Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

On the fixed point theory of soft metric spaces

[EN] The aim of this paper is to show that a soft metric induces a compatible metric on the collection of all soft points of the absolute soft set, when the set of parameters is a finite set. We then show that soft metric extensions of several important fixed point theorems for metric spaces can be directly deduced from comparable existing results. We also present some examples to validate and illustrate our approach.Salvador Romaguera thanks the support of Ministry of Economy and Competitiveness of Spain, Grant MTM2012-37894-C02-01.Abbas, M.; Murtaza, G.; Romaguera Bonilla, S. (2016). On the fixed point theory of soft metric spaces. Fixed Point Theory and Applications. 2016(17):1-11. https://doi.org/10.1186/s13663-016-0502-yS111201617Zadeh, LA: Fuzzy sets. Inf. Control 8, 103-112 (1965)Molodtsov, D: Soft set theory - first results. Comput. Math. Appl. 37, 19-31 (1999)Aktaş, H, Çağman, N: Soft sets and soft groups. Inf. Sci. 177, 2726-2735 (2007)Ali, MI, Feng, F, Liu, X, Min, WK, Shabir, M: On some new operations in soft set theory. Comput. Math. Appl. 57, 1547-1553 (2009)Feng, F, Liu, X, Leoreanu-Fotea, V, Jun, YB: Soft sets and soft rough sets. Inf. Sci. 181, 1125-1137 (2011)Jiang, Y, Tang, Y, Chen, Q, Wang, J, Tang, S: Extending soft sets with description logics. Comput. Math. Appl. 59, 2087-2096 (2009)Jun, YB: Soft BCK/BCI-algebras. Comput. Math. Appl. 56, 1408-1413 (2008)Jun, YB, Lee, KJ, Khan, A: Soft ordered semigroups. Math. Log. Q. 56, 42-50 (2010)Jun, YB, Lee, KJ, Park, CH: Soft set theory applied to ideals in d-algebras. Comput. Math. Appl. 57, 367-378 (2009)Jun, YB, Park, CH: Applications of soft sets in ideal theory of BCK/BCI-algebras. Inf. Sci. 178, 2466-2475 (2008)Kong, Z, Gao, L, Wang, L, Li, S: The normal parameter reduction of soft sets and its algorithm. Comput. Math. Appl. 56, 3029-3037 (2008)Majumdar, P, Samanta, SK: Generalized fuzzy soft sets. Comput. Math. Appl. 59, 1425-1432 (2010)Li, F: Notes on the soft operations. ARPN J. Syst. Softw. 1, 205-208 (2011)Maji, PK, Roy, AR, Biswas, R: An application of soft sets in a decision making problem. Comput. Math. Appl. 44, 1077-1083 (2002)Qin, K, Hong, Z: On soft equality. J. Comput. Appl. Math. 234, 1347-1355 (2010)Xiao, Z, Gong, K, Xia, S, Zou, Y: Exclusive disjunctive soft sets. Comput. Math. Appl. 59, 2128-2137 (2009)Xiao, Z, Gong, K, Zou, Y: A combined forecasting approach based on fuzzy soft sets. J. Comput. Appl. Math. 228, 326-333 (2009)Xu, W, Ma, J, Wang, S, Hao, G: Vague soft sets and their properties. Comput. Math. Appl. 59, 787-794 (2010)Yang, CF: A note on soft set theory. Comput. Math. Appl. 56, 1899-1900 (2008)Yang, X, Lin, TY, Yang, J, Li, Y, Yu, D: Combination of interval-valued fuzzy set and soft set. Comput. Math. Appl. 58, 521-527 (2009)Zhu, P, Wen, Q: Operations on soft sets revisited (2012). arXiv:1205.2857v1Feng, F, Jun, YB, Liu, XY, Li, LF: An adjustable approach to fuzzy soft set based decision making. J. Comput. Appl. Math. 234, 10-20 (2009)Feng, F, Jun, YB, Zhao, X: Soft semirings. Comput. Math. Appl. 56, 2621-2628 (2008)Feng, F, Liu, X: Soft rough sets with applications to demand analysis. In: Int. Workshop Intell. Syst. Appl. (ISA 2009), pp. 1-4. (2009)Herawan, T, Deris, MM: On multi-soft sets construction in information systems. In: Emerging Intelligent Computing Technology and Applications with Aspects of Artificial Intelligence, pp. 101-110. Springer, Berlin (2009)Herawan, T, Rose, ANM, Deris, MM: Soft set theoretic approach for dimensionality