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Anatomical prior-based vertebral landmark detection for spinal disorder diagnosis 基于解剖学先验的椎体标记检测在脊柱疾病诊断中的应用
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-12 DOI: 10.1016/j.artmed.2024.103011
Yukang Yang , Yu Wang , Tianyu Liu , Miao Wang , Ming Sun , Shiji Song , Wenhui Fan , Gao Huang
As one of fundamental ways to interpret spine images, detection of vertebral landmarks is an informative prerequisite for further diagnosis and management of spine disorders such as scoliosis and fractures. Most existing machine learning-based methods for automatic vertebral landmark detection suffer from overlapping landmarks or abnormally long distances between nearby landmarks against anatomical priors, and thus lack sufficient reliability and interpretability. To tackle the problem, this paper systematically utilizes anatomical prior knowledge in vertebral landmark detection. We explicitly formulate anatomical priors of the spine, related to distances among vertebrae and spatial order within the spine, and integrate these geometrical constraints within training loss, inference procedure, and evaluation metrics. First, we introduce an anatomy-constraint loss to regularize the training process with the aforementioned contextual priors explicitly. Second, we propose a simple-yet-effective anatomy-aided inference procedure by employing sequential prediction rather than a parallel counterpart. Third, we provide novel anatomy-related metrics to quantitatively evaluate to which extent landmark predictions follow the anatomical priors, as is not reflected within the widely-used landmark localization error metric. We employ the localization framework on 1410 anterior–posterior radiographic images. Compared with competitive baseline models, we achieve superior landmark localization accuracy and comparable Cobb angle estimation for scoliosis assessment. Ablation studies demonstrate the effectiveness of designed components on the decrease of localization error and improvement of anatomical plausibility. Additionally, we exhibit effective generalization performance by transferring our detection method onto sagittal 2-D slices of CT scans and boost the performance of downstream compression fracture classification at vertebra-level.
作为解读脊柱图像的基本方法之一,椎体地标检测是进一步诊断和治疗脊柱侧凸和骨折等脊柱疾病的重要前提。大多数现有的基于机器学习的椎体标记自动检测方法存在标记重叠或附近标记与解剖先验之间异常长距离的问题,因此缺乏足够的可靠性和可解释性。为了解决这一问题,本文系统地利用解剖先验知识进行椎体标记检测。我们明确地制定了脊柱的解剖学先验,与椎骨之间的距离和脊柱内的空间顺序有关,并将这些几何约束整合到训练损失、推理程序和评估指标中。首先,我们引入解剖约束损失来明确地规范训练过程与上述上下文先验。其次,我们提出了一个简单而有效的解剖辅助推理程序,采用顺序预测而不是并行预测。第三,我们提供了新的解剖学相关指标来定量评估里程碑预测在多大程度上遵循解剖学先验,这在广泛使用的里程碑定位误差指标中没有反映出来。我们将定位框架应用于1410张前后x线图像。与竞争基线模型相比,我们在脊柱侧凸评估中获得了更高的地标定位精度和可比较的Cobb角估计。消融研究表明,设计的组件在减少定位误差和提高解剖合理性方面是有效的。此外,通过将我们的检测方法转移到CT扫描的矢状面二维切片上,我们展示了有效的泛化性能,并提高了椎骨水平下游压缩性骨折分类的性能。
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引用次数: 0
LSSF-Net: Lightweight segmentation with self-awareness, spatial attention, and focal modulation LSSF-Net:具有自我意识、空间注意力和焦点调制功能的轻量级分段。
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-12 DOI: 10.1016/j.artmed.2024.103012
Hamza Farooq , Zuhair Zafar , Ahsan Saadat , Tariq M. Khan , Shahzaib Iqbal , Imran Razzak
Accurate segmentation of skin lesions within dermoscopic images plays a crucial role in the timely identification of skin cancer for computer-aided diagnosis on mobile platforms. However, varying shapes of the lesions, lack of defined edges, and the presence of obstructions such as hair strands and marker colours make this challenge more complex. Additionally, skin lesions often exhibit subtle variations in texture and colour that are difficult to differentiate from surrounding healthy skin, necessitating models that can capture both fine-grained details and broader contextual information. Currently, melanoma segmentation models are commonly based on fully connected networks and U-Nets. However, these models often struggle with capturing the complex and varied characteristics of skin lesions, such as the presence of indistinct boundaries and diverse lesion appearances, which can lead to suboptimal segmentation performance. To address these challenges, we propose a novel lightweight network specifically designed for skin lesion segmentation utilising mobile devices, featuring a minimal number of learnable parameters (only 0.8 million). This network comprises an encoder–decoder architecture that incorporates conformer-based focal modulation attention, self-aware local and global spatial attention, and split channel-shuffle. The efficacy of our model has been evaluated on four well-established benchmark datasets for skin lesion segmentation: ISIC 2016, ISIC 2017, ISIC 2018, and PH2. Empirical findings substantiate its state-of-the-art performance, notably reflected in a high Jaccard index.
