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.

经典的多个实例学习（MIL）方法通常基于实例之间的相同和独立的分布式假设，因此忽略了个人实体以外的潜在丰富的上下文信息。另一方面，已经提出了具有全球自我发场模块的变压器来对所有实例之间的相互依赖性进行建模。但是，在本文中，我们质疑：是否需要使用自我注意力进行全球关系建模，或者我们是否可以适当地将自我注意计算限制为大规模整个幻灯片图像（WSIS）中的本地制度？我们为MIL（LA-MIL）提出了一个通用的基于局部注意力图的变压器，通过在自适应局部任意大小的自适应局部方案中明确化情境化实例，从而引入了归纳偏见。此外，有效适应的损失函数使我们可以学习表达性WSI嵌入的方法，以进行多种生物标志物的联合分析。我们证明，LA-MIL实现了最新的胃肠癌预测，从而超过了重要生物标志物（例如微卫星不稳定性的结直肠癌）的现有模型。我们的发现表明，本地自我注意力足够模型与全球模块相同的依赖性。我们的LA-MIL实施可从https://github.com/agentdr1/la_mil获得。

用于核细胞分割的注释显微镜图像是费力且耗时的。为了利用少数现有的注释，也跨越多种方式，我们提出了一种基于生成的对抗网络（GAN）的新型显微镜式增强技术。与其他风格转移方法不同，它不仅可以处理不同的细胞测定类型和照明条件，还可以与不同的成像方式，例如亮场和荧光显微镜。使用Disentangled表示的内容和风格，我们可以在增强期间改变其风格的同时保留原始图像的结构。我们在2018年数据科学碗数据集上评估我们的数据增强，包括各种细胞测定，照明条件和成像方式。凭借我们的增强，竞争中两个排名排名蒙版R-CNN的核细胞分割算法的分割精度显着增加。因此，我们的增强技术使下游任务更加强大地对测试数据异质性，并有助于抵消类别不平衡而不重新采样少数类。

Machine learning models are typically evaluated by computing similarity with reference annotations and trained by maximizing similarity with such. Especially in the bio-medical domain, annotations are subjective and suffer from low inter- and intra-rater reliability. Since annotations only reflect the annotation entity's interpretation of the real world, this can lead to sub-optimal predictions even though the model achieves high similarity scores. Here, the theoretical concept of Peak Ground Truth (PGT) is introduced. PGT marks the point beyond which an increase in similarity with the reference annotation stops translating to better Real World Model Performance (RWMP). Additionally, a quantitative technique to approximate PGT by computing inter- and intra-rater reliability is proposed. Finally, three categories of PGT-aware strategies to evaluate and improve model performance are reviewed.

Segmentation of regions of interest (ROIs) for identifying abnormalities is a leading problem in medical imaging. Using Machine Learning (ML) for this problem generally requires manually annotated ground-truth segmentations, demanding extensive time and resources from radiologists. This work presents a novel weakly supervised approach that utilizes binary image-level labels, which are much simpler to acquire, to effectively segment anomalies in medical Magnetic Resonance (MR) images without ground truth annotations. We train a binary classifier using these labels and use it to derive seeds indicating regions likely and unlikely to contain tumors. These seeds are used to train a generative adversarial network (GAN) that converts cancerous images to healthy variants, which are then used in conjunction with the seeds to train a ML model that generates effective segmentations. This method produces segmentations that achieve Dice coefficients of 0.7903, 0.7868, and 0.7712 on the MICCAI Brain Tumor Segmentation (BraTS) 2020 dataset for the training, validation, and test cohorts respectively. We also propose a weakly supervised means of filtering the segmentations, removing a small subset of poorer segmentations to acquire a large subset of high quality segmentations. The proposed filtering further improves the Dice coefficients to up to 0.8374, 0.8232, and 0.8136 for training, validation, and test, respectively.