reduction. In: Database Theory and Application, pp. 171-178. Springer, Berlin (2009)Kim, YK, Min, WK: Full soft sets and full soft decision systems. J. Intell. Fuzzy Syst. 26, 925-933 (2014). doi: 10.3233/IFS-130783Mushrif, MM, Sengupta, S, Ray, AK: Texture classification using a novel, soft-set theory based classification algorithm. Lect. Notes Comput. Sci. 3851, 246-254 (2006)Roy, AR, Maji, PK: A fuzzy soft set theoretic approach to decision making problems. J. Comput. Appl. Math. 203, 412-418 (2007)Zhu, P, Wen, Q: Probabilistic soft sets. In: IEEE Conference on Granular Computing (GrC 2010), pp. 635-638 (2010)Zou, Y, Xiao, Z: Data analysis approaches of soft sets under incomplete information. Knowl.-Based Syst. 21, 941-945 (2008)Cagman, N, Karatas, S, Enginoglu, S: Soft topology. Comput. Math. Appl. 62, 351-358 (2011)Das, S, Samanta, SK: Soft real sets, soft real numbers and their properties. J. Fuzzy Math. 20, 551-576 (2012)Das, S, Samanta, SK: Soft metric. Ann. Fuzzy Math. Inform. 6, 77-94 (2013)Abbas, M, Murtaza, G, Romaguera, S: Soft contraction theorem. J. Nonlinear Convex Anal. 16, 423-435 (2015)Chen, CM, Lin, IJ: Fixed point theory of the soft Meir-Keeler type contractive mappings on a complete soft metric space. Fixed Point Theory Appl. 2015, 184 (2015)Feng, F, Li, CX, Davvaz, B, Ali, MI: Soft sets combined with fuzzy sets and rough sets: a tentative approach. Soft Comput. 14, 8999-9911 (2010)Maji, PK, Biswas, R, Roy, AR: Soft set theory. Comput. Math. Appl. 45, 555-562 (2003)Wardowski, D: On a soft mapping and its fixed points. Fixed Point Theory Appl. 2013, 182 (2013)Kannan, R: Some results on fixed points II. Am. Math. Mon. 76, 405-408 (1969)Meir, A, Keeler, E: A theorem on contraction mappings. J. Math. Anal. Appl. 28, 326-329 (1969)Caristi, J: Fixed point theorems for mappings satisfying inwardness conditions. Trans. Am. Math. Soc. 215, 241-251 (1976)Kirk, WA: Caristi’s fixed-point theorem and metric convexity. Colloq. Math. 36, 81-86 (1976

Normal parameter reduction algorithm in soft set based on hybrid binary particle swarm and biogeography optimizer

© 2019, Springer-Verlag London Ltd., part of Springer Nature. Existing classification techniques that are proposed previously for eliminating data inconsistency could not achieve an efficient parameter reduction in soft set theory, which effects on the obtained decisions. Meanwhile, the computational cost made during combination generation process of soft sets could cause machine infinite state, which is known as nondeterministic polynomial time. The contributions of this study are mainly focused on minimizing choices costs through adjusting the original classifications by decision partition order and enhancing the probability of searching domain space using a developed Markov chain model. Furthermore, this study introduces an efficient soft set reduction-based binary particle swarm optimized by biogeography-based optimizer (SSR-BPSO-BBO) algorithm that generates an accurate decision for optimal and sub-optimal choices. The results show that the decision partition order technique is performing better in parameter reduction up to 50%, while other algorithms could not obtain high reduction rates in some scenarios. In terms of accuracy, the proposed SSR-BPSO-BBO algorithm outperforms the other optimization algorithms in achieving high accuracy percentage of a given soft dataset. On the other hand, the proposed Markov chain model could significantly represent the robustness of our parameter reduction technique in obtaining the optimal decision and minimizing the search domain.Published versio