Protein lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification associated with a wide range of biological processes. Identifying Kbhb sites is critical for a better understanding of its mechanism of action. However, biochemical experimental methods for probing Kbhb sites are costly and have a long cycle. Therefore, a feature embedding learning method based on the Transformer encoder was proposed to predict Kbhb sites. In this method, amino acid residues were mapped into numerical vectors according to their amino acid class and position in a learnable feature embedding method. Then the Transformer encoder was used to extract discriminating features, and the bidirectional long short-term memory network (BiLSTM) was used to capture the correlation between different features. In this paper, a benchmark dataset was constructed, and a Kbhb site predictor, AutoTF-Kbhb, was implemented based on the proposed method. Experimental results showed that the proposed feature embedding learning method could extract effective features. AutoTF-Kbhb achieved an area under curve (AUC) of 0.87 and a Matthews correlation coefficient (MCC) of 0.37 on the independent test set, significantly outperforming other methods in comparison. Therefore, AutoTF-Kbhb can be used as an auxiliary means to identify Kbhb sites.
Protein Processing, Post-Translational ; Lysine/chemistry* ; Proteins/chemistry* ; Machine Learning ; Algorithms

With the rising incidence of breast cancer among women, neoadjuvant chemotherapy (NAC) is becoming increasingly crucial as a preoperative treatment modality, enabling tumor downstaging and volume reduction. However, its efficacy varies significantly among patients, underscoring the importance of predicting pathological complete response (pCR) following NAC. Early research relied on statistical methods to integrate clinical data for predicting treatment outcomes. With the advent of artificial intelligence (AI), traditional machine learning approaches were subsequently employed for efficacy prediction. Deep learning emerged to dominate this field, and demonstrated the capability to automatically extract imaging features and integrate multimodal data for pCR prediction. This review comprehensively examined the applications and limitations of these three methodologies in predicting breast cancer pCR. Future efforts must prioritize the development of superior predictive models to achieve precise predictions, integrate them into clinical workflows, enhance patient care, and ultimately improve therapeutic outcomes and quality of life.
Humans ; Breast Neoplasms/pathology* ; Neoadjuvant Therapy ; Artificial Intelligence ; Female ; Machine Learning ; Deep Learning ; Chemotherapy, Adjuvant ; Treatment Outcome

OBJECTIVE: To explore, identify, and develop novel blood-based indicators using machine learning algorithms for accurate preoperative assessment and effective prediction of postoperative complication risks in patients with rheumatoid arthritis (RA) undergoing total knee arthroplasty (TKA). METHODS: A retrospective cohort study was conducted including RA patients who underwent unilateral TKA between January 2019 and December 2024. Inpatient and 30-day postoperative outpatient follow-up data were collected. Six machine learning algorithms, including decision tree, random forest, logistic regression, support vector machine, extreme gradient boosting, and light gradient boosting machine, were used to construct predictive models. Model performance was evaluated using the area under the receiver operating characteristic curve (AUC), F1-score, accuracy, precision, and recall. SHapley Additive exPlanations (SHAP) values were employed to interpret and rank the importance of individual variables. RESULTS: According to the inclusion criteria, a total of 1 548 patients were enrolled. Ultimately, 18 preoperative indicators were identified as effective predictive features, and 8 postoperative complications were defined as prediction labels for inclusion in the study. Within 30 days after surgery, 453 patients (29.2%) developed one or more complications. Considering overall accuracy, precision, recall, and F1-score, the random forest model [AUC=0.930, 95% CI (0.910, 0.950)] and the extreme gradient boosting model [AUC=0.909, 95% CI (0.880, 0.938)] demonstrated the best predictive performance. SHAP analysis revealed that anti-cyclic citrullinated peptide antibody, C-reactive protein, rheumatoid factor, interleukin-6, body mass index, age, and smoking status made significant contributions to the overall prediction of postoperative complications. CONCLUSION Machine learning-based models enable accurate prediction of postoperative complication risks among RA patients undergoing TKA. Inflammatory and immune-related blood biomarkers, such as anti-cyclic citrullinated peptide antibody, C-reactive protein, and rheumatoid factor, interleukin-6, play key predictive roles, highlighting their potential value in perioperative risk stratification and individualized management.
Humans ; Arthroplasty, Replacement, Knee/adverse effects* ; Arthritis, Rheumatoid/blood* ; Machine Learning ; Postoperative Complications/blood* ; Female ; Male ; Retrospective Studies ; Middle Aged ; Aged ; Risk Factors ; Preoperative Period ; C-Reactive Protein/analysis* ; Risk Assessment

