LipidQuant 1.0: automated data processing in lipid class separation—mass spectrometry quantitative workflows

Summary We present the LipidQuant 1.0 tool for automated data processing workflows in lipidomic quantitation based on lipid class separation coupled with high-resolution mass spectrometry. Lipid class separation workflows, such as hydrophilic interaction liquid chromatography or supercritical fluid chromatography, should be preferred in lipidomic quantitation due to the coionization of lipid class internal standards with analytes from the same class. The individual steps in the LipidQuant workflow are explained, including lipid identification, quantitation, isotopic correction, and reporting results. We show the application of LipidQuant data processing to a small cohort of human serum samples. Availability and implementation The LipidQuant 1.0 is freely available at Zenodo https://doi.org/10.5281/zenodo.5151201 and https://holcapek.upce.cz/lipidquant.php. Supplementary information Supplementary data are available at Bioinformatics online.

A new validity function of FCM clustering algorithm based on intra-class compactness and inter-class separation

Fuzzy C-means (FCM) clustering algorithm is a widely used method in data mining. However, there is a big limitation that the predefined number of clustering must be given. So it is very important to find an optimal number of clusters. Therefore, a new validity function of FCM clustering algorithm is proposed to verify the validity of the clustering results. This function is defined based on the intra-class compactness and inter-class separation from the fuzzy membership matrix, the data similarity between classes and the geometric structure of the data set, whose minimum value represents the optimal clustering partition result. The proposed clustering validity function and seven traditional clustering validity functions are experimentally verified on four artificial data sets and six UCI data sets. The simulation results show that the proposed validity function can obtain the optimal clustering number of the data set more accurately, and can still find the more accurate clustering number under the condition of changing the fuzzy weighted index, which has strong adaptability and robustness.

Acoustic Seafloor Classification Using the Weyl Transform of Multibeam Echosounder Backscatter Mosaic

The use of multibeam echosounder systems (MBES) for detailed seafloor mapping is increasing at a fast pace. Due to their design, enabling continuous high-density measurements and the coregistration of seafloor’s depth and reflectivity, MBES has become a fundamental instrument in the advancing field of acoustic seafloor classification (ASC). With these data becoming available, recent seafloor mapping research focuses on the interpretation of the hydroacoustic data and automated predictive modeling of seafloor composition. While a methodological consensus on which seafloor sediment classification algorithm and routine does not exist in the scientific community, it is expected that progress will occur through the refinement of each stage of the ASC pipeline: ranging from the data acquisition to the modeling phase. This research focuses on the stage of the feature extraction; the stage wherein the spatial variables used for the classification are, in this case, derived from the MBES backscatter data. This contribution explored the sediment classification potential of a textural feature based on the recently introduced Weyl transform of 300 kHz MBES backscatter imagery acquired over a nearshore study site in Belgian Waters. The goodness of the Weyl transform textural feature for seafloor sediment classification was assessed in terms of cluster separation of Folk’s sedimentological categories (4-class scheme). Class separation potential was quantified at multiple spatial scales by cluster silhouette coefficients. Weyl features derived from MBES backscatter data were found to exhibit superior thematic class separation compared to other well-established textural features, namely: (1) First-order Statistics, (2) Gray Level Co-occurrence Matrices (GLCM), (3) Wavelet Transform and (4) Local Binary Pattern (LBP). Finally, by employing a Random Forest (RF) categorical classifier, the value of the proposed textural feature for seafloor sediment mapping was confirmed in terms of global and by-class classification accuracies, highest for models based on the backscatter Weyl features. Further tests on different backscatter datasets and sediment classification schemes are required to further elucidate the use of the Weyl transform of MBES backscatter imagery in the context of seafloor mapping.

Robustness of Latent Profile Analysis to Measurement Noninvariance Between Profiles

Latent profile analysis (LPA) identifies heterogeneous subgroups based on continuous indicators that represent different dimensions. It is a common practice to measure each dimension using items, create composite or factor scores for each dimension, and use these scores as indicators of profiles in LPA. In this case, measurement models for dimensions are not included and potential noninvariance across latent profiles is not modeled in LPA. This simulation study examined the robustness of LPA in terms of class enumeration and parameter recovery when the noninvariance was unmodeled by using composite or factor scores as profile indicators. Results showed that correct class enumeration rates of LPA were relatively high with small degree of noninvariance, large class separation, large sample size, and equal proportions. Severe bias in profile indicator mean difference was observed with intercept and loading noninvariance, respectively. Implications for applied researchers are discussed.

Polynomial-Time Random Oracles and Separating Complexity Classes

Bennett and Gill [1981] showed that P A ≠ NP A ≠ coNP A for a random oracle A , with probability 1. We investigate whether this result extends to individual polynomial-time random oracles. We consider two notions of random oracles: p-random oracles in the sense of martingales and resource-bounded measure [Lutz 1992; Ambos-Spies et al. 1997], and p-betting-game random oracles using the betting games generalization of resource-bounded measure [Buhrman et al. 2000]. Every p-betting-game random oracle is also p-random; whether the two notions are equivalent is an open problem. (1) We first show that P A ≠ NP A for every oracle A that is p-betting-game random. Ideally, we would extend (1) to p-random oracles. We show that answering this either way would imply an unrelativized complexity class separation: (2) If P A ≠ NP A relative to every p-random oracle A , then BPP ≠ EXP. (3) If P A ≠ NP A relative to some p-random oracle A , then P ≠ PSPACE. Rossman, Servedio, and Tan [2015] showed that the polynomial-time hierarchy is infinite relative to a random oracle, solving a longstanding open problem. We consider whether we can extend (1) to show that PH A is infinite relative to oracles A that are p-betting-game random. Showing that PH A separates at even its first level would also imply an unrelativized complexity class separation: (4) If NP A ≠ coNP A for a p-betting-game measure 1 class of oracles A , then NP ≠ EXP. (5) If PH A is infinite relative to every p-random oracle A , then PH ≠ EXP. We also consider random oracles for time versus space, for example: (6) L A ≠ P A relative to every oracle A that is p-betting-game random.

Collective Strategy Condensation: When Envy Splits Societies

Human societies are characterized by three constituent features, besides others. (A) Options, as for jobs and societal positions, differ with respect to their associated monetary and non-monetary payoffs. (B) Competition leads to reduced payoffs when individuals compete for the same option as others. (C) People care about how they are doing relatively to others. The latter trait—the propensity to compare one’s own success with that of others—expresses itself as envy. It is shown that the combination of (A)–(C) leads to spontaneous class stratification. Societies of agents split endogenously into two social classes, an upper and a lower class, when envy becomes relevant. A comprehensive analysis of the Nash equilibria characterizing a basic reference game is presented. Class separation is due to the condensation of the strategies of lower-class agents, which play an identical mixed strategy. Upper-class agents do not condense, following individualist pure strategies. The model and results are size-consistent, holding for arbitrary large numbers of agents and options. Analytic results are confirmed by extensive numerical simulations. An analogy to interacting confined classical particles is discussed.