准确分割皮肤镜图像中的皮肤病变对于在移动平台上及时识别皮肤癌以进行计算机辅助诊断起着至关重要的作用。然而,由于皮损形状各异、边缘不清晰以及毛发和标记色等障碍物的存在,这一挑战变得更加复杂。此外,皮肤病变往往在质地和颜色上表现出微妙的变化,很难与周围健康的皮肤区分开来,因此需要能捕捉细微细节和更广泛背景信息的模型。目前,黑色素瘤分割模型通常基于全连接网络和 U 型网络。然而,这些模型往往难以捕捉皮肤病变复杂多样的特征,如边界不清和病变外观多样等,从而导致分割效果不理想。为了应对这些挑战,我们提出了一种新颖的轻量级网络,专门用于利用移动设备进行皮损分割,可学习参数数量极少(仅为 0.8 百万)。该网络由编码器-解码器架构组成,其中包含基于保形剂的焦点调制注意力、自我感知的局部和全局空间注意力以及分裂信道洗牌。我们在四个成熟的皮损分割基准数据集上对模型的功效进行了评估:ISIC 2016、ISIC 2017、ISIC 2018 和 PH2。实证研究结果证实了该模型的一流性能,尤其是高杰卡德指数(Jaccard index)。
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引用次数: 0
Domain generalization for enhanced predictions of hospital readmission on unseen domains among patients with diabetes 通过领域归纳增强对糖尿病患者未见领域的再入院预测能力
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-10 DOI: 10.1016/j.artmed.2024.103010
Ameen Abdel Hai , Mark G. Weiner , Alice Livshits , Jeremiah R. Brown , Anuradha Paranjape , Wenke Hwang , Lester H. Kirchner , Nestoras Mathioudakis , Esra Karslioglu French , Zoran Obradovic , Daniel J. Rubin
A prediction model to assess the risk of hospital readmission can be valuable to identify patients who may benefit from extra care. Developing hospital-specific readmission risk prediction models using local data is not feasible for many institutions. Models developed on data from one hospital may not generalize well to another hospital. There is a lack of an end-to-end adaptable readmission model that can generalize to unseen test domains. We propose an early readmission risk domain generalization network, ERR-DGN, for cross-domain knowledge transfer. ERR-DGN internalizes the shared patterns and characteristics that are consistent across source domains, enabling it to adapt to a new domain. It transforms source datasets to a common embedding space while capturing relevant temporal long-term dependencies of sequential data. Domain generalization is then applied on domain-specific fully connected linear layers. The model is optimized by a loss function that integrates distribution discrepancy loss to match the mean embeddings of multiple source distributions with the task-specific loss.
A model was developed using electronic health record (EHR) data of 201,688 patients with diabetes across urban, suburban, rural, and mixed hospital systems to enhance 30-day readmission predictions among patients with diabetes on 67,066 unseen patients at a rural hospital. We also explored how model performance varied by the number of sites and over time. The proposed method outperformed the baseline models, yielding a 6 % increase in F1-score (0.79 ± 0.006 vs. 0.73 ± 0.007). Model performance peaked with the inclusion of three sites. Performance of the model was relatively stable for 3 years then declined at 4 years. ERR-DGN may be a proficient tool for learning data from multiple sites and subsequently applying a hospitalization readmission prediction model to a new site. Including a relatively small number of varied sites may be sufficient to achieve peak performance. Periodic retraining at least every 3 years may mitigate model degradation over time.