General anesthesia, pivotal for surgical procedures, requires precise depth monitoring to mitigate risks ranging from intraoperative awareness to postoperative cognitive impairments. Traditional assessment methods, relying on physiological indicators or behavioral responses, fall short of accurately capturing the nuanced states of unconsciousness. This study introduces a machine learning-based approach to decode anesthesia depth, leveraging EEG data across different anesthesia states induced by propofol and esketamine in rats. Our findings demonstrate the model's robust predictive accuracy, underscored by a novel intra-subject dataset partitioning and a 5-fold cross-validation method. The research diverges from conventional monitoring by utilizing anesthetic infusion rates as objective indicators of anesthesia states, highlighting distinct EEG patterns and enhancing prediction accuracy. Moreover, the model's ability to generalize across individuals suggests its potential for broad clinical application, distinguishing between anesthetic agents and their depths. Despite relying on rat EEG data, which poses questions about real-world applicability, our approach marks a significant advance in anesthesia monitoring.
Animals ; Machine Learning ; Electroencephalography/methods* ; Ketamine/administration & dosage* ; Rats ; Male ; Propofol/administration & dosage* ; Rats, Sprague-Dawley ; Anesthesia, General/methods* ; Brain/physiology* ; Intraoperative Neurophysiological Monitoring/methods*

Closed-loop neuromodulation, especially using the phase of the electroencephalography (EEG) rhythm to assess the real-time brain state and optimize the brain stimulation process, is becoming a hot research topic. Because the EEG signal is non-stationary, the commonly used EEG phase-based prediction methods have large variances, which may reduce the accuracy of the phase prediction. In this study, we proposed a machine learning-based EEG phase prediction network, which we call EEG phase prediction network (EPN), to capture the overall rhythm distribution pattern of subjects and map the instantaneous phase directly from the narrow-band EEG data. We verified the performance of EPN on pre-recorded data, simulated EEG data, and a real-time experiment. Compared with widely used state-of-the-art models (optimized multi-layer filter architecture, auto-regress, and educated temporal prediction), EPN achieved the lowest variance and the greatest accuracy. Thus, the EPN model will provide broader applications for EEG phase-based closed-loop neuromodulation.
Humans ; Electroencephalography/methods* ; Brain/physiology* ; Machine Learning ; Signal Processing, Computer-Assisted ; Male ; Adult ; Neural Networks, Computer ; Brain Waves/physiology*

In modern society, people are increasingly exposed to chronic stress, leading to various mental disorders. However, the activities of brain regions, especially neural firing patterns related to specific behaviors, remain unclear. In this study, we introduce a novel approach, NeuroSync, which integrates open-field behavioral testing with electrophysiological recordings from emotion-related brain regions, specifically the central amygdala and the paraventricular nucleus of the hypothalamus, to explore the mechanisms of negative emotions induced by chronic stress in mice. By applying machine vision techniques, we quantified behaviors in the open field, and signal processing algorithms elucidated the neural underpinnings of the observed behaviors. Synchronizing behavioral and electrophysiological data revealed significant correlations between neural firing patterns and stress-related behaviors, providing insights into real-time brain activity underlying behavioral responses. This research combines deep learning and machine learning to synchronize high-resolution video and electrophysiological data, offering new insights into neural-behavioral dynamics under chronic stress conditions.
Animals ; Mice ; Male ; Emotions/physiology* ; Stress, Psychological/physiopathology* ; Action Potentials/physiology* ; Mice, Inbred C57BL ; Behavior, Animal/physiology* ; Machine Learning ; Amygdala/physiopathology* ; Neurons/physiology* ; Paraventricular Hypothalamic Nucleus/physiopathology* ; Brain/physiology*

