GABAergic interneuron diversity and organization are crucial for the generation of human-specific functional neural networks in cerebral organoids.

This mini review investigates the importance of GABAergic interneurons for the network function of human-induced pluripotent stem cells (hiPSC)-derived brain organoids. The presented evidence suggests that the abundance, diversity and three-dimensional cortical organization of GABAergic interneurons are the primary elements responsible for the creation of synchronous neuronal firing patterns. Without intricate inhibition, coupled oscillatory patterns cannot reach a sufficient complexity to transfer spatiotemporal information constituting physiological network function. Furthermore, human-specific brain network function seems to be mediated by a more complex and interconnected inhibitory structure that remains developmentally flexible for a longer period when compared to rodents. This suggests that several characteristics of human brain networks cannot be captured by rodent models, emphasizing the need for model systems like organoids that adequately mimic physiological human brain function in vitro.

TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences.

BACKGROUND: MicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the identification of microRNA targets a prominent focus of research. Conventional experimental methods for identifying microRNA targets are both time-consuming and expensive, prompting the development of computational tools for target prediction. However, the existing computational tools exhibit limited performance in meeting the demands of practical applications, highlighting the need to improve the performance of microRNA target prediction models. RESULTS: In this paper, we utilize the most popular natural language processing and computer vision technologies to propose a novel approach, called TEC-miTarget, for microRNA target prediction based on transformer encoder and convolutional neural networks. TEC-miTarget treats RNA sequences as a natural language and encodes them using a transformer encoder, a widely used encoder in natural language processing. It then combines the representations of a pair of microRNA and its candidate target site sequences into a contact map, which is a three-dimensional array similar to a multi-channel image. Therefore, the contact map's features are extracted using a four-layer convolutional neural network, enabling the prediction of interactions between microRNA and its candidate target sites. We applied a series of comparative experiments to demonstrate that TEC-miTarget significantly improves microRNA target prediction, compared with existing state-of-the-art models. Our approach is the first approach to perform comparisons with other approaches at both sequence and transcript levels. Furthermore, it is the first approach compared with both deep learning-based and seed-match-based methods. We first compared TEC-miTarget's performance with approaches at the sequence level, and our approach delivers substantial improvements in performance using the same datasets and evaluation metrics. Moreover, we utilized TEC-miTarget to predict microRNA targets in long mRNA sequences, which involves two steps: selecting candidate target site sequences and applying sequence-level predictions. We finally showed that TEC-miTarget outperforms other approaches at the transcript level, including the popular seed match methods widely used in previous years. CONCLUSIONS: We propose a novel approach for predicting microRNA targets at both sequence and transcript levels, and demonstrate that our approach outperforms other methods based on deep learning or seed match. We also provide our approach as an easy-to-use software, TEC-miTarget, at https://github.com/tingpeng17/TEC-miTarget . Our results provide new perspectives for microRNA target prediction.

Brain tumor segmentation using neuro-technology enabled intelligence-cascaded U-Net model.

According to experts in neurology, brain tumours pose a serious risk to human health. The clinical identification and treatment of brain tumours rely heavily on accurate segmentation. The varied sizes, forms, and locations of brain tumours make accurate automated segmentation a formidable obstacle in the field of neuroscience. U-Net, with its computational intelligence and concise design, has lately been the go-to model for fixing medical picture segmentation issues. Problems with restricted local receptive fields, lost spatial information, and inadequate contextual information are still plaguing artificial intelligence. A convolutional neural network (CNN) and a Mel-spectrogram are the basis of this cough recognition technique. First, we combine the voice in a variety of intricate settings and improve the audio data. After that, we preprocess the data to make sure its length is consistent and create a Mel-spectrogram out of it. A novel model for brain tumor segmentation (BTS), Intelligence Cascade U-Net (ICU-Net), is proposed to address these issues. It is built on dynamic convolution and uses a non-local attention mechanism. In order to reconstruct more detailed spatial information on brain tumours, the principal design is a two-stage cascade of 3DU-Net. The paper's objective is to identify the best learnable parameters that will maximize the likelihood of the data. After the network's ability to gather long-distance dependencies for AI, Expectation-Maximization is applied to the cascade network's lateral connections, enabling it to leverage contextual data more effectively. Lastly, to enhance the network's ability to capture local characteristics, dynamic convolutions with local adaptive capabilities are used in place of the cascade network's standard convolutions. We compared our results to those of other typical methods and ran extensive testing utilising the publicly available BraTS 2019/2020 datasets. The suggested method performs well on tasks involving BTS, according to the experimental data. The Dice scores for tumor core (TC), complete tumor, and enhanced tumor segmentation BraTS 2019/2020 validation sets are 0.897/0.903, 0.826/0.828, and 0.781/0.786, respectively, indicating high performance in BTS.

