Dimensional Representation Research Articles

SeqDPI: A 1D-CNN approach for predicting binding affinity of kinase inhibitors.

Predicting drug target binding affinity has huge relevance in Modern drug discovery and drug repositioning processes which assist doctors to come up with new drugs or even use the existing drugs for new target proteins. In silico models, using advanced deep learning techniques could further assist these prediction tasks by providing most prominent drug target pairs. Considering these factors, a deep learning based algorithmic framework is developed in this study to support drug target interaction prediction. The proposed SeqDPI model extract the relevant drug and protein features from the one dimensional Sequential representation of the dataset considered using optimized CNN networks that deploy convolutions on varying length of amino acid subsequence's to capture hidden pattern, the convolved drug- protein features obtained are then used as an input to L2 penalized feed forward neural network which matches the local residue patterns in protein classes with molecular fingerprints of drugs to predict the binding strength for all drug target pairs. The proposed model reduces the convolution strain typically encountered in existing in silico models that utilize complex 3D structures of drug protein datasets. The result shows that the SeqDPI model achieves a mean square error MSE of (0.167) across cross validation folds, outperforming baseline models such as KronRLS (0.406), Simboost (0.226), and DeepPS (0.214). Additionally, SeqDPI attains a high CI score of 0.9114 on the benchmark KIBA dataset, demonstrating its statistical significance and computational efficiency compared to existing methods. This gives the relevance and effectiveness of SeqDPI model in accurately predicting binding affinities while working with simpler one-dimensional data, making it a robust and computationally cost-effective solution for drug-target interaction prediction.

IGTP: Learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics.

Deep-learning models like Variational AutoEncoder have enabled low dimensional cellular embedding representation for large-scale single-cell transcriptomes and shown great flexibility in downstream tasks. However, biologically meaningful latent space is usually missing if no specific structure is designed. Here, we engineered a novel interpretable generative transcriptional program (iGTP) framework that could model the importance of transcriptional program (TP) space and protein-protein interactions (PPI) between different biological states. We demonstrated the performance of iGTP in a diverse biological context using gene ontology, canonical pathway, and different PPI curation. iGTP not only elucidated the ground truth of cellular responses but also surpassed other deep learning models and traditional bioinformatics methods in functional enrichment tasks. By integrating the latent layer with a graph neural network framework, iGTP could effectively infer cellular responses to perturbations. Lastly, we applied iGTP TP embeddings with a latent diffusion model to accurately generate cell embeddings for specific cell types and states. We anticipate that iGTP will offer insights at both PPI and TP levels and holds promise for predicting responses to novel perturbations.

Contrast and content preserving HDMR-based color-to-gray conversion

Converting a color image into a grayscale image is a complex problem that is based on preserving color contrast, sharpness, and luminance. In this paper, a novel image decolorization algorithm is proposed using High Dimensional Model Representation (HDMR) with an optimization procedure that retains color content and contrast. In the proposed algorithm, a color image is first decomposed into HDMR components and then the components are categorized depending on whether they are colored or colorless. After that, the image is reconstructed by merging the weighted colored and colorless HDMR components. The weight coefficients are determined by an optimization process. The proposed algorithm both visually and quantitatively compared with state-of-the-art methods in the literature using various performance evaluation metrics. As regards all obtained results, the HDMR based image decolorization algorithm is more potent and has better performance in overall comparison. Most importantly, this algorithm has a flexible structure as it is able to produce various grayscale images for different thresholds of visible color contrast which makes this algorithm superior given that it is the only one that accomplishes this feat in the literature to the best of our knowledge.