INTRODUCTION: Obstructive sleep apnoea (OSA) is a serious but underdiagnosed condition. Demand for the gold standard diagnostic polysomnogram (PSG) far exceeds its availability. More efficient diagnostic methods are needed, even in tertiary settings. Machine learning (ML) models have strengths in disease prediction and early diagnosis. We explored the use of ML with oximetry, demographic and anthropometric data to diagnose OSA. METHODS: A total of 2,996 patients were included for modelling and divided into test and training sets. Seven commonly used supervised learning algorithms were trained with the data. Sensitivity (recall), specificity, positive predictive value (PPV) (precision), negative predictive value, area under the receiver operating characteristic curve (AUC) and F1 measure were reported for each model. RESULTS: In the best performing four-class model (neural network model predicting no, mild, moderate or severe OSA), a prediction of moderate and/or severe disease had a combined PPV of 94%; one out of 335 patients had no OSA and 19 had mild OSA. In the best performing two-class model (logistic regression model predicting no-mild vs. moderate-severe OSA), the PPV for moderate-severe OSA was 92%; two out of 350 patients had no OSA and 26 had mild OSA. CONCLUSION Our study showed that the prediction of moderate-severe OSA in a tertiary setting with an ML approach is a viable option to facilitate early identification of OSA. Prospective studies with home-based oximeters and analysis of other oximetry variables are the next steps towards formal implementation.
Humans ; Oximetry/methods* ; Sleep Apnea, Obstructive/diagnosis* ; Male ; Female ; Middle Aged ; Machine Learning ; Polysomnography ; Adult ; Anthropometry ; ROC Curve ; Aged ; Algorithms ; Predictive Value of Tests ; Sensitivity and Specificity ; Neural Networks, Computer ; Demography

OBJECTIVE: To screen the population for acupuncture treatment of neck pain, using functional magnetic resonance imaging (fMRI) technology and based on machine learning algorithms. METHODS: Eighty patients with neck pain were recruited. Using FPX25 handheld pressure algometer, the tender points were detected in the areas with high-frequent onset of neck pain and high degree of acupoint sensitization. Acupuncture was delivered at 4 tender points with the lowest pain threshold, once every two days; and the treatment was given 3 times a week and for 2 consecutive weeks. The amplitude of low-frequency fluctuation (ALFF) of the brain before treatment was taken as a predictive feature to construct support vector machine (SVM), logistic regression (LR), and K-nearest neighbors (KNN) models to predict the responses of neck pain patients to acupuncture treatment. A longitudinal analysis of the ALFF features was performed before and after treatment to reveal the potential biological markers of the reactivity to the acupuncture therapy. RESULTS: The SVM model could successfully distinguish high responders (48 cases) and low responders (32 cases) to acupuncture treatment, and its accuracy rate reached 82.5%. Based on the SVM model, the ALFF values of 4 brain regions were identified as the consistent predictive features, including the right middle temporal gyrus, the right superior occipital gyrus, and the bilateral posterior cingulate gyrus. In the patients with high acupuncture response, the ALFF value in the left posterior cingulate gyrus decreased after treatment (P<0.05), whereas in the patients with low acupuncture response, the ALFF value in the right superior occipital gyrus increased after treatment (P<0.01). The longitudinal functional connectivity (FC) analysis found that compared with those before treatment, the high responders showed the enhanced FC after treatment between the left posterior cingulate gyrus and various regions, including the bilateral Crus1 of the cerebellum, the right insula, the bilateral angular gyrus, the left medial superior frontal gyrus, and the left middle cingulate gyrus (GRF: corrected, voxel level: P<0.05, mass level: P<0.05). In contrast, the low responders exhibited the enhanced FC between the left posterior cingulate gyrus and the left Crus2 of the cerebellum, the left middle temporal gyrus, the right posterior cingulate gyrus, and the left angular gyrus; besides, FC was reduced in low responders between the left posterior cingulate gyrus and the right supramarginal gyrus (GRF: corrected, voxel level: P<0.05, mass level: P<0.05). CONCLUSION This study validates the practicality of pre-treatment ALFF feature prediction for acupuncture efficacy on neck pain. The therapeutic effect of acupuncture on neck pain is potentially associated with its impact on the default mode network, and then, alter the pain perception and emotional regulation.
Humans ; Neck Pain/physiopathology* ; Acupuncture Therapy ; Female ; Male ; Adult ; Middle Aged ; Machine Learning ; Magnetic Resonance Imaging ; Young Adult ; Brain/physiopathology* ; Acupuncture Points ; Aged