Dual-channel deep graph convolutional neural networks.

The dual-channel graph convolutional neural networks based on hybrid features jointly model the different features of networks, so that the features can learn each other and improve the performance of various subsequent machine learning tasks. However, current dual-channel graph convolutional neural networks are limited by the number of convolution layers, which hinders the performance improvement of the models. Graph convolutional neural networks superimpose multi-layer graph convolution operations, which would occur in smoothing phenomena, resulting in performance decreasing as the increasing number of graph convolutional layers. Inspired by the success of residual connections on convolutional neural networks, this paper applies residual connections to dual-channel graph convolutional neural networks, and increases the depth of dual-channel graph convolutional neural networks. Thus, a dual-channel deep graph convolutional neural network (D2GCN) is proposed, which can effectively avoid over-smoothing and improve model performance. D2GCN is verified on CiteSeer, DBLP, and SDBLP datasets, the results show that D2GCN performs better than the comparison algorithms used in node classification tasks.

Multi-scale feature aggregation and fusion network with self-supervised multi-level perceptual loss for textures preserving low-dose CT denoising.

Objective. The textures and detailed structures in computed tomography (CT) images are highly desirable for clinical diagnosis. This study aims to expand the current body of work on textures and details preserving convolutional neural networks for low-dose CT (LDCT) image denoising task.Approach. This study proposed a novel multi-scale feature aggregation and fusion network (MFAF-net) for LDCT image denoising. Specifically, we proposed a multi-scale residual feature aggregation module to characterize multi-scale structural information in CT images, which captures regional-specific inter-scale variations using learned weights. We further proposed a cross-level feature fusion module to integrate cross-level features, which adaptively weights the contributions of features from encoder to decoder by using a spatial pyramid attention mechanism. Moreover, we proposed a self-supervised multi-level perceptual loss module to generate multi-level auxiliary perceptual supervision for recovery of salient textures and structures of tissues and lesions in CT images, which takes advantage of abundant semantic information at various levels. We introduced parameters for the perceptual loss to adaptively weight the contributions of auxiliary features of different levels and we also introduced an automatic parameter tuning strategy for these parameters.Main results. Extensive experimental studies were performed to validate the effectiveness of the proposed method. Experimental results demonstrate that the proposed method can achieve better performance on both fine textures preservation and noise suppression for CT image denoising task compared with other competitive convolutional neural network (CNN) based methods.Significance. The proposed MFAF-net takes advantage of multi-scale receptive fields, cross-level features integration and self-supervised multi-level perceptual loss, enabling more effective recovering of fine textures and detailed structures of tissues and lesions in CT images.

Predicting the wicking rate of nitrocellulose membranes from recipe data: a case study using ANN at a membrane manufacturing in South Korea.

Lateral flow assays have been widely used for detecting coronavirus disease 2019 (COVID-19). A lateral flow assay consists of a Nitrocellulose (NC) membrane, which must have a specific lateral flow rate for the proteins to react. The wicking rate is conventionally used as a method to assess the lateral flow in membranes. We used multiple regression and artificial neural networks (ANN) to predict the wicking rate of NC membranes based on membrane recipe data. The developed ANN predicted the wicking rate with a mean square error of 0.059, whereas the multiple regression had a square error of 0.503. This research also highlighted the significant impact of the water content on the wicking rate through images obtained from scanning electron microscopy. The findings of this research can cut down the research and development costs of novel NC membranes with a specific wicking rate significantly, as the algorithm can predict the wicking rate based on the membrane recipe.

