凭借越来越多的计算建模效率，用于管理和保护大障碍礁的计算建模效率，我们通过重新修复包含APSIM模型的输出的现有大型数据集来对APSIM模型进行机会模型模拟使用深神经网络的使用初探运行。数据集未专门针对模型仿真任务量身定制。我们采用了两个神经网络架构进行了仿真任务：密集连接的前馈神经网络（FFNN），以及进料到FFNN（GRU-FFNN）的门控复发单元，一种经常性神经网络。有试验架构的各种配置。最小相关统计用于识别可以聚合以形成模型仿真的训练集的APSIM场景的集群。我们专注于模拟APSIM模型的4个重要产出：径流，土壤，DINRUNOFF，NLEACHED。具有三个隐藏图层的GRU-FFNN架构和每层128个单位提供良好的径流和DINRUNOFF仿真。但是，在广泛的考虑架构下，肮脏和Nlo张化的仿真相对较差;仿真器未能在这两个输出的较高值下捕获可变性。虽然来自过去建模活动的机会主义数据提供了一个大型和有用的数据集，用于探索APSIM仿真，但它可能无法足够丰富，以便成功地学习更复杂的模型动态。可能需要计算机实验设计来生成更具信息性的数据以模拟所有输出变量的感兴趣。我们还建议使用合成气象设置，以允许模型进入各种输入。这些不需要都代表正常条件，但可以提供更密集的，更多的信息数据集，可以学习输入和输出之间的复杂关系。

An increasing number of public datasets have shown a marked clinical impact on assessing anatomical structures. However, each of the datasets is small, partially labeled, and rarely investigates severe tumor subjects. Moreover, current models are limited to segmenting specific organs/tumors, which can not be extended to novel domains and classes. To tackle these limitations, we introduce embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models, dubbed the CLIP-Driven Universal Model. The Universal Model can better segment 25 organs and 6 types of tumors by exploiting the semantic relationship between abdominal structures. The model is developed from an assembly of 14 datasets with 3,410 CT scans and evaluated on 6,162 external CT scans from 3 datasets. We rank first on the public leaderboard of the Medical Segmentation Decathlon (MSD) and achieve the state-of-the-art results on Beyond The Cranial Vault (BTCV). Compared with dataset-specific models, the Universal Model is computationally more efficient (6x faster), generalizes better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks. The design of CLIP embedding enables the Universal Model to be easily extended to new classes without catastrophically forgetting the previously learned classes.

We present an extension to masked autoencoders (MAE) which improves on the representations learnt by the model by explicitly encouraging the learning of higher scene-level features. We do this by: (i) the introduction of a perceptual similarity term between generated and real images (ii) incorporating several techniques from the adversarial training literature including multi-scale training and adaptive discriminator augmentation. The combination of these results in not only better pixel reconstruction but also representations which appear to capture better higher-level details within images. More consequentially, we show how our method, Perceptual MAE, leads to better performance when used for downstream tasks outperforming previous methods. We achieve 78.1% top-1 accuracy linear probing on ImageNet-1K and up to 88.1% when fine-tuning, with similar results for other downstream tasks, all without use of additional pre-trained models or data.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Background: Encouraged by the success of pretrained Transformer models in many natural language processing tasks, their use for International Classification of Diseases (ICD) coding tasks is now actively being explored. In this study, we investigate three types of Transformer-based models, aiming to address the extreme label set and long text classification challenges that are posed by automated ICD coding tasks. Methods: The Transformer-based model PLM-ICD achieved the current state-of-the-art (SOTA) performance on the ICD coding benchmark dataset MIMIC-III. It was chosen as our baseline model to be further optimised. XR-Transformer, the new SOTA model in the general extreme multi-label text classification domain, and XR-LAT, a novel adaptation of the XR-Transformer model, were also trained on the MIMIC-III dataset. XR-LAT is a recursively trained model chain on a predefined hierarchical code tree with label-wise attention, knowledge transferring and dynamic negative sampling mechanisms. Results: Our optimised PLM-ICD model, which was trained with longer total and chunk sequence lengths, significantly outperformed the current SOTA PLM-ICD model, and achieved the highest micro-F1 score of 60.8%. The XR-Transformer model, although SOTA in the general domain, did not perform well across all metrics. The best XR-LAT based model obtained results that were competitive with the current SOTA PLM-ICD model, including improving the macro-AUC by 2.1%. Conclusion: Our optimised PLM-ICD model is the new SOTA model for automated ICD coding on the MIMIC-III dataset, while our novel XR-LAT model performs competitively with the previous SOTA PLM-ICD model.

