An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

δ-equality of intuitionistic fuzzy sets: a new proximity measure and applications in medical diagnosis

Intuitionistic fuzzy set is capable of handling uncertainty with counterpart falsities which exist in nature. Proximity measure is a convenient way to demonstrate impractical significance of values of memberships in the intuitionistic fuzzy set. However, the related works of Pappis (Fuzzy Sets Syst 39(1):111–115, 1991), Hong and Hwang (Fuzzy Sets Syst 66(3):383–386, 1994), Virant (2000) and Cai (IEEE Trans Fuzzy Syst 9(5):738–750, 2001) did not model the measure in the context of the intuitionistic fuzzy set but in the Zadeh’s fuzzy set instead. In this paper, we examine this problem and propose new notions of δ-equalities for the intuitionistic fuzzy set and δ-equalities for intuitionistic fuzzy relations. Two fuzzy sets are said to be δ-equal if they are equal to an extent of δ. The applications of δ-equalities are important to fuzzy statistics and fuzzy reasoning. Several characteristics of δ-equalities that were not discussed in the previous works are also investigated. We apply the δ-equalities to the application of medical diagnosis to investigate a patient’s diseases from symptoms. The idea is using δ-equalities for intuitionistic fuzzy relations to find groups of intuitionistic fuzzified set with certain equality or similar degrees then combining them. Numerical examples are given to illustrate validity of the proposed algorithm. Further, we conduct experiments on real medical datasets to check the efficiency and applicability on real-world problems. The results obtained are also better in comparison with 10 existing diagnosis methods namely De et al. (Fuzzy Sets Syst 117:209–213, 2001), Samuel and Balamurugan (Appl Math Sci 6(35):1741–1746, 2012), Szmidt and Kacprzyk (2004), Zhang et al. (Procedia Eng 29:4336–4342, 2012), Hung and Yang (Pattern Recogn Lett 25:1603–1611, 2004), Wang and Xin (Pattern Recogn Lett 26:2063–2069, 2005), Vlachos and Sergiadis (Pattern Recogn Lett 28(2):197– 206, 2007), Zhang and Jiang (Inf Sci 178(6):4184–4191, 2008), Maheshwari and Srivastava (J Appl Anal Comput 6(3):772–789, 2016) and Support Vector Machine (SVM)

Interval-valued and intuitionistic fuzzy mathematical morphologies as special cases of L-fuzzy mathematical morphology

Mathematical morphology (MM) offers a wide range of tools for image processing and computer vision. MM was originally conceived for the processing of binary images and later extended to gray-scale morphology. Extensions of classical binary morphology to gray-scale morphology include approaches based on fuzzy set theory that give rise to fuzzy mathematical morphology (FMM). From a mathematical point of view, FMM relies on the fact that the class of all fuzzy sets over a certain universe forms a complete lattice. Recall that complete lattices provide for the most general framework in which MM can be conducted. The concept of L-fuzzy set generalizes not only the concept of fuzzy set but also the concepts of interval-valued fuzzy set and Atanassov’s intuitionistic fuzzy set. In addition, the class of L-fuzzy sets forms a complete lattice whenever the underlying set L constitutes a complete lattice. Based on these observations, we develop a general approach towards L-fuzzy mathematical morphology in this paper. Our focus is in particular on the construction of connectives for interval-valued and intuitionistic fuzzy mathematical morphologies that arise as special, isomorphic cases of L-fuzzy MM. As an application of these ideas, we generate a combination of some well-known medical image reconstruction techniques in terms of interval-valued fuzzy image processing

Intuitionistic fuzzy similarity measures and their role in classification

We present some similarity and distance measures between intuitionistic fuzzy sets (IFSs). Thus, we propose two semi-metric distance measures between IFSs. The measures are applied to classification of shapes and handwritten Arabic sentences described with intuitionistic fuzzy information. The experimental results permitted to do a comparative analysis between intuitionistic fuzzy similarity and distance measures, which can facilitate the selection of such measure in similar applications

Automatic leukocyte nucleus segmentation by intuitionistic fuzzy divergence based thresholding

