Non-adaptive Feature Research Articles

Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively

Of Chargaff’s four rules on DNA base quantity, his second parity rule (PR-2) is the most contentious. Various biometricians (e.g., Sueoka, Lobry) regarded PR-2 compliance as a non-adaptive feature of modern genomes that could be modeled through interrelations among mutation rates. However, PR-2 compliance with stem-loop potential was considered adaptively relevant by biochemists familiar with analyses of nucleic acid structure (e.g., of Crick) and of meiotic recombination (e.g., of Kleckner). Meanwhile, other biometricians had shown that PR-2 complementarity extended beyond individual bases (1-mers) to oligonucleotides (k-mers), possibly reflecting “advantageous DNA structure” (Nussinov). An “introns early” hypothesis (Reanney, Forsdyke) had suggested a primordial nucleic acid world with recombination-mediated error-correction requiring genome-wide stem-loop potential to have evolved prior to localized intrusions of protein-encoding potential (exons). Thus, a primordial genome was equivalent to one long intron. Indeed, when assessed as the base order-dependent component (correcting for local influences of GC%), modern genes, especially when evolving rapidly under positive Darwinian selection, display high intronic stem-loop potential. This suggests forced migration from neighboring exons by competing protein-encoding potential. PR-2 compliance may have first arisen non-adaptively. Primary prototypic structures were later strengthened by their adaptive contribution to recombination. Thus, contentious views may actually be in harmony.

Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly.

Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.

Intelligence and Usability Empowerment of Smartphone Adaptive Features

In adaptivity, the interface of the device automatically adjusts and assists the user. The adaptive user interfaces can adapt their activities by monitoring user status, the state of the system, and the current situation according to the adaptation strategy. Usually, the intensity of adaptation is measured in effectiveness, efficiency, and satisfaction to analyze the smartphone’s adaptive features. The adaptive features of light-emitting diode (LED) notifications, voice commands, face recognition, screen rotation, kid mode, drive mode, night mode, Swift Keyboard, s-health, gesture recognition, and fingerprint are selected for both iOS and Android platforms. Task completion within a specific time frame is used to measure effectiveness and efficiency, while satisfaction is calculated using the after-scenario questionnaire (ASQ). A total of 550 users are involved in the experimentation. The usability evaluation is measured for smartphone features. The effectiveness of adaptive features contains higher adaptivity in face recognition (87%) and voice command (85%). Furthermore, the satisfaction level is greater for adaptive features than non-adaptive features. This study indicates that adaptive features can only be used after a thorough examination of the user’s context. Furthermore, the usability evaluation shows that there is a dire need for adaptive smartphone features to provide ease and satisfaction to the user.

Learning Waveform-Based Acoustic Models Using Deep Variational Convolutional Neural Networks

We investigate the potential of stochastic neural networks for learning effective waveform-based acoustic models. The waveform-based setting, inherent to fully end-to-end speech recognition systems, is motivated by several comparative studies of automatic and human speech recognition that associate standard non-adaptive feature extraction techniques with information loss which can adversely affect robustness. Stochastic neural networks, on the other hand, are a class of models capable of incorporating rich regularization mechanisms into the learning process. We consider a deep convolutional neural network that first decomposes speech into frequency sub-bands via an adaptive parametric convolutional block where filters are specified by cosine modulations of compactly supported windows. The network then employs standard non-parametric 1D convolutions to extract relevant spectro-temporal patterns while gradually compressing the structured high dimensional representation generated by the parametric block. We rely on a probabilistic parametrization of the proposed neural architecture and learn the model using stochastic variational inference. This requires evaluation of an analytically intractable integral defining the Kullback-Leibler divergence term responsible for regularization, for which we propose an effective approximation based on the Gauss-Hermite quadrature. Our empirical results demonstrate a superior performance of the proposed approach over comparable waveform-based baselines and indicate that it could lead to robustness. Moreover, the approach outperforms a recently proposed deep convolutional neural network for learning of robust acoustic models with standard FBANK features.