Deepfakes are computationally-created entities that falsely represent reality. They can take image, video, and audio modalities, and pose a threat to many areas of systems and societies, comprising a topic of interest to various aspects of cybersecurity and cybersafety. In 2020 a workshop consulting AI experts from academia, policing, government, the private sector, and state security agencies ranked deepfakes as the most serious AI threat. These experts noted that since fake material can propagate through many uncontrolled routes, changes in citizen behaviour may be the only effective defence. This study aims to assess human ability to identify image deepfakes of human faces (StyleGAN2:FFHQ) from nondeepfake images (FFHQ), and to assess the effectiveness of simple interventions intended to improve detection accuracy. Using an online survey, 280 participants were randomly allocated to one of four groups: a control group, and 3 assistance interventions. Each participant was shown a sequence of 20 images randomly selected from a pool of 50 deepfake and 50 real images of human faces. Participants were asked if each image was AI-generated or not, to report their confidence, and to describe the reasoning behind each response. Overall detection accuracy was only just above chance and none of the interventions significantly improved this. Participants' confidence in their answers was high and unrelated to accuracy. Assessing the results on a per-image basis reveals participants consistently found certain images harder to label correctly, but reported similarly high confidence regardless of the image. Thus, although participant accuracy was 62% overall, this accuracy across images ranged quite evenly between 85% and 30%, with an accuracy of below 50% for one in every five images. We interpret the findings as suggesting that there is a need for an urgent call to action to address this threat.

Objective: Thigh muscle group segmentation is important for assessment of muscle anatomy, metabolic disease and aging. Many efforts have been put into quantifying muscle tissues with magnetic resonance (MR) imaging including manual annotation of individual muscles. However, leveraging publicly available annotations in MR images to achieve muscle group segmentation on single slice computed tomography (CT) thigh images is challenging. Method: We propose an unsupervised domain adaptation pipeline with self-training to transfer labels from 3D MR to single CT slice. First, we transform the image appearance from MR to CT with CycleGAN and feed the synthesized CT images to a segmenter simultaneously. Single CT slices are divided into hard and easy cohorts based on the entropy of pseudo labels inferenced by the segmenter. After refining easy cohort pseudo labels based on anatomical assumption, self-training with easy and hard splits is applied to fine tune the segmenter. Results: On 152 withheld single CT thigh images, the proposed pipeline achieved a mean Dice of 0.888(0.041) across all muscle groups including sartorius, hamstrings, quadriceps femoris and gracilis. muscles Conclusion: To our best knowledge, this is the first pipeline to achieve thigh imaging domain adaptation from MR to CT. The proposed pipeline is effective and robust in extracting muscle groups on 2D single slice CT thigh images.The container is available for public use at https://github.com/MASILab/DA_CT_muscle_seg

Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explainability tools help provide insights into what models have learned when corresponding histologic features are poorly defined. Here, we present a method for improving explainability of DNN models using synthetic histology generated by a conditional generative adversarial network (cGAN). We show that cGANs generate high-quality synthetic histology images that can be leveraged for explaining DNN models trained to classify molecularly-subtyped tumors, exposing histologic features associated with molecular state. Fine-tuning synthetic histology through class and layer blending illustrates nuanced morphologic differences between tumor subtypes. Finally, we demonstrate the use of synthetic histology for augmenting pathologist-in-training education, showing that these intuitive visualizations can reinforce and improve understanding of histologic manifestations of tumor biology.

The selection of an optimal pacing site, which is ideally scar-free and late activated, is critical to the response of cardiac resynchronization therapy (CRT). Despite the success of current approaches formulating the detection of such late mechanical activation (LMA) regions as a problem of activation time regression, their accuracy remains unsatisfactory, particularly in cases where myocardial scar exists. To address this issue, this paper introduces a multi-task deep learning framework that simultaneously estimates LMA amount and classify the scar-free LMA regions based on cine displacement encoding with stimulated echoes (DENSE) magnetic resonance imaging (MRI). With a newly introduced auxiliary LMA region classification sub-network, our proposed model shows more robustness to the complex pattern cause by myocardial scar, significantly eliminates their negative effects in LMA detection, and in turn improves the performance of scar classification. To evaluate the effectiveness of our method, we tests our model on real cardiac MR images and compare the predicted LMA with the state-of-the-art approaches. It shows that our approach achieves substantially increased accuracy. In addition, we employ the gradient-weighted class activation mapping (Grad-CAM) to visualize the feature maps learned by all methods. Experimental results suggest that our proposed model better recognizes the LMA region pattern.

Pre-trained protein language models have demonstrated significant applicability in different protein engineering task. A general usage of these pre-trained transformer models latent representation is to use a mean pool across residue positions to reduce the feature dimensions to further downstream tasks such as predicting bio-physics properties or other functional behaviours. In this paper we provide a two-fold contribution to machine learning (ML) driven drug design. Firstly, we demonstrate the power of sparsity by promoting penalization of pre-trained transformer models to secure more robust and accurate melting temperature (Tm) prediction of single-chain variable fragments with a mean absolute error of 0.23C. Secondly, we demonstrate the power of framing our prediction problem in a probabilistic framework. Specifically, we advocate for the need of adopting probabilistic frameworks especially in the context of ML driven drug design.