MOTIVATION: Global population aging has led to a rapid increase in neurodegenerative disorders such as Alzheimer's disease (AD). Although existing drugs can temporarily alleviate symptoms, none have been proven to delay or prevent disease progression. Acetylcholinesterase inhibitors (AChEIs) have been shown to mitigate AD symptoms, yet traditional AChEI screening approaches remain time-consuming and inefficient. RESULTS: To address this limitation, we developed multi-species AChEI screening network (MAISNet), an AChEI screening framework based on acetylcholinesterase (AChE) data from six species. In MAISNet, inhibitor molecules were represented as SMILES-derived molecular graphs, whereas AChE protein structures were encoded as residue contact maps. Multi-scale molecular and protein features were extracted using the sample and aggregate (GraphSAGE) network and the graph attention network, respectively, and were subsequently fused through a bidirectional cross-attention mechanism. The integrated representations were then processed by a multilayer perceptron (MLP) to inhibitor classification. On both internal and external validation sets, MAISNet consistently outperformed five baseline models. Furthermore, we applied MAISNet to screen existing small molecules, and Methyl 2-[(3S)-3-(1, 2, 3, 4, 5, 6, 7, 8-octahydro-2-naphthyl)-2-(methoxycarbonyl)-1H-pyrrol-1-yl]acetate subsequently emerged as the top-ranked candidate. Overall, MAISNet significantly improves the accuracy and generalization capability of AChEI screening, providing an efficient and reliable computational tool for accelerating therapeutic discovery for AD. AVAILABILITY AND IMPLEMENTATION: Code that supports the reported results can be found at: https://github.com/liangshengjie111/MAISNet. The archival version of the code is preserved on Zenodo at https://doi.org/10.5281/zenodo.18721665.

Brucellar spondylitis (BS), a prevalent zoonotic disease caused by Brucella, poses a significant global health threat. Accurate and timely diagnosis of BS is crucial for effective treatment; however, no specialized deep learning model has been developed for detecting BS in MR images. In this study, we proposed Brucella Spondylitis MRI Diagnosis Network (BSMRINet), a fully automated diagnostic framework designed for the detection of BS from T2-weighted (T2W) MR images. The model was developed and validated using 582 cohorts collected from four hospitals between January 2018 and August 2023. The BSMRINet architecture comprised two key modules. The vertebral body lesion detection module was designed to detect BS in intact vertebral bodies by integrating a corner detection algorithm with a ResNet-based deep learning model. This module provided accurate identification and localization of potential lesions of Brucella and calculated intervertebral disc height (DH) values. The spine lesion detection module was specifically designed to detect BS in damaged vertebral bodies by utilizing a DenseNet architecture with modified squeeze-and-excitation (scSE) networks. This module further evaluated paravertebral injuries, including abscess formation, soft tissue swelling, and joint involvement. BSMRINet demonstrated strong robustness and generalization across both internal and external validation phases. Additionally, it outperformed two radiologists with 10 to 15 years of experience in diagnosing spinal MR images. The results suggested that BSMRINet can assist in the diagnostic process of BS and enhance the diagnostic capabilities of radiologists.

Positron Emission Tomography (PET) images reflect the metabolic rate of tracers in different tissues of the human body, crucial for early cancer diagnosis and treatment. Accurate tumor segmentation is essential to aid clinicians in determining drug dosages. Due to the low resolution of PET images, prior information (such as CT, MRI or distance information) are often incorporated to assist PET segmentation. In this paper, we propose an automatic 3D PET tumor segmentation framework assisted by geodesic sequences. Specifically, considering the intrinsic characteristics of PET images, we first construct geodesic prior, which effectively enhances the contrast between the tumor and background while suppressing noise and the influence of other tissues. To address the need for seed points in the geodesic prior, an automatic marking strategy is designed that identifies all suspected lesion regions and uses their central points as a series of seeds to generate the corresponding geodesic sequences. Subsequently, we develop a three-branch network architecture to simultaneously process PET images, geodesic sequences, and background geodesic information. To enhance image features, a distance attention mechanism is introduced at the end of the network encoder to effectively measure the similarity between different geodesic features, refining the image features. Finally, the network incorporates spatial regularization and local PET intensity information into the activation function via the Soft Threshold Dynamics with Local Intensity Fitting (STDLIF) module, further improving segmentation accuracy. Experimental results demonstrate that, compared to existing state-of-the-art algorithms, the proposed method shows better segmentation performance on both clinical and public datasets.

