自动放射学报告生成在诊所至关重要，可以缓解来自繁重的工作量的经验丰富的放射科医师，并提醒缺乏误诊或错过诊断的缺乏经验的放射科学家。现有方法主要将放射学报告生成作为图像标题任务，采用编码器解码器框架。但是，在医学领域，这种纯数据驱动方法遭受以下问题：1）视觉和文本偏差问题; 2）缺乏专家知识。在本文中，我们提出了一种知识增强的放射学报告生成方法，介绍了两种类型的医学知识：1）一般知识，这是输入的独立知识，并为报告生成提供了广泛的知识; 2）特定知识，其输入依赖并为报告生成提供了细粒度的知识。为了充分利用一般和具体知识，我们还提出了一种知识增强的多主题注意机制。通过利用一般知识和特定知识来利用放射线图像的视觉特征，所提出的模型可以提高所生成的报告的质量。两种公共数据集IU-X射线和模拟CXR的实验结果表明，所提出的知识增强方法优于基于最先进的图像标题的方法。消融研究还表明，一般和具体知识都可以有助于提高放射学报告生成的表现。

Autonomous robotic surgery has advanced significantly based on analysis of visual and temporal cues in surgical workflow, but relational cues from domain knowledge remain under investigation. Complex relations in surgical annotations can be divided into intra- and inter-relations, both valuable to autonomous systems to comprehend surgical workflows. Intra- and inter-relations describe the relevance of various categories within a particular annotation type and the relevance of different annotation types, respectively. This paper aims to systematically investigate the importance of relational cues in surgery. First, we contribute the RLLS12M dataset, a large-scale collection of robotic left lateral sectionectomy (RLLS), by curating 50 videos of 50 patients operated by 5 surgeons and annotating a hierarchical workflow, which consists of 3 inter- and 6 intra-relations, 6 steps, 15 tasks, and 38 activities represented as the triplet of 11 instruments, 8 actions, and 16 objects, totaling 2,113,510 video frames and 12,681,060 annotation entities. Correspondingly, we propose a multi-relation purification hybrid network (MURPHY), which aptly incorporates novel relation modules to augment the feature representation by purifying relational features using the intra- and inter-relations embodied in annotations. The intra-relation module leverages a R-GCN to implant visual features in different graph relations, which are aggregated using a targeted relation purification with affinity information measuring label consistency and feature similarity. The inter-relation module is motivated by attention mechanisms to regularize the influence of relational features based on the hierarchy of annotation types from the domain knowledge. Extensive experimental results on the curated RLLS dataset confirm the effectiveness of our approach, demonstrating that relations matter in surgical workflow analysis.

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.

The automation of an increasingly large number of software engineering tasks is becoming possible thanks to Machine Learning (ML). One foundational building block in the application of ML to software artifacts is the representation of these artifacts (e.g., source code or executable code) into a form that is suitable for learning. Many studies have leveraged representation learning, delegating to ML itself the job of automatically devising suitable representations. Yet, in the context of Android problems, existing models are either limited to coarse-grained whole-app level (e.g., apk2vec) or conducted for one specific downstream task (e.g., smali2vec). Our work is part of a new line of research that investigates effective, task-agnostic, and fine-grained universal representations of bytecode to mitigate both of these two limitations. Such representations aim to capture information relevant to various low-level downstream tasks (e.g., at the class-level). We are inspired by the field of Natural Language Processing, where the problem of universal representation was addressed by building Universal Language Models, such as BERT, whose goal is to capture abstract semantic information about sentences, in a way that is reusable for a variety of tasks. We propose DexBERT, a BERT-like Language Model dedicated to representing chunks of DEX bytecode, the main binary format used in Android applications. We empirically assess whether DexBERT is able to model the DEX language and evaluate the suitability of our model in two distinct class-level software engineering tasks: Malicious Code Localization and Defect Prediction. We also experiment with strategies to deal with the problem of catering to apps having vastly different sizes, and we demonstrate one example of using our technique to investigate what information is relevant to a given task.

Accurate polyp segmentation is of great importance for colorectal cancer diagnosis and treatment. However, due to the high cost of producing accurate mask annotations, existing polyp segmentation methods suffer from severe data shortage and impaired model generalization. Reversely, coarse polyp bounding box annotations are more accessible. Thus, in this paper, we propose a boosted BoxPolyp model to make full use of both accurate mask and extra coarse box annotations. In practice, box annotations are applied to alleviate the over-fitting issue of previous polyp segmentation models, which generate fine-grained polyp area through the iterative boosted segmentation model. To achieve this goal, a fusion filter sampling (FFS) module is firstly proposed to generate pixel-wise pseudo labels from box annotations with less noise, leading to significant performance improvements. Besides, considering the appearance consistency of the same polyp, an image consistency (IC) loss is designed. Such IC loss explicitly narrows the distance between features extracted by two different networks, which improves the robustness of the model. Note that our BoxPolyp is a plug-and-play model, which can be merged into any appealing backbone. Quantitative and qualitative experimental results on five challenging benchmarks confirm that our proposed model outperforms previous state-of-the-art methods by a large margin.