An Efficient One-Dimensional Texture Representation Approach for Lung Disease Diagnosis

The remarkable increase in published medical imaging datasets for chest X-rays has significantly improved the performance of deep learning techniques to classify lung diseases efficiently. However, large datasets require special arrangements to make them suitable, accessible, and practically usable in remote clinics and emergency rooms. Additionally, it increases the computational time and image-processing complexity. This study investigates the efficiency of converting the 2D chest X-ray into one-dimensional texture representation data using descriptive statistics and local binary patterns, enabling the use of feed-forward neural networks to efficiently classify lung diseases within a short time and with cost effectiveness. This method bridges diagnostic gaps in healthcare services and improves patient outcomes in remote hospitals and emergency rooms. It also could reinforce the crucial role of technology in advancing healthcare. Utilizing the Guangzhou and PA datasets, our one-dimensional texture representation achieved 99% accuracy with a training time of 10.85 s and 0.19 s for testing. In the PA dataset, it achieved 96% accuracy with a training time of 38.14 s and a testing time of 0.17 s, outperforming EfficientNet, EfficientNet-V2-Small, and MobileNet-V3-Small. Therefore, this study suggests that the dimensional texture representation is fast and effective for lung disease classification.

Time series forecasting of multiphase microstructure evolution using deep learning

Microstructure evolution, which plays a critical role in determining materials properties, is commonly simulated by the high-fidelity but computationally expensive phase-field method. To address this, we approximate microstructure evolution as a time series forecasting problem within the domain of deep learning. Our approach involves implementing a cost-effective surrogate model that accurately predicts the spatiotemporal evolution of microstructures, taking an example of spinodal decomposition in binary and ternary mixtures. Our surrogate model combines a convolutional autoencoder to reduce the dimensional representation of these microstructures with convolutional recurrent neural networks to forecast their temporal evolution. We use different variants of recurrent neural networks to compare their efficacy in developing surrogate models for phase-field predictions. On average, our deep learning framework demonstrates excellent accuracy and speedup relative to the “ground truth” phase-field simulations. We use quantitative measures to demonstrate how surrogate model predictions can effectively replace the phase-field timesteps without compromising accuracy in predicting the long-term evolution trajectory. Additionally, by emulating a transfer learning approach, our framework performs satisfactorily in predicting new microstructures resulting from alloy composition and physics unknown to the model. Therefore, our approach offers a useful data-driven alternative and accelerator to the materials microstructure simulation workflow.

Patients' beliefs as predictors of patient satisfaction and health-related quality of life in pediatric rehabilitation.

This study investigated the predictive value of illness and treatment beliefs for patient satisfaction and health-related quality of life (HRQOL) in adolescents receiving inpatient rehabilitation treatment. In addition, we examined the relationship between fulfilled rehabilitation-related treatment expectations and patient satisfaction. In this longitudinal study (recruitment between April 2019 and March 2020), 170 participants (M = 14.3 years [SD = 1.6]) answered self-report questionnaires before and at the end of rehabilitation (6 weeks later). We applied multiple hierarchical regression analyses, controlling for sociodemographic and diagnoses variables. The results showed fulfilled expectations of treatment success and sustainability to be a significant predictor of patient satisfaction (p < .01). The illness belief dimension of emotional representation predicted HRQOL (p < .01). Rehabilitation-related treatment beliefs were not predictive of any outcome. This study provides a first insight into the relationships between these constructs in the context of inpatient pediatric rehabilitation. However, future research is needed to further examine illness and treatment beliefs in this specific treatment setting. Practical implications concern the incorporation of children's and adolescents' beliefs into treatment management to optimize rehabilitation outcomes. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

SGW-YOLOv8n: An Improved YOLOv8n-Based Model for Apple Detection and Segmentation in Complex Orchard Environments

This study addresses the problem of detecting occluded apples in complex unstructured environments in orchards and proposes an apple detection and segmentation model based on improved YOLOv8n-SGW-YOLOv8n. The model improves apple detection and segmentation by combining the SPD-Conv convolution module, the GAM global attention mechanism, and the Wise-IoU loss function, which enhances the accuracy and robustness. The SPD-Conv module preserves fine-grained features in the image by converting spatial information into channel information, which is particularly suitable for small target detection. The GAM global attention mechanism enhances the recognition of occluded targets by strengthening the feature representation of channel and spatial dimensions. The Wise-IoU loss function further optimises the regression accuracy of the target frame. Finally, the pre-prepared dataset is used for model training and validation. The results show that the SGW-YOLOv8n model significantly improves relative to the original YOLOv8n in target detection and instance segmentation tasks, especially in occlusion scenes. The model improves the detection mAP to 75.9% and the segmentation mAP to 75.7% and maintains a processing speed of 44.37 FPS, which can meet the real-time requirements, providing effective technical support for the detection and segmentation of fruits in complex unstructured environments for fruit harvesting robots.

PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods

Background: Phage therapy has a broad application prospect as a novel therapeutic method, and Phage Virion Proteins (PVP) can recognize the host and bind to surface receptors, which is of great significance for the development of antimicrobial drugs for the treatment of infectious diseases caused by bacteria. In recent years, several PVP predictors based on machine learning have been developed, which usually use a single feature to train the learner. In contrast, higher dimensional feature representations tend to contain more potential sequence information. Methods: In this work, we construct a stacking model PredPVP for PVP prediction by combining multiple features and using feature selection methods. Specifically, the sequence is first encoded using seven features. For this high-dimensional feature representation, three feature selection methods wereutilized to remove redundant features, then integrated with eight machine learning algorithms. Finally, probability features and class features (PCFs) generated by 24 base models were put into logistic regression (LR) to train the model. Results: The results of the independent test set indicate that PredPVP has higher performance compared to other existing predictors, with an AUC of 93.4%. Conclusion: We expect PredPVP to be used as a tool for large-scale PVP recognition, providing a new way for the development of novel antimicrobials and accelerating its application in actual treatment. The datasets and source codes used in this study are available at https://github.com/caoqian23/PredPVP.

Modeling takeover time for non-driving related tasks using hybrid deep neural networks in conditionally automated vehicles

To enhance the safety of the transition from autonomous to manual driving control, one of the key factors is quantifying the safe takeover transition, namely the takeover time. Previous studies have focused on factors influencing takeover time and predicting takeover time using traditional methods, but there is a lack of research utilizing deep learning networks and driver physiological factors for takeover time prediction. Toward this end, we propose a hybrid deep learning network model dedicated to predicting drivers’ takeover time with a dataset obtained from a bench experiment involving 46 drivers. Firstly, to address the potential information loss commonly associated with traditional manual feature extraction techniques, a convolutional neural network (CNN) is developed to automatically extract physiological spatial representations from drivers. Additionally, a double-layer bidirectional long short-term memory network (DBiLSTM) is incorporated to model the physiological time representation dimension, enabling a more refined representation of physiological signals. Then, to tackle the complexities introduced by individual driver variations, a self-attention mechanism is enabling the model to automatically prioritize critical features, thereby enhancing the accuracy and reliability of its predictions. The results demonstrate that the proposed approach surpasses traditional machine learning network models in predictive accuracy for takeover time prediction, thereby exhibiting novelty in the field of vehicle takeover control research. This provides a more reliable technical foundation for anticipating the durations of vehicle takeovers.

Luttinger liquid tensor network: Sine versus tangent dispersion of massless Dirac fermions

To apply the powerful many-body techniques of tensor networks to massless Dirac fermions, one wants to discretize the p·σ Hamiltonian and construct a matrix-product-operator (MPO) representation. We compare two alternative discretization schemes, one with a sine dispersion, the other with a tangent dispersion, applied to a one-dimensional Luttinger liquid with Hubbard interaction. Both types of lattice fermions allow for an exact MPO representation of low bond dimension, so they are efficiently computable, but only the tangent dispersion gives a power law decay of the propagator in agreement with the continuum limit: The sine dispersion is gapped by the interactions, evidenced by an exponentially decaying propagator. Our construction of a tensor network with an unpaired Dirac cone works around the fermion-doubling obstruction by exploiting the fact that the Hamiltonian of tangent fermions permits a generalized eigenproblem. Published by the American Physical Society 2024

A new matrix representation of the Maxwell equations based on the Riemann–Silberstein–Weber vector for a linear inhomogeneous medium

