Estimating phytoplankton size classes from their inherent optical properties

Phytoplankton plays a massive role in the regulation of greenhouse gases, with different functional types affecting the carbon cycle differently. The most practical way of synoptically mapping the ocean’s phytoplankton communities is through remote sensing with the aid of ocean-optics algorithms. This thesis is a study of the relationships between the Inherent Optical Properties (IOPs) of the ocean and the physical constituents within it, with a special focus on deriving phytoplankton size classes. Three separate models were developed, each focusing on a different relationship between absorption and phytoplankton size classes, before being combined into a final ensemble model. It was shown that all of the developed models performed better than the baseline model, which only estimates the mean values per size class, and that the results of the final ensemble model is comparable to, and performs better than, most other published models on the NOMAD dataset

Estimating Exerted Hand Force via Force Myography to Interact with a Biaxial Stage in Real-Time by Learning Human Intentions: A Preliminary Investigation

Force myography (FMG) signals can read volumetric changes of muscle movements, while a human participant interacts with the environment. For collaborative activities, FMG signals could potentially provide a viable solution to controlling manipulators. In this paper, a novel method to interact with a two-degree-of-freedom (DoF) system consisting of two perpendicular linear stages using FMG is investigated. The method consists in estimating exerted hand forces in dynamic arm motions of a participant using FMG signals to provide velocity commands to the biaxial stage during interactions. Five different arm motion patterns with increasing complexities, i.e., “x-direction”, “y-direction”, “diagonal”, “square”, and “diamond”, were considered as human intentions to manipulate the stage within its planar workspace. FMG-based force estimation was implemented and evaluated with a support vector regressor (SVR) and a kernel ridge regressor (KRR). Real-time assessments, where 10 healthy participants were asked to interact with the biaxial stage by exerted hand forces in the five intended arm motions mentioned above, were conducted. Both the SVR and the KRR obtained higher estimation accuracies of 90–94% during interactions with simple arm motions (x-direction and y-direction), while for complex arm motions (diagonal, square, and diamond) the notable accuracies of 82–89% supported the viability of the FMG-based interactive control

Affect Lexicon Induction For the Github Subculture Using Distributed Word Representations

Sentiments and emotions play essential roles in small group interactions, especially in self-organized collaborative groups. Many people view sentiments as universal constructs; however, cultural differences exist in some aspects of sentiments. Understanding the features of sentiment space in small group cultures provides essential insights into the dynamics of self-organized collaborations. However, due to the limit of carefully human annotated data, it is hard to describe sentimental divergences across cultures. In this thesis, we present a new approach to inspect cultural differences on the level of sentiments and compare subculture with the general social environment. We use Github, a collaborative software development network, as an example of self-organized subculture. First, we train word embeddings on large corpora and do embedding alignment using linear transformation method. Then we model finer-grained human sentiment in the Evaluation- Potency-Activity (EPA) space and extend subculture EPA lexicon with two-dense-layered neural networks. Finally, we apply Long Short-Term Memory (LSTM) network to analyze the identities’ sentiments triggered by event-based sentences. We evaluate the predicted EPA lexicon for Github community using a recently collected dataset, and the result proves our approach could capture subtle changes in affective dimensions. Moreover, our induced sentiment lexicon shows individuals from two environments have different understandings to sentiment-related words and phrases but agree on nouns and adjectives. The sentiment features of “Github culture” could explain that people in self-organized groups tend to reduce personal sentiment to improve group collaboration

Kernel Multivariate Analysis Framework for Supervised Subspace Learning: A Tutorial on Linear and Kernel Multivariate Methods

Feature extraction and dimensionality reduction are important tasks in many fields of science dealing with signal processing and analysis. The relevance of these techniques is increasing as current sensory devices are developed with ever higher resolution, and problems involving multimodal data sources become more common. A plethora of feature extraction methods are available in the literature collectively grouped under the field of Multivariate Analysis (MVA). This paper provides a uniform treatment of several methods: Principal Component Analysis (PCA), Partial Least Squares (PLS), Canonical Correlation Analysis (CCA) and Orthonormalized PLS (OPLS), as well as their non-linear extensions derived by means of the theory of reproducing kernel Hilbert spaces. We also review their connections to other methods for classification and statistical dependence estimation, and introduce some recent developments to deal with the extreme cases of large-scale and low-sized problems. To illustrate the wide applicability of these methods in both classification and regression problems, we analyze their performance in a benchmark of publicly available data sets, and pay special attention to specific real applications involving audio processing for music genre prediction and hyperspectral satellite images for Earth and climate monitoring

An updated State-of-the-Art Overview of transcriptomic Deconvolution Methods

Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging expression of multiple cell types, RNA-Seq analysis is oblivious to variations in cellular changes, hindering the identification of the internal constituents of tissues, involved in disease progression. On the other hand, single-cell techniques are still time, manpower and resource-consuming analyses.To address the intrinsic limitations of both bulk and single-cell methodologies, computational deconvolution techniques have been developed to estimate the frequencies of cell subtypes within complex tissues. These methods are especially valuable for dissecting intricate tissue niches, with a particular focus on tumour microenvironments (TME).In this paper, we offer a comprehensive overview of deconvolution techniques, classifying them based on their methodological characteristics, the type of prior knowledge required for the algorithm, and the statistical constraints they address. Within each category identified, we delve into the theoretical aspects for implementing the underlying method, while providing an in-depth discussion of their main advantages and disadvantages in supplementary materials.Notably, we emphasise the advantages of cutting-edge deconvolution tools based on probabilistic models, as they offer robust statistical frameworks that closely align with biological realities. We anticipate that this review will provide valuable guidelines for computational bioinformaticians in order to select the appropriate method in alignment with their statistical and biological objectives.We ultimately end this review by discussing open challenges that must be addressed to accurately quantify closely related cell types from RNA sequencing data, and the complementary role of single-cell RNA-Seq to that purpose

Improved Extreme Learning Machine and Its Application in Image Quality Assessment

Extreme learning machine (ELM) is a new class of single-hidden layer feedforward neural network (SLFN), which is simple in theory and fast in implementation. Zong et al. propose a weighted extreme learning machine for learning data with imbalanced class distribution, which maintains the advantages from original ELM. However, the current reported ELM and its improved version are only based on the empirical risk minimization principle, which may suffer from overfitting. To solve the overfitting troubles, in this paper, we incorporate the structural risk minimization principle into the (weighted) ELM, and propose a modified (weighted) extreme learning machine (M-ELM and M-WELM). Experimental results show that our proposed M-WELM outperforms the current reported extreme learning machine algorithm in image quality assessment