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The Bone & Joint Journal Jul 2024To examine whether natural language processing (NLP) using a clinically based large language model (LLM) could be used to predict patient selection for total hip or...
AIMS
To examine whether natural language processing (NLP) using a clinically based large language model (LLM) could be used to predict patient selection for total hip or total knee arthroplasty (THA/TKA) from routinely available free-text radiology reports.
METHODS
Data pre-processing and analyses were conducted according to the Artificial intelligence to Revolutionize the patient Care pathway in Hip and knEe aRthroplastY (ARCHERY) project protocol. This included use of de-identified Scottish regional clinical data of patients referred for consideration of THA/TKA, held in a secure data environment designed for artificial intelligence (AI) inference. Only preoperative radiology reports were included. NLP algorithms were based on the freely available GatorTron model, a LLM trained on over 82 billion words of de-identified clinical text. Two inference tasks were performed: assessment after model-fine tuning (50 Epochs and three cycles of k-fold cross validation), and external validation.
RESULTS
For THA, there were 5,558 patient radiology reports included, of which 4,137 were used for model training and testing, and 1,421 for external validation. Following training, model performance demonstrated average (mean across three folds) accuracy, F1 score, and area under the receiver operating curve (AUROC) values of 0.850 (95% confidence interval (CI) 0.833 to 0.867), 0.813 (95% CI 0.785 to 0.841), and 0.847 (95% CI 0.822 to 0.872), respectively. For TKA, 7,457 patient radiology reports were included, with 3,478 used for model training and testing, and 3,152 for external validation. Performance metrics included accuracy, F1 score, and AUROC values of 0.757 (95% CI 0.702 to 0.811), 0.543 (95% CI 0.479 to 0.607), and 0.717 (95% CI 0.657 to 0.778) respectively. There was a notable deterioration in performance on external validation in both cohorts.
CONCLUSION
The use of routinely available preoperative radiology reports provides promising potential to help screen suitable candidates for THA, but not for TKA. The external validation results demonstrate the importance of further model testing and training when confronted with new clinical cohorts.
Topics: Humans; Arthroplasty, Replacement, Knee; Natural Language Processing; Arthroplasty, Replacement, Hip; Patient Selection; Female; Male; Aged; Middle Aged; Algorithms; Artificial Intelligence
PubMed: 38945535
DOI: 10.1302/0301-620X.106B7.BJJ-2024-0136 -
Risk Analysis : An Official Publication... Jun 2024This article presents a risk analysis of large language models (LLMs), a type of "generative" artificial intelligence (AI) system that produces text, commonly in...
This article presents a risk analysis of large language models (LLMs), a type of "generative" artificial intelligence (AI) system that produces text, commonly in response to textual inputs from human users. The article is specifically focused on the risk of LLMs causing an extreme catastrophe in which they do something akin to taking over the world and killing everyone. The possibility of LLM takeover catastrophe has been a major point of public discussion since the recent release of remarkably capable LLMs such as ChatGPT and GPT-4. This arguably marks the first time when actual AI systems (and not hypothetical future systems) have sparked concern about takeover catastrophe. The article's analysis compares (A) characteristics of AI systems that may be needed for takeover, as identified in prior theoretical literature on AI takeover risk, with (B) characteristics observed in current LLMs. This comparison reveals that the capabilities of current LLMs appear to fall well short of what may be needed for takeover catastrophe. Future LLMs may be similarly incapable due to fundamental limitations of deep learning algorithms. However, divided expert opinion on deep learning and surprise capabilities found in current LLMs suggests some risk of takeover catastrophe from future LLMs. LLM governance should monitor for changes in takeover characteristics and be prepared to proceed more aggressively if warning signs emerge. Unless and until such signs emerge, more aggressive governance measures may be unwarranted.
PubMed: 38945529
DOI: 10.1111/risa.14353 -
American Journal of Preventive Medicine Jun 2024
PubMed: 38945180
DOI: 10.1016/j.amepre.2024.06.021 -
Journal of the Mechanical Behavior of... Jun 2024Recent advancements in biomaterial research conduct artificial intelligence for predicting diverse material properties. However, research predicting the mechanical...
Recent advancements in biomaterial research conduct artificial intelligence for predicting diverse material properties. However, research predicting the mechanical properties of biomaterial based on amino acid sequences have been notably absent. This research pioneers the use of classification models to predict ultimate tensile strength from silk fiber amino acid sequences, employing logistic regression, support vector machines with various kernels, and a deep neural network (DNN). Remarkably, the model demonstrates a high accuracy of 0.83 during the generalization test. The study introduces an innovative approach to predicting biomaterial mechanical properties beyond traditional experimental methods. Recognizing the limitations of conventional linear prediction models, the research emphasizes the future trajectory toward DNNs that can adeptly capture non-linear relationships with high precision. Moreover, through comprehensive performance comparisons among diverse prediction models, the study offers insights into the effectiveness of specific models for predicting the mechanical properties of certain materials. In conclusion, this study serves as a pioneering contribution, laying the groundwork for future endeavors and advocating for the seamless integration of AI methodologies into materials research.