评估再入院风险的预测模型对于识别可能从额外护理中受益的患者很有价值。使用本地数据开发针对特定医院的再入院风险预测模型对许多机构来说并不可行。根据一家医院的数据开发的模型可能无法很好地推广到另一家医院。目前还缺乏一种端到端可调整的再入院模型,这种模型可以推广到未见过的测试领域。我们提出了一种用于跨领域知识转移的早期再入院风险领域泛化网络(ERR-DGN)。ERR-DGN将源领域中一致的共享模式和特征内化,使其能够适应新领域。它将源数据集转换到一个共同的嵌入空间,同时捕捉连续数据的相关时间长期依赖关系。然后将领域泛化应用于特定领域的全连接线性层。我们利用城市、郊区、农村和混合医院系统中 201,688 名糖尿病患者的电子健康记录(EHR)数据开发了一个模型,以提高一家农村医院中 67,066 名未见过的糖尿病患者的 30 天再入院预测。我们还探讨了模型性能随地点数量和时间的变化而变化的情况。拟议方法的性能优于基线模型,F1 分数提高了 6%(0.79 ± 0.006 vs. 0.73 ± 0.007)。加入三个站点后,模型性能达到顶峰。该模型的性能在 3 年中相对稳定,但在 4 年中有所下降。ERR-DGN可能是从多个地点学习数据,然后将住院再入院预测模型应用到新地点的熟练工具。纳入相对较少数量的不同地点可能就足以达到最佳性能。至少每 3 年进行一次定期再训练可减轻模型随时间推移而退化的情况。
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引用次数: 0
Acoustical features as knee health biomarkers: A critical analysis 作为膝关节健康生物标志物的声学特征:批判性分析。
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-10 DOI: 10.1016/j.artmed.2024.103013
Christodoulos Kechris , Jerome Thevenot , Tomas Teijeiro , Vincent A. Stadelmann , Nicola A. Maffiuletti , David Atienza
Acoustical knee health assessment has long promised an alternative to clinically available medical imaging tools, but this modality has yet to be adopted in medical practice. The field is currently led by machine learning models processing acoustical features, which have presented promising diagnostic performances. However, these methods overlook the intricate multi-source nature of audio signals and the underlying mechanisms at play. By addressing this critical gap, the present paper introduces a novel causal framework for validating knee acoustical features. We argue that current machine learning methodologies for acoustical knee diagnosis lack the required assurances and thus cannot be used to classify acoustic features as biomarkers. Our framework establishes a set of essential theoretical guarantees necessary to validate this claim. We apply our methodology to three real-world experiments investigating the effect of researchers’ expectations, the experimental protocol, and the wearable employed sensor. We reveal latent issues such as underlying shortcut learning and performance inflation. This study is the first independent result reproduction study in acoustical knee health evaluation. We conclude by offering actionable insights that address key limitations, providing valuable guidance for future research in knee health acoustics.
长期以来,声学膝关节健康评估一直是临床可用医学成像工具的替代品,但这种模式尚未在医疗实践中得到采用。目前,该领域主要由处理声学特征的机器学习模型主导,这些模型在诊断方面表现出色。然而,这些方法忽略了音频信号错综复杂的多源性质和潜在的作用机制。针对这一关键缺陷,本文引入了一个新颖的因果框架来验证膝关节声学特征。我们认为,目前用于膝关节声学诊断的机器学习方法缺乏必要的保证,因此不能用于将声学特征分类为生物标志物。我们的框架建立了一套必要的基本理论保证来验证这一观点。我们将我们的方法应用到三个真实世界的实验中,调查研究人员的期望、实验方案和采用的可穿戴传感器的影响。我们揭示了潜在的问题,如潜在的捷径学习和性能膨胀。本研究是声学膝关节健康评估领域的首个独立结果再现研究。最后,我们针对关键的局限性提出了可行的见解,为膝关节健康声学的未来研究提供了宝贵的指导。
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引用次数: 0
Exploring the effectiveness of instruction tuning in biomedical language processing 探索生物医学语言处理中指令调整的有效性。
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-07 DOI: 10.1016/j.artmed.2024.103007
Omid Rohanian , Mohammadmahdi Nouriborji , Samaneh Kouchaki , Farhad Nooralahzadeh , Lei Clifton , David A. Clifton
Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset’s composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.2
大型语言模型(LLM),尤其是类似于 ChatGPT 的大型语言模型,对自然语言处理(NLP)领域产生了重大影响。虽然这些模型在一般语言任务中表现出色,但它们在生物医学和临床命名实体识别(NER)、关系提取(RE)和医学自然语言推理(NLI)等特定领域下游任务中的表现仍在不断发展。在这种情况下,我们的研究调查了指令调整在生物医学语言处理方面的潜力,并将这一技术应用于两个具有相当规模的通用 LLM。我们展示了一个基于指令的综合模型,该模型是在一个包含约 20 万个指令样本的数据集上训练出来的。该数据集是对现有数据的精心编辑,经过了细致的调整和重新格式化,以符合我们基于指令的任务的具体要求。这一举措是利用此类模型取得与 BioBERT 和 BioClinicalBERT 等纯编码器专业模型同等结果的重要一步,可用于各种经典的生物医学 NLP 任务。我们的工作包括分析数据集的组成及其对模型性能的影响,从而深入了解指令调整的复杂性。通过分享我们的代码、模型和基于指令的独特数据集,我们希望鼓励这一领域的持续研究和发展。
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引用次数: 0