While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation~(UDA) techniques leverage abundant labeled source data together with unlabeled target data to reduce the domain gap, but these methods degrade significantly with limited source annotations. In this study, we address this underexplored UDA problem, investigating a challenging but valuable realistic scenario, where the source domain not only exhibits domain shift~w.r.t. the target domain but also suffers from label scarcity. In this regard, we propose a novel and generic framework called ``Label-Efficient Unsupervised Domain Adaptation"~(LE-UDA). In LE-UDA, we construct self-ensembling consistency for knowledge transfer between both domains, as well as a self-ensembling adversarial learning module to achieve better feature alignment for UDA. To assess the effectiveness of our method, we conduct extensive experiments on two different tasks for cross-modality segmentation between MRI and CT images. Experimental results demonstrate that the proposed LE-UDA can efficiently leverage limited source labels to improve cross-domain segmentation performance, outperforming state-of-the-art UDA approaches in the literature. Code is available at: https://github.com/jacobzhaoziyuan/LE-UDA.

We develop a wall model for large-eddy simulation (LES) that takes into account various pressure-gradient effects using multi-agent reinforcement learning (MARL). The model is trained using low-Reynolds-number flow over periodic hills with agents distributed on the wall along the computational grid points. The model utilizes a wall eddy-viscosity formulation as the boundary condition, which is shown to provide better predictions of the mean velocity field, rather than the typical wall-shear stress formulation. Each agent receives states based on local instantaneous flow quantities at an off-wall location, computes a reward based on the estimated wall-shear stress, and provides an action to update the wall eddy viscosity at each time step. The trained wall model is validated in wall-modeled LES (WMLES) of flow over periodic hills at higher Reynolds numbers, and the results show the effectiveness of the model on flow with pressure gradients. The analysis of the trained model indicates that the model is capable of distinguishing between the various pressure gradient regimes present in the flow.

Artificial Intelligence (AI) is having a tremendous impact across most areas of science. Applications of AI in healthcare have the potential to improve our ability to detect, diagnose, prognose, and intervene on human disease. For AI models to be used clinically, they need to be made safe, reproducible and robust, and the underlying software framework must be aware of the particularities (e.g. geometry, physiology, physics) of medical data being processed. This work introduces MONAI, a freely available, community-supported, and consortium-led PyTorch-based framework for deep learning in healthcare. MONAI extends PyTorch to support medical data, with a particular focus on imaging, and provide purpose-specific AI model architectures, transformations and utilities that streamline the development and deployment of medical AI models. MONAI follows best practices for software-development, providing an easy-to-use, robust, well-documented, and well-tested software framework. MONAI preserves the simple, additive, and compositional approach of its underlying PyTorch libraries. MONAI is being used by and receiving contributions from research, clinical and industrial teams from around the world, who are pursuing applications spanning nearly every aspect of healthcare.

Finetuning language models on a collection of datasets phrased as instructions has been shown to improve model performance and generalization to unseen tasks. In this paper we explore instruction finetuning with a particular focus on (1) scaling the number of tasks, (2) scaling the model size, and (3) finetuning on chain-of-thought data. We find that instruction finetuning with the above aspects dramatically improves performance on a variety of model classes (PaLM, T5, U-PaLM), prompting setups (zero-shot, few-shot, CoT), and evaluation benchmarks (MMLU, BBH, TyDiQA, MGSM, open-ended generation). For instance, Flan-PaLM 540B instruction-finetuned on 1.8K tasks outperforms PALM 540B by a large margin (+9.4% on average). Flan-PaLM 540B achieves state-of-the-art performance on several benchmarks, such as 75.2% on five-shot MMLU. We also publicly release Flan-T5 checkpoints, which achieve strong few-shot performance even compared to much larger models, such as PaLM 62B. Overall, instruction finetuning is a general method for improving the performance and usability of pretrained language models.

公平性是一个标准，重点是评估不同人口组的算法性能，它引起了自然语言处理，推荐系统和面部识别的关注。由于医学图像样本中有很多人口统计学属性，因此了解公平的概念，熟悉不公平的缓解技术，评估算法的公平程度并认识到医疗图像分析（媒体）中的公平问题中的挑战很重要。在本文中，我们首先给出了公平性的全面和精确的定义，然后通过在媒体中引入当前使用的技术中使用的技术。之后，我们列出了包含人口统计属性的公共医疗图像数据集，以促进公平研究并总结有关媒体公平性的当前算法。为了帮助更好地理解公平性，并引起人们对媒体中与公平性有关的问题的关注，进行了实验，比较公平性和数据失衡之间的差异，验证各种媒体任务中不公平的存在，尤其是在分类，细分和检测以及评估不公平缓解算法的有效性。最后，我们以媒体公平性的机会和挑战得出结论。