We derive a new eight dimensional matrix representation of the Maxwell equations for a linear homogeneous medium and extend it to the case of a linear inhomogneous medium. This derivation starts ab initio with the Maxwell equations and uses arguments based on the algebra of the Pauli matrices. This process leads automatically to the matrix representation based on the Riemann–Silberstein–Weber (RSW) vector. The new representation for the homogeneous medium is a direct sum of four Pauli matrix blocks. This aspect of the new representation should make it suitable for studying the propagation of electromagnetic waves in a linear inhomogeneous medium adopting the techniques of quantum mechanics treating the inhomogeneity as a perturbation. The new representation is used to rederive the Mukunda–Simon–Sudarshan matrix substitution rule for transition from the Helmholtz scalar wave optics to the Maxwell vector wave optics.

An Orbital Basis Set for Double Photoionization of Atoms and Molecules.

The ab initio theoretical treatment of one-photon double photoionization processes has been limited to atoms and diatomic molecules by the challenges posed by large grid-based representations of the double ionized continuum wave function. To provide a path for extensions to polyatomics, an energy-adapted orbital basis approach is demonstrated that reduces the dimensions of such representations and simultaneously allows larger time steps in time-dependent computational descriptions of double ionization. Additionally, an algorithm that exploits the diagonal nature of the two-electron integrals in the grid basis and dramatically accelerates the transformation between grid and orbital representations is presented. Excellent agreement between the present results and benchmark theoretical calculations is found for H- and Be atoms, as well as the hydrogen molecule, including for the triply differential cross sections that relate the angular distribution and energy sharing of all of the particles in the molecular frame.

An advanced high dimensional model representation approach for internal combustion engine modeling and optimization

This work introduces an efficient data-driven approach for engine performance modeling and optimization. A highly accurate and robust high-dimensional model representation (HDMR) surrogate model is developed based on the dataset generated from a coupled KIVA4-CHEMKIN Ⅱ software. The HDMR model is integrated with a multi-objective optimization algorithm, enabling the automatic identification of optimal combustion strategies. Results suggest that the constructed HDMR model is able to accurately predict the engine performance and exhaust gas emissions with negligible CPU costs. Moreover, the model effectively identifies optimal engine operating conditions, leading to enhanced fuel efficiency.

Language proficiency is associated with neural representational dimensionality of semantic concepts

Previous studies suggest that semantic concepts are characterized by high-dimensional neural representations and that language proficiency affects semantic processing. However, it is not clear whether language proficiency modulates the dimensional representations of semantic concepts at the neural level. To address this question, the present study adopted principal component analysis (PCA) and representational similarity analysis (RSA) to examine the differences in representational dimensionalities (RDs) and in semantic representations between words in highly proficient (Chinese) and less proficient (English) language. PCA results revealed that language proficiency increased the dimensions of lexical representations in the left inferior frontal gyrus, temporal pole, inferior temporal gyrus, supramarginal gyrus, angular gyrus, and fusiform gyrus. RSA results further showed that these regions represented semantic information and that higher semantic representations were observed in highly proficient language relative to less proficient language. These results suggest that language proficiency is associated with the neural representational dimensionality of semantic concepts.

Genetic and clinical correlates of two neuroanatomical AI dimensions in the Alzheimer’s disease continuum

