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.

Body fluid proteome has been intensively studied as a primary source for disease biomarker discovery. Using advanced proteomics technologies, early research success has resulted in increasingly accumulated proteins detected in different body fluids, among which many are promising biomarkers. However, despite a handful of small-scale and specific data resources, current research is clearly lacking effort compiling published body fluid proteins into a centralized and sustainable repository that can provide users with systematic analytic tools. In this study, we developed a new database of human body fluid proteome (HBFP) that focuses on experimentally validated proteome in 17 types of human body fluids. The current database archives 11 827 unique proteins reported by 164 scientific publications, with a maximal false discovery rate of 0.01 on both the peptide and protein levels since 2001, and enables users to query, analyze and download protein entries with respect to each body fluid. Three unique features of this new system include the following: (i) the protein annotation page includes detailed abundance information based on relative qualitative measures of peptides reported in the original references, (ii) a new score is calculated on each reported protein to indicate the discovery confidence and (iii) HBFP catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of nine amino acids according to the Human Proteome Project Data Interpretation Guidelines, while the remaining 4473 proteins have more than two unique peptides without given sequence information. As an important resource for human protein secretome, we anticipate that this new HBFP database can be a powerful tool that facilitates research in clinical proteomics and biomarker discovery. Database URL: https://bmbl.bmi.osumc.edu/HBFP/

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. 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. DeepSec is available at https://bmbl.bmi.osumc.edu/deepsec/. Supplementary data are available at Bioinformatics online.

Fire detection presents considerable challenges due to the destructive and unpredictable characteristics of fires. These difficulties are amplified by the small size and low-resolution nature of fire and smoke targets in images captured from a distance, making it hard for models to extract relevant features. To address this, we introduce a novel method for small-target fire and smoke detection named YOLOv7scb. This approach incorporates two key improvements to the YOLOv7 framework: the use of space-to-depth convolution (SPD-Conv) and C3 modules, enhancing the model’s ability to extract features from small targets effectively. Additionally, a weighted bidirectional feature pyramid network (BiFPN) is integrated into the feature-extraction network to merge features across scales efficiently without increasing the model’s complexity. We also replace the conventional complete intersection over union (CIoU) loss function with Focal-CIoU, which reduces the degrees of freedom in the loss function and improves the model’s robustness. Given the limited size of the initial fire and smoke dataset, a transfer-learning strategy is applied during training. Experimental results demonstrate that our proposed model surpasses others in metrics such as precision and recall. Notably, it achieves a precision of 98.8% for small-target flame detection and 90.6% for small-target smoke detection. These findings underscore the model’s effectiveness and its broad potential for fire detection and mitigation applications.

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.

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.