Individualised recovery trajectories of patients with impeded mobility, using distance between probability distributions of learnt graphs 利用学习图的概率分布之间的距离,为行动不便的患者制定个性化的康复轨迹。
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-01 DOI: 10.1016/j.artmed.2024.103005
Chuqiao Zhang , Crina Grosan , Dalia Chakrabarty
Patients who are undergoing physical rehabilitation, benefit from feedback that follows from reliable assessment of their cumulative performance attained at a given time. In this paper, we provide a method for the learning of the recovery trajectory of an individual patient, as they undertake exercises as part of their physical therapy towards recovery of their loss of movement ability, following a critical illness. The difference between the Movement Recovery Scores (MRSs) attained by a patient, when undertaking a given exercise routine on successive instances, is given by a statistical distance/divergence between the (posterior) probabilities of random graphs that are Bayesianly learnt using time series data on locations of 20 of the patient’s joints, recorded on an e-platform as the patient exercises. This allows for the computation of the MRS on every occasion the patient undertakes this exercise, using which, the recovery trajectory is drawn. We learn each graph as a Random Geometric Graph drawn in a probabilistic metric space, and identify the closed-form marginal posterior of any edge of the graph, given the correlation structure of the multivariate time series data on joint locations. On the basis of our recovery learning, we offer recommendations on the optimal exercise routines for patients with given level of mobility impairment.
正在接受物理康复治疗的病人,可以从对他们在特定时间内取得的累积成绩进行可靠评估后得到的反馈中获益。在本文中,我们提供了一种方法,用于了解个别病人的康复轨迹,因为他们在进行锻炼时,是恢复危重病人丧失的运动能力的物理治疗的一部分。病人在连续进行给定锻炼时获得的运动恢复得分(MRS)之间的差异,是由随机图(后置)概率之间的统计距离/分歧给出的,而随机图是利用病人锻炼时在电子平台上记录的病人 20 个关节位置的时间序列数据以贝叶斯方式学习的。这样就能计算出患者每次运动时的 MRS,并据此绘制出恢复轨迹。我们将每个图作为在概率度量空间中绘制的随机几何图形来学习,并根据关节位置多变量时间序列数据的相关结构,确定图中任何边的闭式边际后验。在恢复学习的基础上,我们为具有特定行动障碍程度的患者提供了最佳运动程序建议。
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引用次数: 0
From pre-training to fine-tuning: An in-depth analysis of Large Language Models in the biomedical domain 从预训练到微调:深入分析生物医学领域的大型语言模型。
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-01 DOI: 10.1016/j.artmed.2024.103003
Agnese Bonfigli , Luca Bacco , Mario Merone , Felice Dell’Orletta
In this study, we delve into the adaptation and effectiveness of Transformer-based, pre-trained Large Language Models (LLMs) within the biomedical domain, a field that poses unique challenges due to its complexity and the specialized nature of its data. Building on the foundation laid by the transformative architecture of Transformers, we investigate the nuanced dynamics of LLMs through a multifaceted lens, focusing on two domain-specific tasks, i.e., Natural Language Inference (NLI) and Named Entity Recognition (NER). Our objective is to bridge the knowledge gap regarding how these models’ downstream performances correlate with their capacity to encapsulate task-relevant information. To achieve this goal, we probed and analyzed the inner encoding and attention mechanisms in LLMs, both encoder- and decoder-based, tailored for either general or biomedical-specific applications. This examination occurs before and after the models are fine-tuned across various data volumes. Our findings reveal that the models’ downstream effectiveness is intricately linked to specific patterns within their internal mechanisms, shedding light on the nuanced ways in which LLMs process and apply knowledge in the biomedical context. The source code for this paper is available at https://github.com/agnesebonfigli99/LLMs-in-the-Biomedical-Domain.
