BackgroundThe stability of Variable Importance Measures (VIMs) based on random forest has recently received increased attention. Despite the extensive attention on traditional stability of data perturbations or parameter variations, few studies include influences coming from the intrinsic randomness in generating VIMs, i.e. bagging, randomization and permutation. To address these influences, in this paper we introduce a new concept of intrinsic stability of VIMs, which is defined as the self-consistence among feature rankings in repeated runs of VIMs without data perturbations and parameter variations. Two widely used VIMs, i.e., Mean Decrease Accuracy (MDA) and Mean Decrease Gini (MDG) are comprehensively investigated. The motivation of this study is two-fold. First, we empirically verify the prevalence of intrinsic stability of VIMs over many real-world datasets to highlight that the instability of VIMs does not originate exclusively from data perturbations or parameter variations, but also stems from the intrinsic randomness of VIMs. Second, through Spearman and Pearson tests we comprehensively investigate how different factors influence the intrinsic stability.ResultsThe experiments are carried out on 19 benchmark datasets with diverse characteristics, including 10 high-dimensional and small-sample gene expression datasets. Experimental results demonstrate the prevalence of intrinsic stability of VIMs. Spearman and Pearson tests on the correlations between intrinsic stability and different factors show that #feature (number of features) and #sample (size of sample) have a coupling effect on the intrinsic stability. The synthetic indictor, #feature/#sample, shows both negative monotonic correlation and negative linear correlation with the intrinsic stability, while OOB accuracy has monotonic correlations with intrinsic stability. This indicates that high-dimensional, small-sample and high complexity datasets may suffer more from intrinsic instability of VIMs. Furthermore, with respect to parameter settings of random forest, a large number of trees is preferred. No significant correlations can be seen between intrinsic stability and other factors. Finally, the magnitude of intrinsic stability is always smaller than that of traditional stability.ConclusionFirst, the prevalence of intrinsic stability of VIMs demonstrates that the instability of VIMs not only comes from data perturbations or parameter variations, but also stems from the intrinsic randomness of VIMs. This finding gives a better understanding of VIM stability, and may help reduce the instability of VIMs. Second, by investigating the potential factors of intrinsic stability, users would be more aware of the risks and hence more careful when using VIMs, especially on high-dimensional, small-sample and high complexity datasets.

Background: Most machine-learning classifiers output label predictions for new instances without indicating how reliable the predictions are. The applicability of these classifiers is limited in critical domains where incorrect predictions have serious consequences, like medical diagnosis. Further, the default assumption of equal misclassification costs is most likely violated in medical diagnosis.

The Drosophila genome encodes three BEN-solo proteins including Insensitive (Insv), Elba1 and Elba2 that possess activities in transcriptional repression and chromatin insulation. A fourth protein—Elba3—bridges Elba1 and Elba2 to form an ELBA complex. Here, we report comprehensive investigation of these proteins in Drosophila embryos. We assess common and distinct binding sites for Insv and ELBA and their genetic interdependencies. While Elba1 and Elba2 binding generally requires the ELBA complex, Elba3 can associate with chromatin independently of Elba1 and Elba2. We further demonstrate that ELBA collaborates with other insulators to regulate developmental patterning. Finally, we find that adjacent gene pairs separated by an ELBA bound sequence become less differentially expressed in ELBA mutants. Transgenic reporters confirm the insulating activity of ELBA- and Insv-bound sites. These findings define ELBA and Insv as general insulator proteins in Drosophila and demonstrate the functional importance of insulators to partition transcription units.

We present two new neighbor query algorithms, including range query (RNN) and nearest neighbor (NN) query, based on revised k-d tree by using two techniques. The first technique is proposed for decreasing unnecessary distance computations by checking whether the cell of a node is inside or outside the specified neighborhood of query

In the biomineralization of NiCO3, the secondary structure of extracellular proteins changed from α-helices to β structures.

BackgroundBenefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and deep neural networks. The advent of electronic medical records (EMRs) has not only changed the format of medical records but also helped users to obtain information faster. However, there are many challenges regarding researching directly using Chinese EMRs, such as low quality, huge quantity, imbalance, semi-structure and non-structure, particularly the high density of the Chinese language compared with English. Therefore, effective word segmentation, word representation and model architecture are the core technologies in the literature on Chinese EMRs.ResultsIn this paper, we propose a deep learning framework to study intelligent diagnosis using Chinese EMR data, which incorporates a convolutional neural network (CNN) into an EMR classification application. The novelty of this paper is reflected in the following: (1) We construct a pediatric medical dictionary based on Chinese EMRs. (2) Word2vec adopted in word embedding is used to achieve the semantic description of the content of Chinese EMRs. (3) A fine-tuning CNN model is constructed to feed the pediatric diagnosis with Chinese EMR data. Our results on real-world pediatric Chinese EMRs demonstrate that the average accuracy and F1-score of the CNN models are up to 81%, which indicates the effectiveness of the CNN model for the classification of EMRs. Particularly, a fine-tuning one-layer CNN performs best among all CNNs, recurrent neural network (RNN) (long short-term memory, gated recurrent unit) and CNN-RNN models, and the average accuracy and F1-score are both up to 83%.ConclusionThe CNN framework that includes word segmentation, word embedding and model training can serve as an intelligent auxiliary diagnosis tool for pediatricians. Particularly, a fine-tuning one-layer CNN performs well, which indicates that word order does not appear to have a useful effect on our Chinese EMRs.Electronic supplementary materialThe online version of this article (10.1186/s12859-019-2617-8) contains supplementary material, which is available to authorized users.

ObjectiveChronic Fatigue (CF) still remains unclear about its etiology, pathophysiology, nomenclature and diagnostic criteria in the medical community. Traditional Chinese medicine (TCM) adopts a unique diagnostic method, namely ‘bian zheng lun zhi’ or syndrome differentiation, to diagnose the CF with a set of syndrome factors, which can be regarded as the Multi-Label Learning (MLL) problem in the machine learning literature. To obtain an effective and reliable diagnostic tool, we use Conformal Predictor (CP), Random Forest (RF) and Problem Transformation method (PT) for the syndrome differentiation of CF.Methods and MaterialsIn this work, using PT method, CP-RF is extended to handle MLL problem. CP-RF applies RF to measure the confidence level (p-value) of each label being the true label, and then selects multiple labels whose p-values are larger than the pre-defined significance level as the region prediction. In this paper, we compare the proposed CP-RF with typical CP-NBC(Naïve Bayes Classifier), CP-KNN(K-Nearest Neighbors) and ML-KNN on CF dataset, which consists of 736 cases. Specifically, 95 symptoms are used to identify CF, and four syndrome factors are employed in the syndrome differentiation, including ‘spleen deficiency’, ‘heart deficiency’, ‘liver stagnation’ and ‘qi deficiency’.The ResultsCP-RF demonstrates an outstanding performance beyond CP-NBC, CP-KNN and ML-KNN under the general metrics of subset accuracy, hamming loss, one-error, coverage, ranking loss and average precision. Furthermore, the performance of CP-RF remains steady at the large scale of confidence levels from 80% to 100%, which indicates its robustness to the threshold determination. In addition, the confidence evaluation provided by CP is valid and well-calibrated.ConclusionCP-RF not only offers outstanding performance but also provides valid confidence evaluation for the CF syndrome differentiation. It would be well applicable to TCM practitioners and facilitate the utilities of objective, effective and reliable computer-based diagnosis tool.

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