Tumor Segmentation in Intraoperative Fluorescence Images Based on Transfer Learning and Convolutional Neural Networks.

OBJECTIVE: To propose a transfer learning based method of tumor segmentation in intraoperative fluorescence images, which will assist surgeons to efficiently and accurately identify the boundary of tumors of interest. METHODS: We employed transfer learning and deep convolutional neural networks (DCNNs) for tumor segmentation. Specifically, we first pre-trained four networks on the ImageNet dataset to extract low-level features. Subsequently, we fine-tuned these networks on two fluorescence image datasets (ABFM and DTHP) separately to enhance the segmentation performance of fluorescence images. Finally, we tested the trained models on the DTHL dataset. The performance of this approach was compared and evaluated against DCNNs trained end-to-end and the traditional level-set method. RESULTS: The transfer learning-based UNet++ model achieved high segmentation accuracies of 82.17% on the ABFM dataset, 95.61% on the DTHP dataset, and 85.49% on the DTHL test set. For the DTHP dataset, the pre-trained Deeplab v3 + network performed exceptionally well, with a segmentation accuracy of 96.48%. Furthermore, all models achieved segmentation accuracies of over 90% when dealing with the DTHP dataset. CONCLUSION: To the best of our knowledge, this study explores tumor segmentation on intraoperative fluorescent images for the first time. The results show that compared to traditional methods, deep learning has significant advantages in improving segmentation performance. Transfer learning enables deep learning models to perform better on small-sample fluorescence image data compared to end-to-end training. This discovery provides strong support for surgeons to obtain more reliable and accurate image segmentation results during surgery.

Convolutional neural networks develop major organizational principles of early visual cortex when enhanced with retinal sampling.

Primate visual cortex exhibits key organizational principles: cortical magnification, eccentricity-dependent receptive field size and spatial frequency tuning as well as radial bias. We provide compelling evidence that these principles arise from the interplay of the non-uniform distribution of retinal ganglion cells, and a quasi-uniform convergence rate from the retina to the cortex. We show that convolutional neural networks outfitted with a retinal sampling layer, which resamples images according to retinal ganglion cell density, develop these organizational principles. Surprisingly, our results indicate that radial bias is spatial-frequency dependent and only manifests for high spatial frequencies. For low spatial frequencies, the bias shifts towards orthogonal orientations. These findings introduce a novel hypothesis about the origin of radial bias. Quasi-uniform convergence limits the range of spatial frequencies (in retinal space) that can be resolved, while retinal sampling determines the spatial frequency content throughout the retina.

DNA shape features improve prediction of CRISPR/Cas9 activity.

The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine learning models have been proposed for the prediction of Cas9 activity at unintended sites, yet feature engineering plays a major role in the outcome of the predictors. This study evaluates the improvement in the performance of similar predictors upon inclusion of epigenetic and DNA shape feature groups in the conventionally used sequence-based Cas9 target and off-target datasets. The approach involved the utilization of neural networks trained on a diverse range of parameters, allowing us to systematically assess the performance increase for the meticulously designed datasets- (i) sequence only, (ii) sequence and epigenetic features, and (iii) sequence, epigenetic and DNA shape feature datasets. The addition of DNA shape information significantly improved predictive performance, evaluated by Akaike and Bayesian information criteria. The evaluation of individual feature importance by permutation and LIME-based methods also indicates that not only sequence features like mismatches and nucleotide composition, but also base pairing parameters like opening and stretch, that are indicative of distortion in the DNA-RNA hybrid in the presence of mismatches, influence model outcomes.

ALL classification using neural ensemble and memetic deep feature optimization.