PubMed: 38945120
DOI: 10.1016/j.jmbbm.2024.106643 -
Computerized Medical Imaging and... Jun 2024Despite sharing the same histologic classification, individual tumors in multi metastatic patients may present with different characteristics and varying sensitivities...
Despite sharing the same histologic classification, individual tumors in multi metastatic patients may present with different characteristics and varying sensitivities to anticancer therapies. In this study, we investigate the utility of radiomic biomarkers for prediction of lesion-specific treatment resistance in multi metastatic leiomyosarcoma patients. Using a dataset of n=202 lung metastases (LM) from n=80 patients with 1648 pre-treatment computed tomography (CT) radiomics features and LM progression determined from follow-up CT, we developed a radiomic model to predict the progression of each lesion. Repeat experiments assessed the relative predictive performance across LM volume groups. Lesion-specific radiomic models indicate up to a 4.5-fold increase in predictive capacity compared with a no-skill classifier, with an area under the precision-recall curve of 0.70 for the most precise model (FDR = 0.05). Precision varied by administered drug and LM volume. The effect of LM volume was controlled by removing radiomic features at a volume-correlation coefficient threshold of 0.20. Predicting lesion-specific responses using radiomic features represents a novel strategy by which to assess treatment response that acknowledges biological diversity within metastatic subclones, which could facilitate management strategies involving selective ablation of resistant clones in the setting of systemic therapy.
PubMed: 38945043
DOI: 10.1016/j.compmedimag.2024.102413 -
European Journal of Medicinal Chemistry Jun 2024Macrocyclic peptides possess unique features, making them highly promising as a drug modality. However, evaluating their bioactivity through wet lab experiments is...
Macrocyclic peptides possess unique features, making them highly promising as a drug modality. However, evaluating their bioactivity through wet lab experiments is generally resource-intensive and time-consuming. Despite advancements in artificial intelligence (AI) for bioactivity prediction, challenges remain due to limited data availability and the interpretability issues in deep learning models, often leading to less-than-ideal predictions. To address these challenges, we developed PepExplainer, an explainable graph neural network based on substructure mask explanation (SME). This model excels at deciphering amino acid substructures, translating macrocyclic peptides into detailed molecular graphs at the atomic level, and efficiently handling non-canonical amino acids and complex macrocyclic peptide structures. PepExplainer's effectiveness is enhanced by utilizing the correlation between peptide enrichment data from selection-based focused library and bioactivity data, and employing transfer learning to improve bioactivity predictions of macrocyclic peptides against IL-17C/IL-17 RE interaction. Additionally, PepExplainer underwent further validation for bioactivity prediction using an additional set of thirteen newly synthesized macrocyclic peptides. Moreover, it enabled the optimization of the IC of a macrocyclic peptide, reducing it from 15 nM to 5.6 nM based on the contribution score provided by PepExplainer. This achievement underscores PepExplainer's skill in deciphering complex molecular patterns, highlighting its potential to accelerate the discovery and optimization of macrocyclic peptides.
PubMed: 38944933
DOI: 10.1016/j.ejmech.2024.116628 -
Computers in Biology and Medicine Jun 2024Virtual and augmented reality surgical simulators, integrated with machine learning, are becoming essential for training psychomotor skills, and analyzing surgical...
BACKGROUND
Virtual and augmented reality surgical simulators, integrated with machine learning, are becoming essential for training psychomotor skills, and analyzing surgical performance. Despite the promise of methods like the Connection Weights Algorithm, the small sample sizes (small number of participants (N)) typical of these trials challenge the generalizability and robustness of models. Approaches like data augmentation and transfer learning from models trained on similar surgical tasks address these limitations.
OBJECTIVE
To demonstrate the efficacy of artificial neural network and transfer learning algorithms in evaluating virtual surgical performances, applied to a simulated oblique lateral lumbar interbody fusion technique in an augmented and virtual reality simulator.
DESIGN
The study developed and integrated artificial neural network algorithms within a novel simulator platform, using data from the simulated tasks to generate 276 performance metrics across motion, safety, and efficiency. Innovatively, it applies transfer learning from a pre-trained ANN model developed for a similar spinal simulator, enhancing the training process, and addressing the challenge of small datasets.
SETTING
Musculoskeletal Biomechanics Research Lab; Neurosurgical Simulation and Artificial Intelligence Learning Centre, McGill University, Montreal, Canada.
PARTICIPANTS
Twenty-seven participants divided into 3 groups: 9 post-residents, 6 senior and 12 junior residents.
RESULTS
Two models, a stand-alone model trained from scratch and another leveraging transfer learning, were trained on nine selected surgical metrics achieving 75 % and 87.5 % testing accuracy respectively.
CONCLUSIONS
This study presents a novel blueprint for addressing limited datasets in surgical simulations through the strategic use of transfer learning and data augmentation. It also evaluates and reinforces the application of the Connection Weights Algorithm from our previous publication. Together, these methodologies not only enhance the precision of performance classification but also advance the validation of surgical training platforms.
