Matching Pursuit for Denoising Raman Spectra, Based on Genetic Algorithm and Hermite Atoms.

Due to its various advantages, Raman spectroscopy has become a powerful tool in different fields of science and engineering; however, in specific applications, this technique's limiting factor is closely related to the inherent noise of the Raman spectra. To eliminate the noise of a Raman spectrum, preserving its position, intensity, and width characteristic, we propose using a genetic matching pursuit-Hermite atoms (GMP-HAs) algorithm in this work. This algorithm helps recover Raman spectra immersed in Gaussian noise with the least number of atoms. The noise-free Raman signal is reconstructed with the GMP-HAs algorithm, transforming the typical best-matching atom search into an optimization problem. Specifically, we maximize the fitness function, defined as the correlation between current residual and Hermite atoms, with the genetic algorithm MI-LXPM encoded in a real domain and avoiding local maxima, by adding a stopping criterion based on an exponential adjustment according to the algorithm's behavior in the presence of noise. Simulated and biological Raman spectra are used to evaluate the proposed algorithm and compare its performance with typically known methods for denoising, such as the Savitzky- Golay filter (SG) and basis pursuit denoising. Using the signal-to-noise ratio (S/N)metric resulted in a 0.31 dB advantage in the S/N product for the proposed algorithm with respect to SG. Additionally, it is shown that the algorithm uses only 25.3% of the number of atoms needed by the matching pursuit algorithm. The results indicate that the GMP-HAs algorithm has better denoising capabilities, and at the same time, the Raman spectra are decomposed with fewer atoms compared to known sparse algorithms.

Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences.

Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), and cytosine (C). Genes are DNA sequences containing the information to synthesize proteins. The genes of higher eukaryotic organisms contain coding sequences, known as exons and non-coding sequences, known as introns, which are removed on splice sites after the DNA is transcribed into RNA. Genome annotation is the process of identifying the location of coding regions and determining their function. This process is fundamental for understanding gene structure; however, it is time-consuming and expensive when done by biochemical methods. With technological advances, splice site detection can be done computationally. Although various software tools have been developed to predict splice sites, they need to improve accuracy and reduce false-positive rates. The main goal of this research was to generate Deep Splicer, a deep learning model to identify splice sites in the genomes of humans and other species. This model has good performance metrics and a lower false-positive rate than the currently existing tools. Deep Splicer achieved an accuracy between 93.55% and 99.66% on the genetic sequences of different organisms, while Splice2Deep, another splice site detection tool, had an accuracy between 90.52% and 98.08%. Splice2Deep surpassed Deep Splicer on the accuracy obtained after evaluating C. elegans genomic sequences (97.88% vs. 93.62%) and A. thaliana (95.40% vs. 94.93%); however, Deep Splicer's accuracy was better for H. sapiens (98.94% vs. 97.15%) and D. melanogaster (97.14% vs. 92.30%). The rate of false positives was 0.11% for human genetic sequences and 0.25% for other species' genetic sequences. Another splice prediction tool, Splice Finder, had between 1% and 3% of false positives for human sequences, while other species' sequences had around 4% and 10%.

An Approach of Anomaly Detection and Neural Network Classifiers to Measure Cellulolytic Activity.

AIM AND OBJECTIVE: A common method used for massive detection of cellulolytic microorganisms is based on the formation of halos on solid medium. However, this is a subjective method and real-time monitoring is not possible. The objective of this work was to develop a method of computational analysis of the visual patterns created by cellulolytic activity through artificial neural networks description. MATERIALS AND METHODS: Our method learns by an adaptive prediction model and automatically determines when enzymatic activity on a chromogenic indicator such as the hydrolysis halo occurs. To achieve this goal, we generated a data library with absorbance readings and RGB values of enzymatic hydrolysis, obtained by spectrophotometry and a prototype camera-based equipment (Enzyme Vision), respectively. We used the first part of the library to generate a linear regression model, which was able to predict theoretical absorbances using the RGB color patterns, which agreed with values obtained by spectrophotometry. The second part was used to train, validate, and test the neural network model in order to predict cellulolytic activity based on color patterns. RESULTS: As a result of our model, we were able to establish six new descriptors useful for the prediction of the temporal changes in the enzymatic activity. Finally, our model was evaluated on one halo from cellulolytic microorganisms, achieving the regional classification of the generated halo in three of the six classes learned by our model. CONCLUSION: We assume that our approach can be a viable alternative for high throughput screening of enzymatic activity in real time.

Inversion method based on stochastic optimization for particle sizing.

A stochastic inverse method is presented based on a hybrid evolutionary optimization algorithm (HEOA) to retrieve a monomodal particle-size distribution (PSD) from the angular distribution of scattered light. By solving an optimization problem, the HEOA (with the Fraunhofer approximation) retrieves the PSD from an intensity pattern generated by Mie theory. The analyzed light-scattering pattern can be attributed to unimodal normal, gamma, or lognormal distribution of spherical particles covering the interval of modal size parameters 46≤α≤150. The HEOA ensures convergence to the near-optimal solution during the optimization of a real-valued objective function by combining the advantages of a multimember evolution strategy and locally weighted linear regression. The numerical results show that our HEOA can be satisfactorily applied to solve the inverse light-scattering problem.

Numerical study of particle-size distributions retrieved from angular light-scattering data using an evolution strategy with the Fraunhofer approximation.

An algorithm is presented based on an evolution strategy to retrieve a particle size distribution from angular light-scattering data. The analyzed intensity patterns are generated using the Mie theory, and the algorithm retrieves a series of known normal, gamma, and lognormal distributions by using the Fraunhofer approximation. The distributions scan the interval of modal size parameters 100 < or = alpha < or = 150. The numerical results show that the evolution strategy can be successfully applied to solve this kind of inverse problem, obtaining a more accurate solution than, for example, the Chin-Shifrin inversion method, and avoiding the use of a priori information concerning the domain of the distribution, commonly necessary for reconstructing the particle size distribution when this analytical inversion method is used.

Obtaining the phase of an interferogram by use of an evolution strategy: part I.

We present a method for obtaining the phase of a noisy simulated interferogram. We find the wave-front aberrations by transforming the problem of fitting a polynomial into an optimization problem, which is then solved using an evolutionary algorithm. Our experimental results show that our method yields a more accurate solution than other methods commonly used to solve this problem.