在本研究中,我们深入探讨了基于 Transformer 的预训练大型语言模型(LLM)在生物医学领域的适应性和有效性,该领域因其数据的复杂性和专业性而面临独特的挑战。在 Transformers 的转换架构所奠定的基础上,我们通过多角度视角研究 LLM 的细微动态,重点关注两个特定领域的任务,即自然语言推理(NLI)和命名实体识别(NER)。我们的目标是填补知识空白,了解这些模型的下游性能与其封装任务相关信息的能力之间的关系。为了实现这一目标,我们探究并分析了基于编码器和解码器的 LLM 中的内部编码和注意机制,这些 LLM 都是为一般应用或生物医学特定应用量身定制的。这种检查发生在对各种数据量的模型进行微调之前和之后。我们的研究结果表明,模型的下游效果与其内部机制的特定模式密切相关,从而揭示了 LLM 在生物医学环境中处理和应用知识的细微方式。本文的源代码可在 https://github.com/agnesebonfigli99/LLMs-in-the-Biomedical-Domain 上获取。
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引用次数: 0
Intelligent wearable-assisted digital healthcare industry 5.0 智能可穿戴设备辅助数字医疗行业 5.0
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-01 DOI: 10.1016/j.artmed.2024.103000
Vrutti Tandel , Aparna Kumari , Sudeep Tanwar , Anupam Singh , Ravi Sharma , Nagendar Yamsani
The latest evolution of the healthcare industry from Industry 1.0 to 5.0, incorporating smart wearable devices and digital technologies, has revolutionized healthcare delivery and improved patient treatment. Integrating smart wearables such as fitness trackers, smartwatches, and biosensors has endowed healthcare Industry 5.0 with numerous advantages, including remote patient monitoring, personalized healthcare, patient empowerment and engagement, telemedicine, and virtual care. This digital healthcare paradigm embraces promising technologies like Machine Learning (ML) and the Internet of Medical Things (IoMT) to enhance patient care. The key contribution of digital healthcare Industry 5.0 lies in its ability to revolutionize patient care by leveraging smart wearables and digital technologies to provide personalized, proactive, and patient-centric healthcare solutions. Despite the remarkable growth of smart wearables, the exploration of ML-based applications still needs to be expanded. Motivated by this gap, our paper conducts a comprehensive examination and evaluation of advanced ML techniques pertinent to the digital healthcare Industry 5.0 and wearable technology. We propose a detailed taxonomy for digital healthcare Industry 5.0, transforming it into an innovative process model highlighting key research challenges such as wearable modes for data collection, health tracking, security, and privacy issues. The proposed ML-based process comprises data collection from wearables like smartwatches and performs data pre-processing. Several ML models are applied, such as Support Vector Machine (SVM), Decision Tree (DT), and Random Forest(RF), to predict and classify the activity of the person. ML algorithms are capable of analyzing extensive healthcare data encompassing electronic health records (EHR) from sensors to offer valuable insights to improve decision-making processes. A comparative study of the existing work is discussed in detail. Lastly, a case study is presented to render the process model, where the RF-based model shows its efficacy by obtaining the lowest RMSE of 0.94, MSE of 0.88, and MAE of 0.27 for the prediction of activity.