PubMed: 38944904
DOI: 10.1016/j.compbiomed.2024.108809 -
Clinical Nutrition ESPEN Jun 2024Accurate diagnosis of sarcopenia requires evaluation of muscle quality, which refers to the amount of fat infiltration in muscle tissue. In this study, we aim to...
Low muscle quality on a procedural computed tomography scan assessed with deep learning as a practical useful predictor of mortality in patients with severe aortic valve stenosis.
BACKGROUND & AIMS
Accurate diagnosis of sarcopenia requires evaluation of muscle quality, which refers to the amount of fat infiltration in muscle tissue. In this study, we aim to investigate whether we can independently predict mortality risk in transcatheter aortic valve implantation (TAVI) patients, using automatic deep learning algorithms to assess muscle quality on procedural computed tomography (CT) scans.
METHODS
This study included 1199 patients with severe aortic stenosis who underwent transcatheter aortic valve implantation (TAVI) between January 2010 and January 2020. A procedural CT scan was performed as part of the preprocedural-TAVI evaluation, and the scans were analyzed using deep-learning-based software to automatically determine skeletal muscle density (SMD) and intermuscular adipose tissue (IMAT). The association of SMD and IMAT with all-cause mortality was analyzed using a Cox regression model, adjusted for other known mortality predictors, including muscle mass.
RESULTS
The mean age of the participants was 80 ± 7 years, 53% were female. The median observation time was 1084 days, and the overall mortality rate was 39%. We found that the lowest tertile of muscle quality, as determined by SMD, was associated with an increased risk of mortality (HR 1.40 [95%CI: 1.15-1.70], p < 0.01). Similarly, low muscle quality as defined by high IMAT in the lowest tertile was also associated with increased mortality risk (HR 1.24 [95%CI: 1.01-1.52], p = 0.04).
CONCLUSIONS
Our findings suggest that deep learning-assessed low muscle quality, as indicated by fat infiltration in muscle tissue, is a practical, useful and independent predictor of mortality after TAVI.
PubMed: 38944828
DOI: 10.1016/j.clnesp.2024.06.013 -
Advances in Gerontology = Uspekhi... 2024Multi-omics methods for analysing postgenomic data have become firmly established in the tools of molecular gerontology only in recent years, since previously there were... (Review)
Review
Multi-omics methods for analysing postgenomic data have become firmly established in the tools of molecular gerontology only in recent years, since previously there were no comprehensive integrative approaches adequate to the task of calculating biological age. This paper provides an overview of existing papers on multi-omics integrative approaches in calculating the biological age of a human. An analysis of the most common options for integrating methylomic, transcriptomic, proteomic, microbiomic and metabolomic datasets was carried out. We defined (1) concatenation (machine learning), in which models are developed using a concatenated data matrix, formed by combining multiple omics data sets; (2) fusion model approaches that create multiple intermediate submodels for different omics data to then build a final integrated model from the various intermediate submodels; and (3) transformation methods (via artificial intelligence) that first transform each of the single omics data sets into core plots or matrices, and then combine them all into one graph before building an integral complex model. It is unlikely that multi-omics approaches will find application in anti-aging personalized medicine, but they will undoubtedly deepen and expand the understanding of the fundamental processes standing behind the phenomenon of the biological aging clocks.
Topics: Humans; Aging; Proteomics; Metabolomics; Genomics; Computational Biology; Machine Learning; Multiomics
PubMed: 38944768
DOI: No ID Found -
International Journal of Gynaecology... Jun 2024To establish reference ranges of fetal intracranial markers during the first trimester and develop the first novel artificial intelligence (AI) model to measure key...
OBJECTIVE
To establish reference ranges of fetal intracranial markers during the first trimester and develop the first novel artificial intelligence (AI) model to measure key markers automatically.
METHODS
This retrospective study used two-dimensional (2D) ultrasound images from 4233 singleton normal fetuses scanned at 11-13 weeks of gestation at the Affiliated Suzhou Hospital of Nanjing Medical University from January 2018 to July 2022. We analyzed 10 key markers in three important planes of the fetal head. Based on these, reference ranges of 10 fetal intracranial markers were established and an AI model was developed for automated marker measurement. AI and manual measurements were compared to evaluate differences, correlations, consistency, and time consumption based on mean error, Pearson correlation analysis, intraclass correlation coefficients (ICCs), and average measurement time.
RESULTS
The results of AI and manual methods had strong consistency and correlation (all ICC values >0.75, all r values >0.75, and all P values <0.001). The average absolute error of both only ranged from 0.124 to 0.178 mm. AI achieved a 100% detection rate for abnormal cases. Additionally, the average measurement time of AI was only 0.49 s, which was more than 65 times faster than the manual measurement method.
CONCLUSION
The present study first established the normal standard reference ranges of fetal intracranial markers based on a large Chinese population data set. Furthermore, the proposed AI model demonstrated its capability to measure multiple fetal intracranial markers automatically, serving as a highly effective tool to streamline sonographer tasks and mitigate manual measurement errors, which can be generalized to first-trimester scanning.
PubMed: 38944698
DOI: 10.1002/ijgo.15762