Acute lymphoblastic leukemia (ALL) is a fatal blood disorder characterized by the excessive proliferation of immature white blood cells, originating in the bone marrow. An effective prognosis and treatment of ALL calls for its accurate and timely detection. Deep convolutional neural networks (CNNs) have shown promising results in digital pathology. However, they face challenges in classifying different subtypes of leukemia due to their subtle morphological differences. This study proposes an improved pipeline for binary detection and sub-type classification of ALL from blood smear images. At first, a customized, 88 layers deep CNN is proposed and trained using transfer learning along with GoogleNet CNN to create an ensemble of features. Furthermore, this study models the feature selection problem as a combinatorial optimization problem and proposes a memetic version of binary whale optimization algorithm, incorporating Differential Evolution-based local search method to enhance the exploration and exploitation of feature search space. The proposed approach is validated using publicly available standard datasets containing peripheral blood smear images of various classes of ALL. An overall best average accuracy of 99.15% is achieved for binary classification of ALL with an 85% decrease in the feature vector, together with 99% precision and 98.8% sensitivity. For B-ALL sub-type classification, the best accuracy of 98.69% is attained with 98.7% precision and 99.57% specificity. The proposed methodology shows better performance metrics as compared with several existing studies.

BP neural network-based analysis of the applicability of NMF in side-step cutting.

Background: Although the spatio-temporal structure of muscle activation in cutting have been studied extensively, including time-varying motor primitives and time-invariant motor modules under various conditions, the factorisation methods suitable for cutting are unclear, and the extent to which each factorisation method loses information about movement during dimensionality reduction is uncertain. Research question: To clarify the extent to which NMF, PCA and ICA retain information about movement when downscaling, and to explore the factorisation method suitable for cutting. Methods: The kinematic data during cutting was captured with a Vicon motion capture system, from which the kinematic features of the pelvic centre of mass were calculated. NMF, PCA and ICA were used to obtain muscle synergies based on sEMG of the cutting at different angles, respectively. A back propagation neural network was constructed using temporal component of synergy as input and the kinematics data of pelvic as output. Calculation of the Hurst index using fractal analysis based on the temporal component of muscle synergy. Results: The quality of sEMG reconstruction is significantly higher with ICA (P < 0.01) than with NMF and PCA for the cutting. The NMF reconstruction has a high degree of preservation of movement, whereas the ICA loses movement information about the most of the swing phase, and the PCA loses information related to the change of direction. Hurst index less than 0.5 for all three angles of cutting. Significance: NMF is suitable for extracting muscle synergies in all directions of cutting. Information related to movement may be lost when using PCA and ICA to extract the synergy of cutting. The high individual variability of muscle synergy in cutting may be responsible for the loss of movement information in muscle synergy.

A novel approach to texture recognition combining deep learning orthogonal convolution with regional input features.

Textures provide a powerful segmentation and object detection cue. Recent research has shown that deep convolutional nets like Visual Geometry Group (VGG) and ResNet perform well in non-stationary texture datasets. Non-stationary textures have local structures that change from one region of the image to the other. This is consistent with the view that deep convolutional networks are good at detecting local microstructures disguised as textures. However, stationary textures are textures that have statistical properties that are constant or slow varying over the entire region are not well detected by deep convolutional networks. This research demonstrates that simple seven-layer convolutional networks can obtain better results than deep networks using a novel convolutional technique called orthogonal convolution with pre-calculated regional features using grey level co-occurrence matrix. We obtained an average of 8.5% improvement in accuracy in texture recognition on the Outex dataset over GoogleNet, ResNet, VGG and AlexNet.

KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography.

Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.

Statistical data pre-processing and time series incorporation for high-efficacy calibration of low-cost NO2 sensor using machine learning.