The machine learning is used increasingly and widely in acupuncture prescription optimization, intelligent treatment and precision medicine, and has obtained a certain achievement. But, there are still some problems remained to be solved such as the poor interpretability of the model, the inconsistency of data quality of acupuncture research, and the clinical application of constructed models. Researches in future should focus on the acquisition of high-quality clinical and experimental data sets, take various machine learning algorithms as the basis, and construct professional models to solve various problems, so as to drive the high-quality development of acupuncture research.
Acupuncture Therapy/trends* ; Machine Learning ; Humans ; Algorithms

OBJECTIVE: To construct a prediction model for the clinical effect of eye acupuncture combined with rehabilitation therapy on ischemic stroke based on interpretable machine learning. METHODS: From January 1st, 2020 to October 1st, 2024, the clinical data of 470 patients with ischemic stroke were collected in the the Second Department of Encephalopathy Rehabilitation of the Affiliated Hospital of Liaoning University of TCM. The modified Barthel index (MBI) score before and after treatment was used to divide the patients into an effect group (291 cases) and a non-effect group (179 cases). Random forest and recursive feature elimination with cross-validation were combined to screen the predictors of the therapeutic effect of patients. Seven representative machine learning models with different principles were established according to the screening results. The predictive effect of the best model was evaluated by receiver operating characteristics (ROC), calibration, and clinical decision-making (DCA) curves. Finally, the Shapley additive explanation (SHAP) framework was used to interpret the prediction results of the best model. RESULT: ①All the machine learning models presented the area under curve (AUC) to be above 85%. Of these models, the random forest model showed the best prediction ability, with AUC of 0.96 and the precision of 0.87. ②The prediction probability of calibration curve and the actual probability showed a good prediction consistency. ③The net benefit rate of DCA curve in the range of 0.1 to 1.0 was higher than the risk threshold, indicating a good effect of model. ④SHAP explained the characteristic values of variables that affected the prediction effect of the model, meaning, more days of treatment, lower MBI score before treatment, lower level of fibrinogen, shorter days of onset and younger age. These values demonstrated the better effect of eye acupuncture rehabilitation therapy. CONCLUSION The rehabilitation effect prediction model constructed in this study presents a good performance, which is conductive to assisting doctors in formulating targeted personalized rehabilitation programs, and identifying the benefit groups of eye acupuncture combined with rehabilitation therapy and finding the advantageous groups with clinical effect. It provides more ideas for the treatment of ischemic stroke with eye acupuncture combined with rehabilitation therapy.
Humans ; Acupuncture Therapy ; Machine Learning ; Male ; Female ; Middle Aged ; Ischemic Stroke/rehabilitation* ; Aged ; Stroke Rehabilitation ; Adult ; Eye