通过一系列联邦举措和命令，美国政府一直在努力确保美国在AI中的领导。这些广泛的战略文件影响了美国空军美国部（DAF）等组织。DAF-MIT AI加速器是DAF和MIT之间的一项计划，以弥合AI研究人员与DAF任务要求之间的差距。DAF-MIT AI加速器支持的几个项目正在开发公共挑战问题，这些问题解决了许多联邦AI研究的重点。这些挑战是通过公开可用的大型AI-Ready数据集，激励开源解决方案，并为可以激发进一步研究的双重使用技术创建需求信号，来针对优先事项。在本文中，我们描述了正在开发的这些公共挑战以及它们的应用如何促进科学进步。

深度学习（DL）模型为各种医学成像基准挑战提供了最先进的性能，包括脑肿瘤细分（BRATS）挑战。然而，局灶性病理多隔室分割（例如，肿瘤和病变子区）的任务特别具有挑战性，并且潜在的错误阻碍DL模型转化为临床工作流程。量化不确定形式的DL模型预测的可靠性，可以实现最不确定的地区的临床审查，从而建立信任并铺平临床翻译。最近，已经引入了许多不确定性估计方法，用于DL医学图像分割任务。开发指标评估和比较不确定性措施的表现将有助于最终用户制定更明智的决策。在本研究中，我们探索并评估在Brats 2019-2020任务期间开发的公制，以对不确定量化量化（Qu-Brats），并旨在评估和排列脑肿瘤多隔室分割的不确定性估计。该公制（1）奖励不确定性估计，对正确断言产生高置信度，以及在不正确的断言处分配低置信水平的估计数，（2）惩罚导致更高百分比的无关正确断言百分比的不确定性措施。我们进一步基准测试由14个独立参与的Qu-Brats 2020的分割不确定性，所有这些都参与了主要的Brats细分任务。总体而言，我们的研究结果证实了不确定性估计提供了分割算法的重要性和互补价值，因此突出了医学图像分析中不确定性量化的需求。我们的评估代码在HTTPS://github.com/ragmeh11/qu-brats公开提供。

语音神经调节物有可能为患有扰动或休闲症的人提供沟通。最近的进展已经证明了从放置在皮质表面上的电加电网的高质量文本解码和语音合成。在这里，我们研究了较少的侵入性测量模态，即立体定向脑电图（SEEG），其提供来自多个脑区的稀疏抽样，包括皮质区域。为了评估Seeg是否也可用于综合神经录音的高质量音频，我们采用了一种基于现代深度学习方法的经常性编码器 - 解码器框架。我们证明，尽管有限的训练数据，但是可以从这些微创录音来重建高质量的言论。最后，我们利用变分特征丢失来成功识别最具信息丰富的电极触点。

The BERT family of neural language models have become highly popular due to their ability to provide sequences of text with rich context-sensitive token encodings which are able to generalise well to many NLP tasks. We introduce gaBERT, a monolingual BERT model for the Irish language. We compare our gaBERT model to multilingual BERT and the monolingual Irish WikiBERT, and we show that gaBERT provides better representations for a downstream parsing task. We also show how different filtering criteria, vocabulary size and the choice of subword tokenisation model affect downstream performance. We compare the results of fine-tuning a gaBERT model with an mBERT model for the task of identifying verbal multiword expressions, and show that the fine-tuned gaBERT model also performs better at this task. We release gaBERT and related code to the community.

成语与大多数短语不同。首先，成语中的单词具有非规范含义。其次，习语中单词的非传统含义取决于习惯中其他单词的存在。语言理论在这些特性是否相互依赖，以及是否需要特殊的理论机制来容纳成语方面有所不同。我们定义了与上述属性相对应的两个度量，并使用BERT（Devlin等，2019）和XLNet实施它们（Yang等，2019）。我们表明，成语落在两个维度的预期交集处，但是尺寸本身并不相关。我们的结果表明，处理习语的特殊机械可能不保证。