Air pollution stands as a significant modern-day challenge impacting life quality, the environment, and the economy. It comprises various pollutants like gases, particulate matter, biological molecules, and more, stemming from sources such as vehicle emissions, industrial operations, agriculture, and natural events. Nitrogen dioxide (NO2), among these harmful gases, is notably prevalent in densely populated urban regions. Given its adverse effects on health and the environment, accurate monitoring of NO2 levels becomes imperative for devising effective risk mitigation strategies. However, the precise measurement of NO2 poses challenges as it traditionally relies on costly and bulky equipment. This has prompted the development of more affordable alternatives, although their reliability is often questionable. The aim of this article is to introduce a groundbreaking method for precisely calibrating cost-effective NO2 sensors. This technique involves statistical preprocessing of low-cost sensor readings, aligning their distribution with reference data. Central to this calibration is an artificial neural network (ANN) surrogate designed to predict sensor correction coefficients. It utilizes environmental variables (temperature, humidity, atmospheric pressure), cross-references auxiliary NO2 sensors, and incorporates short time series of previous readings from the primary sensor. These methods are complemented by global data scaling. Demonstrated using a custom-designed cost-effective monitoring platform and high-precision public reference station data collected over 5 months, every component of our calibration framework proves crucial, contributing to its exceptional accuracy (with a correlation coefficient near 0.95 concerning the reference data and an RMSE below 2.4 µg/m3). This level of performance positions the calibrated sensor as a viable, cost-effective alternative to traditional monitoring approaches.

Micro-and mesoscale aspects of neurodegeneration in engineered human neural networks carrying the LRRK2 G2019S mutation.

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been widely linked to Parkinson's disease, where the G2019S variant has been shown to contribute uniquely to both familial and sporadic forms of the disease. LRRK2-related mutations have been extensively studied, yet the wide variety of cellular and network events related to these mutations remain poorly understood. The advancement and availability of tools for neural engineering now enable modeling of selected pathological aspects of neurodegenerative disease in human neural networks in vitro. Our study revealed distinct pathology associated dynamics in engineered human cortical neural networks carrying the LRRK2 G2019S mutation compared to healthy isogenic control neural networks. The neurons carrying the LRRK2 G2019S mutation self-organized into networks with aberrant morphology and mitochondrial dynamics, affecting emerging structure-function relationships both at the micro-and mesoscale. Taken together, the findings of our study points toward an overall heightened metabolic demand in networks carrying the LRRK2 G2019S mutation, as well as a resilience to change in response to perturbation, compared to healthy isogenic controls.

A review of algorithms and software for real-time electric field modeling techniques for transcranial magnetic stimulation.

Transcranial magnetic stimulation (TMS) is a device-based neuromodulation technique increasingly used to treat brain diseases. Electric field (E-field) modeling is an important technique in several TMS clinical applications, including the precision stimulation of brain targets with accurate stimulation density for the treatment of mental disorders and the localization of brain function areas for neurosurgical planning. Classical methods for E-field modeling usually take a long computation time. Fast algorithms are usually developed with significantly lower spatial resolutions that reduce the prediction accuracy and limit their usage in real-time or near real-time TMS applications. This review paper discusses several modern algorithms for real-time or near real-time TMS E-field modeling and their advantages and limitations. The reviewed methods include techniques such as basis representation techniques and deep neural-network-based methods. This paper also provides a review of software tools that can integrate E-field modeling with navigated TMS, including a recent software for real-time navigated E-field mapping based on deep neural-network models.

Lexical-Semantic Content, Not Syntactic Structure, Is the Main Contributor to ANN-Brain Similarity of fMRI Responses in the Language Network.