Local binary pattern variants-based adaptive texture features analysis for posed and nonposed facial expression recognition

Facial expression recognition (FER) is an important task for various computer vision applications. The task becomes challenging when it requires the detection and encoding of macro- and micropatterns of facial expressions. We present a two-stage texture feature extraction framework based on the local binary pattern (LBP) variants and evaluate its significance in recognizing posed and nonposed facial expressions. We focus on the parametric limitations of the LBP variants and investigate their effects for optimal FER. The size of the local neighborhood is an important parameter of the LBP technique for its extraction in images. To make the LBP adaptive, we exploit the granulometric information of the facial images to find the local neighborhood size for the extraction of center-symmetric LBP (CS-LBP) features. Our two-stage texture representations consist of an LBP variant and the adaptive CS-LBP features. Among the presented two-stage texture feature extractions, the binarized statistical image features and adaptive CS-LBP features were found showing high FER rates. Evaluation of the adaptive texture features shows competitive and higher performance than the nonadaptive features and other state-of-the-art approaches, respectively.

Seilacher, Konstruktions‐Morphologie, Morphodynamics, and the Evolution of form

Adolf Seilacher (1925-2014) was a German paleontologist who made the concept of Konstruktions-Morphologie (constructional morphology) his own, recognizing that organism morphology is not simply an adaptive response to selection pressure but incorporates phylogenetic and structural influences as well. He was particularly interested in "fabricational noise," nonadaptive features that are a consequence of available materials and modes of growth, but he also elucidated the nature of adaptive radiations-in bivalves and sand dollars, for example. His interpretations relied on detailed study of specimens, and during a long international career he investigated examples from almost every invertebrate fossil group resulting in his 2015 book Morphodynamics, a compilation of his observations and iconic drawings that was published after his death. Seilacher's insights and observations on fossils have the potential to generate hypotheses about evolutionary development that may eventually be tested experimentally.

An Experimental Study on Pedestrian Classification

Detecting people in images is key for several important application domains in computer vision. This paper presents an in-depth experimental study on pedestrian classification; multiple feature-classifier combinations are examined with respect to their ROC performance and efficiency. We investigate global versus local and adaptive versus nonadaptive features, as exemplified by PCA coefficients, Haar wavelets, and local receptive fields (LRFs). In terms of classifiers, we consider the popular Support Vector Machines (SVMs), feed-forward neural networks, and k-nearest neighbor classifier. Experiments are performed on a large data set consisting of 4,000 pedestrian and more than 25,000 nonpedestrian (labeled) images captured in outdoor urban environments. Statistically meaningful results are obtained by analyzing performance variances caused by varying training and test sets. Furthermore, we investigate how classification performance and training sample size are correlated. Sample size is adjusted by increasing the number of manually labeled training data or by employing automatic bootstrapping or cascade techniques. Our experiments show that the novel combination of SVMs with LRF features performs best. A boosted cascade of Haar wavelets can, however, reach quite competitive results, at a fraction of computational cost. The data set used in this paper is made public, establishing a benchmark for this important problem.

Adaptive On-line Classification for EEG-based Brain Computer Interfaces with AAR parameters and band power estimates / Adaptive On-line Classification einer EEG-basierenden Gehirn-Computer Schnittstelle mit Adaptive Autoregressiven und Bandleistungsparametern

We present the result of on-line feedback Brain Computer Interface experiments using adaptive and non-adaptive feature extraction methods with an on-line adaptive classifier based on Quadratic Discriminant Analysis. Experiments were performed with 12 naïve subjects, feedback was provided from the first moment and no training sessions were needed. Experiments run in three different days with each subject. Six of them received feedback with Adaptive Autoregressive parameters and the rest with logarithmic Band Power estimates. The study was done using single trial analysis of each of the sessions and the value of the Error Rate and the Mutual Information of the classification were used to discuss the results. Finally, it was shown that even subjects starting with a low performance were able to control the system in a few hours: and contrary to previous results no differences between AAR and BP estimates were found.

