red blood cells. In our case we used samples of patients with sickle-cell disease which can be generalized for other study cases. To trust the behavior of the proposed system, we also analyzed the interpretability. We pre-processed and segmented microscopic images, to ensure high feature quality. We applied the methods used in the literature to extract the features from blood cells and the machine learning methods to classify their morphology. Next, we searched for their best parameters from the resulting data in the feature extraction phase. Then, we found the best parameters for every classifier using Randomized and Grid search. For the sake of scientific progress, we published parameters for each classifier, the implemented code library, the confusion matrices with the raw data, and we used the public erythrocytesIDB dataset for validation. We also defined how to select the most important features for classification to decrease the complexity and the training time, and for interpretability purpose in opaque models. Finally, comparing the best performing classification methods with the state-of-the-art, we obtained better results even with interpretable model classifiers.

Nataša Petrović, Gabriel Moyà-Alcover, Antoni Jaume-i-Capó, Manuel González-Hidalgo


General General

Studying social media language changes associated with pregnancy status, trimester, and parity from medical records.

In Women's health (London, England)

We sought to evaluate whether there was variability in language used on social media across different time points of pregnancy (before, during, and after pregnancy, as well as by trimester and parity). Consenting patients shared access to their individual Facebook posts and electronic medical records. Random forest models trained on Facebook posts could differentiate first trimester of pregnancy from 3 months before pregnancy (F1 score = .63) and from a random 3-month time period (F1 score = .64). Posts during pregnancy were more likely to include themes about family (β = .22), food craving (β = .14), and date/times (β = .13), while posts 3 months prior to pregnancy included themes about social life (β = .30), sleep (β = .31), and curse words (β = .27), and 3 months post-pregnancy included themes of gratitude (β = .17), health appointments (β = .21), and religiosity (β = .18). Users who were pregnant for the first time were more likely to post about lack of sleep (β = .15), activities of daily living (β = .09), and communication (β = .08) compared with those who were pregnant after having a child who posted about others' birthdays (β = .16) and life events (.12). A better understanding about social media timelines can provide insight into lifestyle choices that are specific to pregnancy.

Guntuku Sharath Chandra, Gaulton Jessica S, Seltzer Emily K, Asch David A, Srinivas Sindhu K, Ungar Lyle H, Mancheno Christina, Klinger Elissa V, Merchant Raina M

Facebook, language, machine learning, pregnancy, social media, trimester