Identifying aggregation-prone proteins or peptides is essential for advancing our understanding of amyloid aggregation processes and their related pathogenic mechanisms. Recognizing potential amyloid hexapeptides can also support peptide-based drug design and reduce experimental costs. In this study, we proposed TSLAmy, a computational model designed to predict amyloid hexapeptides using a two-stage learning framework. In the first stage, we performed feature extraction on the hexapeptides, and in the second stage, we presented prediction model for amyloid hexapeptide aggregation. Firstly, to ensure balanced dataset partitioning, we applied a clustering-based method by training two autoencoders on all possible hexapeptides using their sequence and physicochemical features, respectively. The resulting clusters were used to stratify the data into training and testing datasets. Then, in the first stage, we extracted features from hexapeptides based on their sequence and physicochemical properties. The feature extraction module was used to obtain physicochemical features, while the ESM-2 module was responsible for extracting sequence features for each hexapeptide. Finally, in the second stage, the aggregation prediction module was employed to predict the aggregation potential of hexapeptides. The experimental results demonstrated that the accuracy of TSLAmy reached 0.8493 (0.8447-0.8539), outperforming other state-of-the-art methods. Furthermore, we predicted the aggregation potential of all 64,000,000 possible hexapeptides and analyzed the amino acids that form aggregation-prone hexapeptides. We anticipate that TSLAmy can offer new insights into the identification of aggregation-prone peptides, contributing to advancements in peptide drug development.

Bronchoalveolar lavage fluid (BALF) is a liquid obtained from the alveoli and bronchi, often used to study pulmonary diseases. So far, proteomic analyses have identified over three thousand proteins in BALF. However, the comprehensive characterization of these proteins remains challenging due to their complexity and technological limitations. This paper presented a novel deep learning framework called SecProGNN, designed to predict secretory proteins in BALF. Firstly, SecProGNN represented proteins as graph-structured data, with amino acids connected based on their interactions. Then, these graphs were processed through graph neural networks (GNNs) model to extract graph features. Finally, the extracted feature vectors were fed into a multi-layer perceptron (MLP) module to predict BALF secreted proteins. Additionally, by utilizing SecProGNN, we investigated potential biomarkers for lung adenocarcinoma and identified 16 promising candidates that may be secreted into BALF.

In the field of diagnosing lung diseases, the application of neural networks (NNs) in image classification exhibits significant potential. However, NNs are considered "black boxes," making it difficult to discern their decision-making processes, thereby leading to skepticism and concern regarding NNs. This compromises model reliability and hampers intelligent medicine's development. To tackle this issue, we introduce the Evolutionary Neural Architecture Search (EvoNAS). In image classification tasks, EvoNAS initially utilizes an Evolutionary Algorithm to explore various Convolutional Neural Networks, ultimately yielding an optimized network that excels at separating between redundant texture features and the most discriminative ones. Retaining the most discriminative features improves classification accuracy, particularly in distinguishing similar features. This approach illuminates the intrinsic mechanics of classification, thereby enhancing the accuracy of the results. Subsequently, we incorporate a Differential Evolution algorithm based on distribution estimation, significantly enhancing search efficiency. Employing visualization techniques, we demonstrate the effectiveness of EvoNAS, endowing the model with interpretability. Finally, we conduct experiments on the diffuse lung disease texture dataset using EvoNAS. Compared to the original network, the classification accuracy increases by 0.56%. Moreover, our EvoNAS approach demonstrates significant advantages over existing methods in the same dataset.

