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.

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.

Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realize global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissues structures. Inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting anatomies of 133 structures in brain, 14 organs in abdomen, 4 hierarchical components in kidney, and inter-connected kidney tumors). We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in single network, outperforms prior state-of-the-art method SLANT27 ensembled with 27 network tiles, our model performance increases the mean DSC score of the publicly available Colin and CANDI dataset from 0.7264 to 0.7444 and from 0.6968 to 0.7025, respectively.

培训广泛和深度神经网络（DNN）需要大量的存储资源，例如内存，因为在转发传播期间必须在存储器中保存中间激活数据，然后恢复以便向后传播。然而，由于硬件设计约束，诸如GPU之类的最先进的加速器（例如GPU）仅配备了非常有限的存储容量，这显着限制了在训练大规模DNN时的最大批量大小和性能加速。传统的记忆保存技术均受性能开销或受限互连带宽或特定互连技术的约束。在本文中，我们提出了一种新颖的记忆高效的CNN训练框架（称为Comet），利用错误界限的损耗压缩来显着降低训练的内存要求，以允许培训更大的模型或加速培训。不同于采用基于图像的有损压缩机（例如JPEG）的最先进的解决方案来压缩激活数据，我们的框架故意采用严格的错误控制机制来采用错误界限的损耗压缩。具体而言，我们对从改变的激活数据传播到梯度的压缩误差传播的理论分析，并经验探讨改变梯度对训练过程的影响。基于这些分析，我们优化了误报的损耗压缩，并提出了一种用于激活数据压缩的自适应误差控制方案。我们评估我们对最先进的解决方案的设计，其中包含五个广泛采用的CNN和Imagenet DataSet。实验表明，我们所提出的框架可以在基线训练中显着降低13.5倍，并分别在另一个最先进的基于压缩框架上的1.8倍，几乎没有准确性损失。

我们介绍了Amazon Berkeley对象（ABO），这是一个新的大型数据集，旨在帮助弥合真实和虚拟3D世界之间的差距。ABO包含产品目录图像，元数据和艺术家创建的3D模型，具有复杂的几何形状和与真实的家用物体相对应的物理基础材料。我们得出了具有挑战性的基准，这些基准利用ABO的独特属性，并测量最先进的对象在三个开放问题上的最新限制，以了解实际3D对象：单视3D 3D重建，材料估计和跨域多视图对象检索。

我们介绍了可以由具有Maxout单位的人造馈电神经网络表示的功能线性区域的数量。排名kaxout单元是一个函数，计算$ k $线性函数的最大值。对于具有单层Maxout单元的网络，线性区域对应于Minkowski多型的上顶点。我们根据热带超曲面的交点或部分Minkowski总和的上面数，以及任何输入维度的区域数，任何单位数量，任何等级，任何等级，任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，以及任何等级，在有和没有偏见的情况下。基于这些结果，我们还为具有多层的网络获得了渐近的上限。

With the rise of AI in recent years and the increase in complexity of the models, the growing demand in computational resources is starting to pose a significant challenge. The need for higher compute power is being met with increasingly more potent accelerators and the use of large compute clusters. However, the gain in prediction accuracy from large models trained on distributed and accelerated systems comes at the price of a substantial increase in energy demand, and researchers have started questioning the environmental friendliness of such AI methods at scale. Consequently, energy efficiency plays an important role for AI model developers and infrastructure operators alike. The energy consumption of AI workloads depends on the model implementation and the utilized hardware. Therefore, accurate measurements of the power draw of AI workflows on different types of compute nodes is key to algorithmic improvements and the design of future compute clusters and hardware. To this end, we present measurements of the energy consumption of two typical applications of deep learning models on different types of compute nodes. Our results indicate that 1. deriving energy consumption directly from runtime is not accurate, but the consumption of the compute node needs to be considered regarding its composition; 2. neglecting accelerator hardware on mixed nodes results in overproportional inefficiency regarding energy consumption; 3. energy consumption of model training and inference should be considered separately - while training on GPUs outperforms all other node types regarding both runtime and energy consumption, inference on CPU nodes can be comparably efficient. One advantage of our approach is that the information on energy consumption is available to all users of the supercomputer, enabling an easy transfer to other workloads alongside a raise in user-awareness of energy consumption.

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

In this paper we prove Gamma-convergence of a nonlocal perimeter of Minkowski type to a local anisotropic perimeter. The nonlocal model describes the regularizing effect of adversarial training in binary classifications. The energy essentially depends on the interaction between two distributions modelling likelihoods for the associated classes. We overcome typical strict regularity assumptions for the distributions by only assuming that they have bounded $BV$ densities. In the natural topology coming from compactness, we prove Gamma-convergence to a weighted perimeter with weight determined by an anisotropic function of the two densities. Despite being local, this sharp interface limit reflects classification stability with respect to adversarial perturbations. We further apply our results to deduce Gamma-convergence of the associated total variations, to study the asymptotics of adversarial training, and to prove Gamma-convergence of graph discretizations for the nonlocal perimeter.

Single-cell reference atlases are large-scale, cell-level maps that capture cellular heterogeneity within an organ using single cell genomics. Given their size and cellular diversity, these atlases serve as high-quality training data for the transfer of cell type labels to new datasets. Such label transfer, however, must be robust to domain shifts in gene expression due to measurement technique, lab specifics and more general batch effects. This requires methods that provide uncertainty estimates on the cell type predictions to ensure correct interpretation. Here, for the first time, we introduce uncertainty quantification methods for cell type classification on single-cell reference atlases. We benchmark four model classes and show that currently used models lack calibration, robustness, and actionable uncertainty scores. Furthermore, we demonstrate how models that quantify uncertainty are better suited to detect unseen cell types in the setting of atlas-level cell type transfer.