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.

Daytime deliveries observed for the ring-tailed lemurs of the berenty reserve, Madagascar

In the Berenty Reserve, Southern Madagascar, of the 16 deliveries recorded for ring-tailed lemurs from 1995 and 1997, 10 cases occurred during daytime hours (07:00 – 16:59). Four mothers lost contact with their troop members during parturition, but were able to rejoin them after about one hour. No attack from the individuals of the neighboring groups or predators on the mothers or their newborn infants was observed, whereas, other females of the mother’s own troop attacked them after delivery in two cases. Such daytime delivery may have originated from the circadian rhythm of the species’ nocturnal ancestors, who might have given birth during the daytime. This pattern may now be a non-adaptive feature, in agreement with the “evolutionary disequilibrium hypothesis (EVDH).”

Polyphyly and Convergent Morphological Evolution in Commelinales and Commelinidae: Evidence from rbcL Sequence Data

Phylogenetic relationships of the five families of the order Commelinales remain an area of deep uncertainty in higher-level monocot systematics, despite intensive morphological and anatomical study. To test the monophyly of the Commelinales and the subclass Commelinidae, evaluate their relationships, and analyze evolutionary trends in their morphology, ecology, and biogeography, we conducted parsimony analyses on 95 rbcL sequences representing 17 taxa of Commelinales, 16 taxa of other Commelinidae, and 63 taxa from Arecidae, Liliidae, and Zingiberidae. Commelinales is polyphyletic and Commelinidae paraphyletic, with Eriocaulaceae and Xyridaceae sister to Poaceae and its relatives, Rapateaceae sister to Bromeliaceae and Mayacaceae, and Commelinaceae sister to Philydrales and allies. Thurnia is sister to Prionium at the base of Cyperaceae–Juncaceae; only 1 of Cronquist's multifamily commelinoid orders is diagnosed as monophyletic. We propose a revised Commelinidae, incorporating 4 revised superorders (Bromelianae, Commelinanae, Dasypogonanae, Arecanae) and 10 orders ((Poales, Eriocaulales, Cyperales, Typhales, Bromeliales), (Commelinales, Philydrales, Zingiberales), (Dasypogonales), (Arecales)). Morphological and anatomical characters used to define the original Commelinales and Commelinidae appear to be plesiomorphic or to reflect convergence or recurrent mutation; several characters supporting our revised classification are anatomical traits that seem relatively insulated from environmental selection pressures. The Commelinidae distal to the Arecales arose in South America, with amphiatlantic Bromeliaceae–Mayacaceae–Rapateaceae originating in the Guayana Shield. Ecological diversification involved the repeated invasion of shady, infertile, or arid microsites. The numbers of species in families of the revised Commelinidae are related partly to the extent of adaptive radiation in those families, but seem more strongly related to nonadaptive features promoting speciation, such as restricted seed dispersal (especially in forest interior groups with fleshy fruits), polyploidy, aneuploidy, and apomixis. Species diversity is unrelated to the rate/amount of rbcL sequence evolution.

The evolution of leks through female choice

It is generally acknowledged that female preferences for mating in large groups of displaying males could cause the evolution of leks. Recent hypotheses differ on what selective advantage would accrue to females with such preferences, but they agree on the need for some such advantage if these preferences are to select for larger lek sizes. A model developed here, adapted from models of female preferences for individual male traits, shows that female preferences for larger leks can evolve and be maintained without any direct selective advantage. Like the individual choice models, it also demonstrates a number of arbitrary or non-adaptive features inherent in such systems. Most notably, instead of a single optimal outcome, there may exist a curve of possible equilibria. These equilibria can be stable or unstable depending on the nature of the female preferences.