Eddy current pulsed thermography (ECPT) has attracted much attention in nondestructive testing for its noncontact and large field of view. However, the ECPT images usually suffer from the thermal diffusion blurs. The fusion of temperature spatial and temporal features is the hotspot in the new research of ECPT enhancing methods, but these two features are contradictory on the speed and the accuracy of algorithms. Specifically, spatial features process fast but perform poorly in accuracy and antinoise ability, while temporal features are usually calculated from the whole ECPT video sequence, which inevitably increases the demand for data storage and the time cost, especially in the detection of large workpieces, such as engine blades or pressure pipelines. In this article, an enhanced diffusion-based method (EDBM) is proposed to solve this issue, which maps the temporal features through the spatial features of a single ECPT image, significantly reduces the input data volume and shows great potential in ECPT online detection. Experiments on multiple artificial and natural samples verify that, compared with raw ECPT image, the proposed EDBM can reduce root-mean-square error by 51.7%–86.5% (73.2% on average) and improve signal-to-noise ratio by 3.70–16.8 times (6.82 times on average), which performs better than the commonly spatial-based and temporal-based ECPT enhancement algorithms, such as enhanced Canny and independent component analysis, close to the latest sparse-model decomposition methods, but with two orders of magnitude less time cost.

Several factors, including advances in computational algorithms, the availability of high-performance computing hardware, and the assembly of large community-based databases, have led to the extensive application of Artificial Intelligence (AI) in the biomedical domain for nearly 20 years. AI algorithms have attained expert-level performance in cancer research. However, only a few AI-based applications have been approved for use in the real world. Whether AI will eventually be capable of replacing medical experts has been a hot topic. In this article, we first summarize the cancer research status using AI in the past two decades, including the consensus on the procedure of AI based on an ideal paradigm and current efforts of the expertise and domain knowledge. Next, the available data of AI process in the biomedical domain are surveyed. Then, we review the methods and applications of AI in cancer clinical research categorized by the data types including radiographic imaging, cancer genome, medical records, drug information and biomedical literatures. At last, we discuss challenges in moving AI from theoretical research to real-world cancer research applications and the perspectives toward the future realization of AI participating cancer treatment.

In recent years, supervised deep learning-based denoising methods have been popularized and developed rapidly in the field of seismic data processing. Supervised training, however, is limited by the quality and quantity of the paired training data (noisy clean or noisy noise). Data labeling is a time-consuming and expensive work. Compared with raw seismic data, only a small amount of seismic data have been correctly labeled, which, to some extent, limits the long-term development of supervised deep learning-based methods in the field of seismic data denoising. In this letter, we propose an improved denoising framework based on an unsupervised deep learning-based denoising method Noise2Noise, which only needs unprocessed raw seismic data to train the denoising model. Moreover, unlike Noise2Noise, the proposed method does not need to repeatedly collect seismic data to obtain a training pair with similar signal, which is more convenient and effective. Specifically, we propose a block random sampler that can generate training pairs using raw seismic data, which satisfies the training assumption of Noise2Noise that the training pair has a similar signal. In addition, our method has no requirements for the network structure and noise distribution prior and is flexible. Both synthetic seismic data and field seismic data denoising results show that our method can effectively suppress the random noise, and the denoising performance is equivalent to that of supervised deep learning-based denoising methods. In addition, our method may provide a certain reference for geophysical-related research.