医疗保健行业从工业 1.0 到 5.0 的最新发展,融合了智能可穿戴设备和数字技术,彻底改变了医疗保健服务,改善了患者治疗。整合健身追踪器、智能手表和生物传感器等智能可穿戴设备,赋予了医疗保健行业 5.0 众多优势,包括远程患者监控、个性化医疗保健、患者赋权和参与、远程医疗和虚拟护理。这种数字医疗模式采用了机器学习(ML)和医疗物联网(IoMT)等前景广阔的技术,以加强对患者的护理。数字医疗行业 5.0 的主要贡献在于,它能够利用智能可穿戴设备和数字技术,提供个性化、前瞻性和以患者为中心的医疗解决方案,从而彻底改变患者护理方式。尽管智能可穿戴设备的发展令人瞩目,但基于 ML 的应用探索仍有待拓展。基于这一差距,我们的论文对与数字医疗行业 5.0 和可穿戴技术相关的先进 ML 技术进行了全面的研究和评估。我们为数字医疗行业 5.0 提出了一个详细的分类标准,并将其转化为一个创新的流程模型,突出了关键的研究挑战,如用于数据收集、健康跟踪、安全和隐私问题的可穿戴模式。拟议的基于 ML 的流程包括从智能手表等可穿戴设备收集数据,并进行数据预处理。应用支持向量机(SVM)、决策树(DT)和随机森林(RF)等多种 ML 模型对人的活动进行预测和分类。ML 算法能够分析广泛的医疗保健数据,包括来自传感器的电子健康记录 (EHR),从而为改进决策过程提供有价值的见解。本文详细讨论了现有工作的比较研究。最后,介绍了一个案例研究,以呈现过程模型,其中基于射频的模型在预测活动方面获得了最低的 RMSE(0.94)、MSE(0.88)和 MAE(0.27),显示了其功效。
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引用次数: 0
Efficiency at scale: Investigating the performance of diminutive language models in clinical tasks 规模效率:研究微型语言模型在临床任务中的表现。
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-01 DOI: 10.1016/j.artmed.2024.103002
Niall Taylor , Upamanyu Ghose , Omid Rohanian , Mohammadmahdi Nouriborji , Andrey Kormilitzin , David A. Clifton , Alejo Nevado-Holgado
The entry of large language models (LLMs) into research and commercial spaces has led to a trend of ever-larger models, with initial promises of generalisability. This was followed by a widespread desire to downsize and create specialised models without the need for complete fine-tuning, using Parameter Efficient Fine-tuning (PEFT) methods. We present an investigation into the suitability of different PEFT methods to clinical decision-making tasks, across a range of model sizes, including extremely small models with as few as 25 million parameters.
Our analysis shows that the performance of most PEFT approaches varies significantly from one task to another, with the exception of LoRA, which maintains relatively high performance across all model sizes and tasks, typically approaching or matching full fine-tuned performance. The effectiveness of PEFT methods in the clinical domain is evident, particularly for specialised models which can operate on low-cost, in-house computing infrastructure. The advantages of these models, in terms of speed and reduced training costs, dramatically outweighs any performance gain from large foundation LLMs. Furthermore, we highlight how domain-specific pre-training interacts with PEFT methods and model size, finding the domain pre-training to be particularly important in smaller models and discuss how these factors interplay to provide the best efficiency-performance trade-off. Full code available at: https://github.com/nlpie-research/efficient-ml.