Representations from artificial neural network (ANN) language models have been shown to predict human brain activity in the language network. To understand what aspects of linguistic stimuli contribute to ANN-to-brain similarity, we used an fMRI data set of responses to n = 627 naturalistic English sentences (Pereira et al., 2018) and systematically manipulated the stimuli for which ANN representations were extracted. In particular, we (i) perturbed sentences' word order, (ii) removed different subsets of words, or (iii) replaced sentences with other sentences of varying semantic similarity. We found that the lexical-semantic content of the sentence (largely carried by content words) rather than the sentence's syntactic form (conveyed via word order or function words) is primarily responsible for the ANN-to-brain similarity. In follow-up analyses, we found that perturbation manipulations that adversely affect brain predictivity also lead to more divergent representations in the ANN's embedding space and decrease the ANN's ability to predict upcoming tokens in those stimuli. Further, results are robust as to whether the mapping model is trained on intact or perturbed stimuli and whether the ANN sentence representations are conditioned on the same linguistic context that humans saw. The critical result-that lexical-semantic content is the main contributor to the similarity between ANN representations and neural ones-aligns with the idea that the goal of the human language system is to extract meaning from linguistic strings. Finally, this work highlights the strength of systematic experimental manipulations for evaluating how close we are to accurate and generalizable models of the human language network.

Nonlinear Growth Dynamics of Neuronal Cells Cultured on Directional Surfaces.

During the development of the nervous system, neuronal cells extend axons and dendrites that form complex neuronal networks, which are essential for transmitting and processing information. Understanding the physical processes that underlie the formation of neuronal networks is essential for gaining a deeper insight into higher-order brain functions such as sensory processing, learning, and memory. In the process of creating networks, axons travel towards other recipient neurons, directed by a combination of internal and external cues that include genetic instructions, biochemical signals, as well as external mechanical and geometrical stimuli. Although there have been significant recent advances, the basic principles governing axonal growth, collective dynamics, and the development of neuronal networks remain poorly understood. In this paper, we present a detailed analysis of nonlinear dynamics for axonal growth on surfaces with periodic geometrical patterns. We show that axonal growth on these surfaces is described by nonlinear Langevin equations with speed-dependent deterministic terms and gaussian stochastic noise. This theoretical model yields a comprehensive description of axonal growth at both intermediate and long time scales (tens of hours after cell plating), and predicts key dynamical parameters, such as speed and angular correlation functions, axonal mean squared lengths, and diffusion (cell motility) coefficients. We use this model to perform simulations of axonal trajectories on the growth surfaces, in turn demonstrating very good agreement between simulated growth and the experimental results. These results provide important insights into the current understanding of the dynamical behavior of neurons, the self-wiring of the nervous system, as well as for designing innovative biomimetic neural network models.

Photorefraction Simulates Well the Plasticity of Neural Synaptic Connections.

In recent years, the need for systems capable of achieving the dynamic learning and information storage efficiency of the biological brain has led to the emergence of neuromorphic research. In particular, neuromorphic optics was born with the idea of reproducing the functional and structural properties of the biological brain. In this context, solitonic neuromorphic research has demonstrated the ability to reproduce dynamic and plastic structures capable of learning and storing through conformational changes in the network. In this paper, we demonstrate that solitonic neural networks are capable of mimicking the functional behaviour of biological neural tissue, in terms of synaptic formation procedures and dynamic reinforcement.

A Time-Frequency Domain Mixed Attention-Based Approach for Classifying Wood-Boring Insect Feeding Vibration Signals Using a Deep Learning Model.

Wood borers, such as the emerald ash borer and holcocerus insularis staudinger, pose a significant threat to forest ecosystems, causing damage to trees and impacting biodiversity. This paper proposes a neural network for detecting and classifying wood borers based on their feeding vibration signals. We utilize piezoelectric ceramic sensors to collect drilling vibration signals and introduce a novel convolutional neural network (CNN) architecture named Residual Mixed Domain Attention Module Network (RMAMNet).The RMAMNet employs both channel-domain attention and time-domain attention mechanisms to enhance the network's capability to learn meaningful features. The proposed system outperforms established networks, such as ResNet and VGG, achieving a recognition accuracy of 95.34% and an F1 score of 0.95. Our findings demonstrate that RMAMNet significantly improves the accuracy of wood borer classification, indicating its potential for effective pest monitoring and classification tasks. This study provides a new perspective and technical support for the automatic detection, classification, and early warning of wood-boring pests in forestry.