Generally, microscopy image analysis in biology relies on the segmentation of individual nuclei, using a dedicated stained image, to identify individual cells. However stained nuclei have drawbacks like the need for sample preparation, and specific equipment on the microscope but most importantly, and as it is in most cases, the nuclear stain is not relevant to the biological questions of interest but is solely used for the segmentation task. In this study, we used non-stained brightfield images for nuclei segmentation with the advantage that they can be acquired on any microscope from both live or fixed samples and do not necessitate specific sample preparation. Nuclei semantic segmentation from brightfield images was obtained, on four distinct cell lines with U-Net-based architectures. We tested systematically deep pre-trained encoders to identify the best performing in combination with the different neural network architectures used. Additionally, two distinct and effective strategies were employed for instance segmentation, followed by thorough instance evaluation. We obtained effective semantic and instance segmentation of nuclei in brightfield images from standard test sets as well as from very diverse biological contexts triggered upon treatment with various small molecule inhibitor. The code used in this study was made public to allow further use by the community.

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.

自动生物医学图像分析的领域至关重要地取决于算法验证的可靠和有意义的性能指标。但是，当前的度量使用通常是不明智的，并且不能反映基本的域名。在这里，我们提出了一个全面的框架，该框架指导研究人员以问题意识的方式选择绩效指标。具体而言，我们专注于生物医学图像分析问题，这些问题可以解释为图像，对象或像素级别的分类任务。该框架首先编译域兴趣 - 目标结构 - ，数据集和算法与输出问题相关的属性的属性与问题指纹相关，同时还将其映射到适当的问题类别，即图像级分类，语义分段，实例，实例细分或对象检测。然后，它指导用户选择和应用一组适当的验证指标的过程，同时使他们意识到与个人选择相关的潜在陷阱。在本文中，我们描述了指标重新加载推荐框架的当前状态，目的是从图像分析社区获得建设性的反馈。当前版本是在由60多个图像分析专家的国际联盟中开发的，将在社区驱动的优化之后公开作为用户友好的工具包提供。

机器学习方法利用多参数生物标志物，特别是基于神经影像动物，具有改善痴呆早期诊断的巨大潜力，并预测哪些个体存在发展痴呆的风险。对于机器学习领域的基准算法和痴呆症中的神经影像症，并评估他们在临床实践中使用的潜力和临床试验，七年的大挑战已经在过去十年中组织：Miriad，Alzheimer的疾病大数据梦，Caddementia，机器学习挑战，MCI神经影像动物，蝌蚪和预测分析竞争。基于两个挑战评估框架，我们分析了这些大挑战如何互相补充研究问题，数据集，验证方法，结果和影响。七个大挑战解决了与（临床前）痴呆症（临床）痴呆症的筛查，诊断，预测和监测有关的问题。临床问题，任务和性能指标几乎没有重叠。然而，这具有提供对广泛问题的洞察力的优势，它也会限制对挑战的结果的验证。通常，获胜算法执行严格的数据预处理并组合了广泛的输入特征。尽管最先进的表演，但临床上没有挑战评估的大部分方法。为了增加影响，未来的挑战可以更加关注统计分析，对其与高于阿尔茨海默病的临床问题，以及使用超越阿尔茨海默病神经影像疾病的临床问题，以及超越阿尔茨海默病的临床问题。鉴于过去十年中汲取的潜力和经验教训，我们在未来十年及其超越的机器学习和神经影像中的大挑战前景兴奋。

尽管自动图像分析的重要性不断增加，但最近的元研究揭示了有关算法验证的主要缺陷。性能指标对于使用的自动算法的有意义，客观和透明的性能评估和验证尤其是关键，但是在使用特定的指标进行给定的图像分析任务时，对实际陷阱的关注相对较少。这些通常与（1）无视固有的度量属性，例如在存在类不平衡或小目标结构的情况下的行为，（2）无视固有的数据集属性，例如测试的非独立性案例和（3）无视指标应反映的实际生物医学领域的兴趣。该动态文档的目的是说明图像分析领域通常应用的性能指标的重要局限性。在这种情况下，它重点介绍了可以用作图像级分类，语义分割，实例分割或对象检测任务的生物医学图像分析问题。当前版本是基于由全球60多家机构的国际图像分析专家进行的关于指标的Delphi流程。

The recent increase in public and academic interest in preserving biodiversity has led to the growth of the field of conservation technology. This field involves designing and constructing tools that utilize technology to aid in the conservation of wildlife. In this article, we will use case studies to demonstrate the importance of designing conservation tools with human-wildlife interaction in mind and provide a framework for creating successful tools. These case studies include a range of complexities, from simple cat collars to machine learning and game theory methodologies. Our goal is to introduce and inform current and future researchers in the field of conservation technology and provide references for educating the next generation of conservation technologists. Conservation technology not only has the potential to benefit biodiversity but also has broader impacts on fields such as sustainability and environmental protection. By using innovative technologies to address conservation challenges, we can find more effective and efficient solutions to protect and preserve our planet's resources.