The paper proposes a robust approach to automatic segmentation of leukocyte‟s nucleus from microscopic blood smear images under normal as well as noisy environment by employing a new exponential intuitionistic fuzzy divergence based thresholding technique. The algorithm minimizes the divergence between the actual image and the ideally thresholded image to search for the final threshold. A new divergence formula based on exponential intuitionistic fuzzy entropy has been proposed. Further, to increase its noise handling capacity, a neighborhood-based membership function for the image pixels has been designed. The proposed scheme has been applied on 110 normal and 54 leukemia (chronic myelogenous leukemia) affected blood samples. The nucleus segmentation results have been validated by three expert haematologists. The algorithm achieves an average segmentation accuracy of 98.52% in noise-free environment. It beats the competitor algorithms in terms of several other metrics. The proposed scheme with neighborhood based membership function outperforms the competitor algorithms in terms of segmentation accuracy under noisy environment. It achieves 93.90% and 94.93% accuracies for Speckle and Gaussian noises respectively. The average area under the ROC curves comes out to be 0.9514 in noisy conditions, which proves the robustness of the proposed algorithm

Hybrid learning for interval type-2 intuitionistic fuzzy logic systems as applied to identification and prediction problems

This paper presents a novel application of a hybrid learning approach to the optimisation of membership and non-membership functions of a newly developed interval type-2 intuitionistic fuzzy logic system (IT2 IFLS) of a Takagi-Sugeno-Kang (TSK) fuzzy inference system with neural network learning capability. The hybrid algorithms consisting of decou- pled extended Kalman filter (DEKF) and gradient descent (GD) are used to tune the parameters of the IT2 IFLS for the first time. The DEKF is used to tune the consequent parameters in the forward pass while the GD method is used to tune the antecedents parts during the backward pass of the hybrid learning. The hybrid algorithm is described and evaluated, prediction and identification results together with the runtime are compared with similar existing studies in the literature. Performance comparison is made between the proposed hybrid learning model of IT2 IFLS, a TSK-type-1 intuitionistic fuzzy logic system (IFLS-TSK) and a TSK-type interval type-2 fuzzy logic system (IT2 FLS-TSK) on two instances of the datasets under investigation. The empirical comparison is made on the designed systems using three artificially generated datasets and three real world datasets. Analysis of results reveal that IT2 IFLS outperforms its type-1 variants, IT2 FLS and most of the existing models in the literature. Moreover, the minimal run time of the proposed hybrid learning model for IT2 IFLS also puts this model forward as a good candidate for application in real time systems

Enhancement of dronogram aid to visual interpretation of target objects via intuitionistic fuzzy hesitant sets

In this paper, we address the hesitant information in enhancement task often caused by differences in image contrast. Enhancement approaches generally use certain filters which generate artifacts or are unable to recover all the objects details in images. Typically, the contrast of an image quantifies a unique ratio between the amounts of black and white through a single pixel. However, contrast is better represented by a group of pix- els. We have proposed a novel image enhancement scheme based on intuitionistic hesi- tant fuzzy sets (IHFSs) for drone images (dronogram) to facilitate better interpretations of target objects. First, a given dronogram is divided into foreground and background areas based on an estimated threshold from which the proposed model measures the amount of black/white intensity levels. Next, we fuzzify both of them and determine the hesitant score indicated by the distance between the two areas for each point in the fuzzy plane. Finally, a hyperbolic operator is adopted for each membership grade to improve the pho- tographic quality leading to enhanced results via defuzzification. The proposed method is tested on a large drone image database. Results demonstrate better contrast enhancement, improved visual quality, and better recognition compared to the state-of-the-art methods.Web of Science500866

An Application of Single-Valued Neutrosophic Sets in Medical Diagnosis

In this paper, we present the use of single-valued neutrosophic sets in medical diagnosis by using distance measures and similarity measures. Using interconnection between single-valued neutrosophic sets and symptoms of patient, we determine the type of disease. We define new distance formulas for single valued neutrosophic sets. We develop two new medical diagnosis algorithms under neutrosophic environment. We also solve a numerical example to illustrate the proposed algorithms and finally, we compare the obtained results