随着大型语言模型(LLM)进入研究和商业领域,最初承诺具有通用性的模型呈现出越来越大的趋势。随后,人们普遍希望使用参数高效微调(PEFT)方法缩小并创建无需完全微调的专用模型。我们对不同的 PEFT 方法是否适用于临床决策任务进行了调查,调查涉及各种规模的模型,包括参数少至 2,500 万的极小模型。我们的分析表明,大多数 PEFT 方法的性能在不同任务中差异很大,但 LoRA 除外,它在所有模型大小和任务中都能保持相对较高的性能,通常接近或匹配完全微调性能。PEFT 方法在临床领域的有效性是显而易见的,特别是对于可在低成本内部计算基础设施上运行的专业模型。这些模型在速度和降低训练成本方面的优势,大大超过了大型基础 LLM 所带来的性能提升。此外,我们还强调了特定领域的预训练如何与 PEFT 方法和模型大小相互作用,发现领域预训练对较小的模型尤为重要,并讨论了这些因素如何相互作用以提供最佳的效率-性能权衡。完整代码见:https://github.com/nlpie-research/efficient-ml。
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引用次数: 0
Fully automatic deep convolutional approaches for the screening of neurodegeneratives diseases using multi-view OCT images 利用多视角 OCT 图像筛查神经退行性疾病的全自动深度卷积方法
IF 6.1 2区 医学 Q1 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE Pub Date : 2024-11-01 DOI: 10.1016/j.artmed.2024.103006
Lorena Álvarez-Rodríguez , Ana Pueyo , Joaquim de Moura , Elisa Vilades , Elena Garcia-Martin , Clara I. Sánchez , Jorge Novo , Marcos Ortega
The prevalence of neurodegenerative diseases (NDDs) such as Alzheimer’s (AD), Parkinson’s (PD), Essential tremor (ET), and Multiple Sclerosis (MS) is increasing alongside the aging population. Recent studies suggest that these disorders can be identified through retinal imaging, allowing for early detection and monitoring via Optical Coherence Tomography (OCT) scans. This study is at the forefront of research, pioneering the application of multi-view OCT and 3D information to the neurological diseases domain. Our methodology consists of two main steps. In the first one, we focus on the segmentation of the retinal nerve fiber layer (RNFL) and a class layer grouping between the ganglion cell layer and Bruch’s membrane (GCL-BM) in both macular and optic disc OCT scans. These are the areas where changes in thickness serve as a potential indicator of NDDs. The second phase is to select patients based on information about the retinal layers. We explore how the integration of both views (macula and optic disc) improves each screening scenario: Healthy Controls (HC) vs. NDD, AD vs. NDD, ET vs. NDD, MS vs. NDD, PD vs. NDD, and a final multi-class approach considering all four NDDs. For the segmentation task, we obtained satisfactory results for both 2D and 3D approaches in macular segmentation, in which 3D performed better due to the inclusion of depth and cross-sectional information. As for the optic disc view, transfer learning did not improve the metrics over training from scratch, but it did provide a faster training. As for screening, 3D computational biomarkers provided better results than 2D ones, and multi-view methods were usually better than the single-view ones. Regarding separability among diseases, MS and PD were the ones that provided better results in their screening approaches, being also the most represented classes. In conclusion, our methodology has been successfully validated with an extensive experimentation of configurations, techniques and OCT views, becoming the first multi-view analysis that merges data from both macula-centered and optic disc-centered perspectives. Besides, it is also the first effort to examine key retinal layers across four major NDDs within the framework of pathological screening.
随着人口老龄化的加剧,神经退行性疾病(NDDs),如阿尔茨海默氏症(AD)、帕金森氏症(PD)、原发性震颤(ET)和多发性硬化症(MS)的发病率也在不断上升。最近的研究表明,这些疾病可以通过视网膜成像进行识别,从而通过光学相干断层扫描(OCT)进行早期检测和监测。这项研究走在研究前沿,率先将多视角光学相干断层扫描和三维信息应用于神经疾病领域。我们的方法包括两个主要步骤。第一步,我们重点关注黄斑和视盘 OCT 扫描中视网膜神经纤维层(RNFL)的分割以及神经节细胞层和布鲁氏膜之间的类层分组(GCL-BM)。这些区域的厚度变化可作为 NDD 的潜在指标。第二阶段是根据视网膜层的信息选择患者。我们探讨了两种视图(黄斑和视盘)的整合如何改善每种筛选方案:健康对照组 (HC) vs. NDD、AD vs. NDD、ET vs. NDD、MS vs. NDD、PD vs. NDD,以及最后一种考虑所有四种 NDD 的多类方法。在黄斑分割任务中,二维和三维方法都取得了令人满意的结果,其中三维方法由于包含了深度和横截面信息而表现更好。至于视盘视图,与从头开始训练相比,迁移学习并没有改善指标,但它确实提供了更快的训练。在筛查方面,三维计算生物标志物比二维生物标志物提供了更好的结果,多视角方法通常比单视角方法更好。关于疾病之间的可分离性,多发性硬化症和帕金森病是筛选方法中结果较好的疾病,也是代表性最强的类别。总之,通过对配置、技术和 OCT 视图的广泛实验,我们的方法得到了成功的验证,成为首个融合了以黄斑为中心和以视盘为中心的数据的多视图分析方法。此外,这也是首次在病理筛查框架内对四种主要 NDD 的关键视网膜层进行检查。
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Artificial Intelligence in Medicine
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