We present the interpretable meta neural ordinary differential equation (iMODE) method to rapidly learn generalizable (i.e., not parameter-specific) dynamics from trajectories of multiple dynamical systems that vary in their physical parameters. The iMODE method learns meta-knowledge, the functional variations of the force field of dynamical system instances without knowing the physical parameters, by adopting a bi-level optimization framework: an outer level capturing the common force field form among studied dynamical system instances and an inner level adapting to individual system instances. A priori physical knowledge can be conveniently embedded in the neural network architecture as inductive bias, such as conservative force field and Euclidean symmetry. With the learned meta-knowledge, iMODE can model an unseen system within seconds, and inversely reveal knowledge on the physical parameters of a system, or as a Neural Gauge to "measure" the physical parameters of an unseen system with observed trajectories. We test the validity of the iMODE method on bistable, double pendulum, Van der Pol, Slinky, and reaction-diffusion systems.

While the brain connectivity network can inform the understanding and diagnosis of developmental dyslexia, its cause-effect relationships have not yet enough been examined. Employing electroencephalography signals and band-limited white noise stimulus at 4.8 Hz (prosodic-syllabic frequency), we measure the phase Granger causalities among channels to identify differences between dyslexic learners and controls, thereby proposing a method to calculate directional connectivity. As causal relationships run in both directions, we explore three scenarios, namely channels' activity as sources, as sinks, and in total. Our proposed method can be used for both classification and exploratory analysis. In all scenarios, we find confirmation of the established right-lateralized Theta sampling network anomaly, in line with the temporal sampling framework's assumption of oscillatory differences in the Theta and Gamma bands. Further, we show that this anomaly primarily occurs in the causal relationships of channels acting as sinks, where it is significantly more pronounced than when only total activity is observed. In the sink scenario, our classifier obtains 0.84 and 0.88 accuracy and 0.87 and 0.93 AUC for the Theta and Gamma bands, respectively.

Variational autoencoders model high-dimensional data by positing low-dimensional latent variables that are mapped through a flexible distribution parametrized by a neural network. Unfortunately, variational autoencoders often suffer from posterior collapse: the posterior of the latent variables is equal to its prior, rendering the variational autoencoder useless as a means to produce meaningful representations. Existing approaches to posterior collapse often attribute it to the use of neural networks or optimization issues due to variational approximation. In this paper, we consider posterior collapse as a problem of latent variable non-identifiability. We prove that the posterior collapses if and only if the latent variables are non-identifiable in the generative model. This fact implies that posterior collapse is not a phenomenon specific to the use of flexible distributions or approximate inference. Rather, it can occur in classical probabilistic models even with exact inference, which we also demonstrate. Based on these results, we propose a class of latent-identifiable variational autoencoders, deep generative models which enforce identifiability without sacrificing flexibility. This model class resolves the problem of latent variable non-identifiability by leveraging bijective Brenier maps and parameterizing them with input convex neural networks, without special variational inference objectives or optimization tricks. Across synthetic and real datasets, latent-identifiable variational autoencoders outperform existing methods in mitigating posterior collapse and providing meaningful representations of the data.

We introduce Argoverse 2 (AV2) - a collection of three datasets for perception and forecasting research in the self-driving domain. The annotated Sensor Dataset contains 1,000 sequences of multimodal data, encompassing high-resolution imagery from seven ring cameras, and two stereo cameras in addition to lidar point clouds, and 6-DOF map-aligned pose. Sequences contain 3D cuboid annotations for 26 object categories, all of which are sufficiently-sampled to support training and evaluation of 3D perception models. The Lidar Dataset contains 20,000 sequences of unlabeled lidar point clouds and map-aligned pose. This dataset is the largest ever collection of lidar sensor data and supports self-supervised learning and the emerging task of point cloud forecasting. Finally, the Motion Forecasting Dataset contains 250,000 scenarios mined for interesting and challenging interactions between the autonomous vehicle and other actors in each local scene. Models are tasked with the prediction of future motion for "scored actors" in each scenario and are provided with track histories that capture object location, heading, velocity, and category. In all three datasets, each scenario contains its own HD Map with 3D lane and crosswalk geometry - sourced from data captured in six distinct cities. We believe these datasets will support new and existing machine learning research problems in ways that existing datasets do not. All datasets are released under the CC BY-NC-SA 4.0 license.