Alzheimer’s disease (AD) is associated with heterogeneous atrophy patterns. We employed a semi-supervised representation learning technique known as Surreal-GAN, through which we identified two latent dimensional representations of brain atrophy in symptomatic mild cognitive impairment (MCI) and AD patients: the “diffuse-AD” (R1) dimension shows widespread brain atrophy, and the “MTL-AD” (R2) dimension displays focal medial temporal lobe (MTL) atrophy. Critically, only R2 was associated with widely known sporadic AD genetic risk factors (e.g., APOE ε4) in MCI and AD patients at baseline. We then independently detected the presence of the two dimensions in the early stages by deploying the trained model in the general population and two cognitively unimpaired cohorts of asymptomatic participants. In the general population, genome-wide association studies found 77 genes unrelated to APOE differentially associated with R1 and R2. Functional analyses revealed that these genes were overrepresented in differentially expressed gene sets in organs beyond the brain (R1 and R2), including the heart (R1) and the pituitary gland, muscle, and kidney (R2). These genes were enriched in biological pathways implicated in dendritic cells (R2), macrophage functions (R1), and cancer (R1 and R2). Several of them were “druggable genes” for cancer (R1), inflammation (R1), cardiovascular diseases (R1), and diseases of the nervous system (R2). The longitudinal progression showed that APOEε4, amyloid, and tau were associated with R2 at early asymptomatic stages, but this longitudinal association occurs only at late symptomatic stages in R1. Our findings deepen our understanding of the multifaceted pathogenesis of AD beyond the brain. In early asymptomatic stages, the two dimensions are associated with diverse pathological mechanisms, including cardiovascular diseases, inflammation, and hormonal dysfunction—driven by genes different from APOE—which may collectively contribute to the early pathogenesis of AD. All results are publicly available at https://labs-laboratory.com/medicine/.

Pathological personality dimensions and neurobiological emotional reactivity.

The Hierarchical Taxonomy of Psychopathology (HiTOP) offers a promising framework to identify the neurobiological mechanisms of psychopathology. Many forms of psychopathology are characterized by dysfunctional emotional reactivity. The late positive potential (LPP) is an event-related potential component that provides an index of neurobiological emotional reactivity. Several categorical disorders have demonstrated a similar association with the emotion-modulated LPP. It is possible that higher-order dimensional representations of psychopathology might explain the comparable results. The present study examined the association between HiTOP-consistent pathological personality dimensions across multiple levels of the hierarchy and neurobiological emotional reactivity. The sample included 215 18-35-year-old adults (86% female) who were oversampled for psychopathology. Participants completed the emotional interrupt task while electroencephalography was recorded to examine the LPP. Participants also completed the Comprehensive Assessment of Traits relevant to Personality Disorders to assess pathological personality. At the spectra level, higher negative emotionality was associated with a larger emotion-modulated LPP, while higher detachment was associated with a smaller emotion-modulated LPP. There were no associations between higher-order psychopathology levels and the emotion-modulated LPP. Compared to categorical diagnoses, spectra-level personality pathology dimensions significantly improved the prediction of the emotion-modulated LPP. The present study indicates that HiTOP spectra levels of negative emotionality and detachment demonstrate unique associations with neurobiological emotional reactivity. The study highlights the utility of examining dimensional and hierarchical, rather than categorical, representations of psychopathology in the attempt to identify the neurobiological origins of psychopathology.

Autoencoder-based inverse design and surrogate-based optimization of an integrated wet granulation manufacturing process

In pharmaceutical manufacturing, integrating model-based design and optimization can be beneficial for accelerating process development. This study explores the utilization of Machine Learning (ML) techniques as a surrogate model for the optimization of a three-unit wet-granulation based flowsheet model for solid dosage form manufacturing. First, a reduced representation of a wet granulation flowsheet model is developed, incorporating a granulation and milling process, along with a novel dissolution model that accounts for the effect of particle size, porosity, and microstructure on dissolution rate. Two optimization approaches are compared, including an autoencoder-based inverse design and a surrogate-based forward optimization. Both methods address the bi-objective problem of maximizing dissolution time and product yield by identifying the optimal granulation and mill process parameters. For this case study, both approaches were effective and incurred a similar computational cost, averaging under 4 s. However, the autoencoder approach offers an advantage through dimensionality reduction, a feature not available in surrogate-based optimization. Dimensional reduction is particularly beneficial for complex process designs with numerous inputs and outputs. The lower dimensional representation helps improve process understanding through enhanced visualization of the process design space and facilitates feasibility studies involving multiple constraints. The autoencoder-based inverse design introduced in this work showcases an implementation of AI and ML in pharmaceutical process development, demonstrating the potential to enhance process efficiency and product quality in complex manufacturing scenarios.

Nine Neuroimaging-AI Endophenotypes Unravel Disease Heterogeneity and Partial Overlap across Four Brain Disorders: A Dimensional Neuroanatomical Representation.