With the goal of obtaining high-quality downhole distributed acoustic sensing (DAS) data from multiple types of complex noise, denoising plays an important role. However, conventional denoising methods cannot achieve a satisfactory effect toward multiple types of complex noise. Recently, convolutional neural networks (CNNs) exhibit dramatic improvements over conventional methods. The existing CNN-based methods typically operate through incorporation with conventional methods for adaptive threshold, additional multiscale idea, or attentional mechanism for more features extraction. In these cases, serious signal loss or artificial events are usually generated. Maybe, the recovered events are not continuous with some breakpoints and derangement. To resolve these problems in current networks, we propose a novel iterative parallel-attention guided multibranch residual network (PA-MRNet) with the collective goals of suppressing multiple types of complex noise and recovering buried weak signals. The core of our method is an attentional multibranch residual block (AMRB) containing: parallel multiresolution convolution streams for multiresolution features extraction, proposed parallel attention block (PAB) design for interested features capture, and novel parallel-attention guided fusion block for features fusion. In a word, our method can learn an enriched set of features to suppress multiple types of complex noise and simultaneously recover weak signals continuously with less energy loss. Experiments on synthetic and field DAS data demonstrate the better performance of the proposed iterative PA-MRNet.

Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.

MOTIVATION: Human proteins that are secreted into different body fluids from various cells and tissues can be promising disease indicators. Modern proteomics research empowered by both qualitative and quantitative profiling techniques has made great progress in protein discovery in various human fluids. However, due to the large number of proteins and diverse modifications present in the fluids, as well as the existing technical limits of major proteomics platforms (e.g. mass spectrometry), large discrepancies are often generated from different experimental studies. As a result, a comprehensive proteomics landscape across major human fluids are not well determined. RESULTS: To bridge this gap, we have developed a deep learning framework, named DeepSec, to identify secreted proteins in 12 types of human body fluids. DeepSec adopts an end-to-end sequence-based approach, where a Convolutional Neural Network is built to learn the abstract sequence features followed by a Bidirectional Gated Recurrent Unit with fully connected layer for protein classification. DeepSec has demonstrated promising performances with average area under the ROC curves of 0.85-0.94 on testing datasets in each type of fluids, which outperforms existing state-of-the-art methods available mostly on blood proteins. As an illustration of how to apply DeepSec in biomarker discovery research, we conducted a case study on kidney cancer by using genomics data from the cancer genome atlas and have identified 104 possible marker proteins. AVAILABILITY: DeepSec is available at https://bmbl.bmi.osumc.edu/deepsec/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Research on body fluid proteomes has led to the discoveries of context-dependent proteomics profiles and numerous novel disease biomarkers. Common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational efforts have shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first reviewed published computational methods on this topic and then presented a new database system and a novel deep learning-based method for predicting body-fluid proteins in 16 types of human fluids. The results show that our new system outperforms existing methods and provides a highly promising tool to facilitate clinical proteomic discovery.

Summary form only given. Anthropomatics addresses the symbiosis between humans and machines, focusing on a deeper understanding of the cooperation, interaction and coexistence between humans and machines stimulating and strengthen advanced and deep research in response to the challenges of increasingly smart environments and multimodal access to various complex technical systems. At KIT the Focus Anthropomatics and Robotics - APR has been set up by a number of research groups focusing on the research field of Anthropomatics and Robotics with more than 250 researchers. Modelling humans and their capabilities requires a deep understanding of the principle of biomechanics and kinematics, as well as the underlaying neural control principles and the perceptive and actuatoric system. Modelling and understanding of the sensomotoric mechanisms, learning and developement of skills and cognititve capabilities to enable humans to interact with the world is of high importance to design technical systems operating closely and interactively with humans via various modalities like speech, haptics, vision, grasping and locomotion. Typical research fields are related to active vision, interpretation of scenes and human activities, recognition and tracking technologies multimodal & perceptual user interfaces, understanding and translation of speech. Complementary research needed is related to the retrieval & access and summarization of multimedia data sources, translation of spoken text, context aware learning computers, implicit services and many more. The robotics application field ranges from interactive industrial robotics, service robotic companions, humanoids and medical robotics. In all domains the integrating aspects are focusing on algorithms processing real word data as well as open self-organizing architectures which allow autonomy, skill an