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.

Many current approaches to machine learning in particle physics use generic architectures that require large numbers of parameters and disregard underlying physics principles, limiting their applicability as scientific modeling tools. In this work, we present a machine learning architecture that uses a set of inputs maximally reduced with respect to the full 6-dimensional Lorentz symmetry, and is fully permutation-equivariant throughout. We study the application of this network architecture to the standard task of top quark tagging and show that the resulting network outperforms all existing competitors despite much lower model complexity. In addition, we present a Lorentz-covariant variant of the same network applied to a 4-momentum regression task.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

使用自然语言处理方法自动汇总患者的主要进度注释中的主要问题，有助于与医院环境中的信息和认知超负荷作斗争，并可能为提供者提供计算机化的诊断决策支持。问题列表摘要需要一个模型来理解，抽象和生成临床文档。在这项工作中，我们提出了一项新的NLP任务，旨在在住院期间使用提供者进度注释的意见来在患者的日常护理计划中生成一系列问题。我们研究了两个最先进的SEQ2SEQ变压器体系结构T5和Bart的性能，以解决此问题。我们提供了一个基于公开可用的电子健康记录进度注释MART MART（MIMIC）-III中的公开电子健康记录进度注释的语料库。 T5和BART对通用域文本进行了培训，我们尝试了数据增强方法和域适应性预训练方法，以增加医学词汇和知识的接触。评估方法包括胭脂，Bertscore，嵌入句子上的余弦相似性以及对医学概念的F评分。结果表明，与基于规则的系统和通用域预训练的语言模型相比，具有领域自适应预训练的T5可实现显着的性能增长，这表明可以解决问题摘要任务的有希望的方向。

语言模型既展示了定量的改进，又展示了新的定性功能，随着规模的增加。尽管它们具有潜在的变革性影响，但这些新能力的特征却很差。为了为未来的研究提供信息，为破坏性的新模型能力做准备，并改善社会有害的效果，至关重要的是，我们必须了解目前和近乎未来的能力和语言模型的局限性。为了应对这一挑战，我们介绍了超越模仿游戏基准（Big Bench）。 Big Bench目前由204个任务组成，由132家机构的442位作者贡献。任务主题是多样的，从语言学，儿童发展，数学，常识性推理，生物学，物理学，社会偏见，软件开发等等。 Big-Bench专注于被认为超出当前语言模型的功能的任务。我们评估了OpenAI的GPT型号，Google内部密集变压器体系结构和大型基础上的开关稀疏变压器的行为，跨越了数百万到数十亿个参数。此外，一个人类专家评估者团队执行了所有任务，以提供强大的基准。研究结果包括：模型性能和校准都随规模改善，但绝对的术语（以及与评估者的性能相比）；在模型类中的性能非常相似，尽管带有稀疏性。逐渐和预测的任务通常涉及大量知识或记忆成分，而在临界规模上表现出“突破性”行为的任务通常涉及多个步骤或组成部分或脆性指标；社交偏见通常会随着含糊不清的环境而随着规模而增加，但这可以通过提示来改善。

在本文中，我们展示了我们参与生物重建VII轨道3的工作 - 在推文中自动提取药物名称，在那里我们实施了一个多任务学习模型，这些模型是在文本分类和序列标记上进行的联合培训的多任务学习模型。我们最好的系统运行达到了80.4的严格F1，比所有参与者的平均分数排名第一，排名超过10点。我们的分析表明，集合技术，多任务学习和数据增强都是有益于推文中的药物检测。

Optical coherence tomography (OCT) captures cross-sectional data and is used for the screening, monitoring, and treatment planning of retinal diseases. Technological developments to increase the speed of acquisition often results in systems with a narrower spectral bandwidth, and hence a lower axial resolution. Traditionally, image-processing-based techniques have been utilized to reconstruct subsampled OCT data and more recently, deep-learning-based methods have been explored. In this study, we simulate reduced axial scan (A-scan) resolution by Gaussian windowing in the spectral domain and investigate the use of a learning-based approach for image feature reconstruction. In anticipation of the reduced resolution that accompanies wide-field OCT systems, we build upon super-resolution techniques to explore methods to better aid clinicians in their decision-making to improve patient outcomes, by reconstructing lost features using a pixel-to-pixel approach with an altered super-resolution generative adversarial network (SRGAN) architecture.

Regularising the parameter matrices of neural networks is ubiquitous in training deep models. Typical regularisation approaches suggest initialising weights using small random values, and to penalise weights to promote sparsity. However, these widely used techniques may be less effective in certain scenarios. Here, we study the Koopman autoencoder model which includes an encoder, a Koopman operator layer, and a decoder. These models have been designed and dedicated to tackle physics-related problems with interpretable dynamics and an ability to incorporate physics-related constraints. However, the majority of existing work employs standard regularisation practices. In our work, we take a step toward augmenting Koopman autoencoders with initialisation and penalty schemes tailored for physics-related settings. Specifically, we propose the "eigeninit" initialisation scheme that samples initial Koopman operators from specific eigenvalue distributions. In addition, we suggest the "eigenloss" penalty scheme that penalises the eigenvalues of the Koopman operator during training. We demonstrate the utility of these schemes on two synthetic data sets: a driven pendulum and flow past a cylinder; and two real-world problems: ocean surface temperatures and cyclone wind fields. We find on these datasets that eigenloss and eigeninit improves the convergence rate by up to a factor of 5, and that they reduce the cumulative long-term prediction error by up to a factor of 3. Such a finding points to the utility of incorporating similar schemes as an inductive bias in other physics-related deep learning approaches.

Micro-CT images of the renal arteries of intact rat kidneys, which had their vasculature injected with the contrast agent polymer Microfil, were characterized. Measurement of inter-branch segment properties and the hierarchical structure of the vessel trees were computed by an automated algorithmic approach. The perfusion territories of the different kidneys, as well as the local diameters of the segmented vasculature were mapped onto the representative structures and visually explored. Various parameters were compared in order to outline key geometrical properties, properties which were shown to not have a wide range of inter-specimen variation. It is shown that the fractal scaling in non-symmetric branching reveals itself differently, than in symmetric branching (e.g., in the lung the mean bronchial diameters at each generation are closely related). Also, perfused tissue is shown to have very little inter-specimen variation and therefore could be used in future studies related to characterizing various disease states of tissues and organs based on vascular branching geometry.

We present NusaCrowd, a collaborative initiative to collect and unite existing resources for Indonesian languages, including opening access to previously non-public resources. Through this initiative, we have has brought together 137 datasets and 117 standardized data loaders. The quality of the datasets has been assessed manually and automatically, and their effectiveness has been demonstrated in multiple experiments. NusaCrowd's data collection enables the creation of the first zero-shot benchmarks for natural language understanding and generation in Indonesian and its local languages. Furthermore, NusaCrowd brings the creation of the first multilingual automatic speech recognition benchmark in Indonesian and its local languages. Our work is intended to help advance natural language processing research in under-represented languages.