Disease heterogeneity poses a significant challenge for precision diagnostics. Recent work leveraging artificial intelligence has offered promise to dissect this heterogeneity by identifying complex intermediate brain phenotypes, herein called dimensional neuroimaging endophenotypes (DNEs). We advance the argument that these DNEs capture the degree of expression of respective neuroanatomical patterns measured, offering a dimensional neuroanatomical representation for studying disease heterogeneity and similarities of neurologic and neuropsychiatric diseases. We investigate the presence of nine such DNEs derived from independent yet harmonized studies on Alzheimer's disease (AD1-2)1, autism spectrum disorder (ASD1-3)2, late-life depression (LLD1-2)3, and schizophrenia (SCZ1-2)4, in the general population of 39,178 participants in the UK Biobank study. Phenome-wide associations revealed prominent associations between the nine DNEs and phenotypes related to the brain and other human organ systems. This phenotypic landscape aligns with the SNP-phenotype genome-wide associations, revealing 31 genomic loci associated with the nine DNEs (Bonferroni corrected P-value < 5×10-8/9). The DNEs exhibited significant genetic correlations, colocalization, and causal relationships with multiple human organ systems and chronic diseases. A causal effect (odds ratio=1.25 [1.11, 1.40], P-value=8.72×10-4) was established from AD2, characterized by focal medial temporal lobe atrophy, to AD. The nine DNEs, along with their polygenic risk scores, significantly enhanced the predictive accuracy for 14 systemic disease categories, particularly for conditions related to mental health and the central nervous system, as well as mortality outcomes. These findings underscore the potential of the nine DNEs to capture the expression of disease-related brain phenotypes in individuals of the general population and to relate such measures with genetics, lifestyle factors, and chronic diseases. All results are publicly available at https://labs-laboratory.com/medicine/.

"I Want Lower Tone for Work-Related Notifications": Exploring the Effectiveness of User-Assigned Notification Alerts in Improving User Speculation of and Attendance to Mobile Notifications

Research indicates that smartphone users often speculate about notifications upon sensing their arrival, aiding their decision to attend to them. This speculation, however, relies on the presence of sufficient clues to associate with the notification, which are not always available. To address this challenge, through an experience sampling study, we investigated the effectiveness of delivering user-assigned alerts in influencing users' speculation accuracy, attendance effectiveness, and perceived disturbance. Our findings suggest that while user-assigned alerts enhanced the accuracy of speculation and improved participants' decisions to attend to notifications, the increased notification awareness sometimes led participants to view their decision to ignore notifications as less favorable. Moreover, we found that sporadic alert delivery disrupted the association between the alert and the notification, leading to no reduction in perceived disturbance nor improvement in speculation accuracy. In assigning alerts to notifications, participants considered five strategies: familiarity, distinctiveness, disturbance, emotional resonance, and dimension representation.

Higher-order sensitivity analyses to understand the role of FE input parameters on the simulation of composites in progressive fracture tests

With the rise of data-driven engineering methods, such as machine learning, a comprehensive understanding of the underlying data fed into these algorithms is required for effectively applying these methods. This study presents two highly efficient Finite Element (FE) models that operate at different length scales, based on Continuum Damage Mechanics (CDM). The combination with Random Sampling-High Dimensional Model Representation (RS-HDMR) enables the determination of influential FE input parameters and their correlations to simulate Fibre Reinforced Polymer (FRP) composites subjected to a variety of progressive fracture tests in tension and compression. The results indicate that laminate-based models utilise the FE input parameters efficiently where all parameters are found to be influential. On the other hand, only fibre-related properties are relevant in ply-based FE models, with all input parameters related to transverse properties deemed to be non-influential. The findings of this study aid in identifying suitable fracture tests for a meaningful calibration and validation of CDM-based FE models. Moreover, the study lays the foundation for understanding the role of input parameters within data-driven methods, and for developing efficient reduced-order models or surrogates for uncertainty quantification on the damage tolerance of FRP composites.