机器学习（ML）为生物处理工程的发展做出了重大贡献，但其应用仍然有限，阻碍了生物过程自动化的巨大潜力。用于模型构建自动化的ML可以看作是引入另一种抽象水平的一种方式，将专家的人类集中在生物过程开发的最认知任务中。首先，概率编程用于预测模型的自动构建。其次，机器学习会通过计划实验来测试假设并进行调查以收集信息性数据来自动评估替代决策，以收集基于模型预测不确定性的模型选择的信息数据。这篇评论提供了有关生物处理开发中基于ML的自动化的全面概述。一方面，生物技术和生物工程社区应意识到现有ML解决方案在生物技术和生物制药中的应用的限制。另一方面，必须确定缺失的链接，以使ML和人工智能（AI）解决方案轻松实施在有价值的生物社区解决方案中。我们总结了几个重要的生物处理系统的ML实施，并提出了两个至关重要的挑战，这些挑战仍然是生物技术自动化的瓶颈，并减少了生物技术开发的不确定性。没有一个合适的程序；但是，这项综述应有助于确定结合生物技术和ML领域的潜在自动化。

The release of ChatGPT, a language model capable of generating text that appears human-like and authentic, has gained significant attention beyond the research community. We expect that the convincing performance of ChatGPT incentivizes users to apply it to a variety of downstream tasks, including prompting the model to simplify their own medical reports. To investigate this phenomenon, we conducted an exploratory case study. In a questionnaire, we asked 15 radiologists to assess the quality of radiology reports simplified by ChatGPT. Most radiologists agreed that the simplified reports were factually correct, complete, and not potentially harmful to the patient. Nevertheless, instances of incorrect statements, missed key medical findings, and potentially harmful passages were reported. While further studies are needed, the initial insights of this study indicate a great potential in using large language models like ChatGPT to improve patient-centered care in radiology and other medical domains.

Local patterns play an important role in statistical physics as well as in image processing. Two-dimensional ordinal patterns were studied by Ribeiro et al. who determined permutation entropy and complexity in order to classify paintings and images of liquid crystals. Here we find that the 2 by 2 patterns of neighboring pixels come in three types. The statistics of these types, expressed by two parameters, contains the relevant information to describe and distinguish textures. The parameters are most stable and informative for isotropic structures.

Many dialogue systems (DSs) lack characteristics humans have, such as emotion perception, factuality, and informativeness. Enhancing DSs with knowledge alleviates this problem, but, as many ways of doing so exist, keeping track of all proposed methods is difficult. Here, we present the first survey of knowledge-enhanced DSs. We define three categories of systems - internal, external, and hybrid - based on the knowledge they use. We survey the motivation for enhancing DSs with knowledge, used datasets, and methods for knowledge search, knowledge encoding, and knowledge incorporation. Finally, we propose how to improve existing systems based on theories from linguistics and cognitive science.

Attention-based multiple instance learning (AMIL) algorithms have proven to be successful in utilizing gigapixel whole-slide images (WSIs) for a variety of different computational pathology tasks such as outcome prediction and cancer subtyping problems. We extended an AMIL approach to the task of survival prediction by utilizing the classical Cox partial likelihood as a loss function, converting the AMIL model into a nonlinear proportional hazards model. We applied the model to tissue microarray (TMA) slides of 330 lung cancer patients. The results show that AMIL approaches can handle very small amounts of tissue from a TMA and reach similar C-index performance compared to established survival prediction methods trained with highly discriminative clinical factors such as age, cancer grade, and cancer stage

Nucleolar organizer regions (NORs) are parts of the DNA that are involved in RNA transcription. Due to the silver affinity of associated proteins, argyrophilic NORs (AgNORs) can be visualized using silver-based staining. The average number of AgNORs per nucleus has been shown to be a prognostic factor for predicting the outcome of many tumors. Since manual detection of AgNORs is laborious, automation is of high interest. We present a deep learning-based pipeline for automatically determining the AgNOR-score from histopathological sections. An additional annotation experiment was conducted with six pathologists to provide an independent performance evaluation of our approach. Across all raters and images, we found a mean squared error of 0.054 between the AgNOR- scores of the experts and those of the model, indicating that our approach offers performance comparable to humans.

Mitotic activity is key for the assessment of malignancy in many tumors. Moreover, it has been demonstrated that the proportion of abnormal mitosis to normal mitosis is of prognostic significance. Atypical mitotic figures (MF) can be identified morphologically as having segregation abnormalities of the chromatids. In this work, we perform, for the first time, automatic subtyping of mitotic figures into normal and atypical categories according to characteristic morphological appearances of the different phases of mitosis. Using the publicly available MIDOG21 and TUPAC16 breast cancer mitosis datasets, two experts blindly subtyped mitotic figures into five morphological categories. Further, we set up a state-of-the-art object detection pipeline extending the anchor-free FCOS approach with a gated hierarchical subclassification branch. Our labeling experiment indicated that subtyping of mitotic figures is a challenging task and prone to inter-rater disagreement, which we found in 24.89% of MF. Using the more diverse MIDOG21 dataset for training and TUPAC16 for testing, we reached a mean overall average precision score of 0.552, a ROC AUC score of 0.833 for atypical/normal MF and a mean class-averaged ROC-AUC score of 0.977 for discriminating the different phases of cells undergoing mitosis.

Modern machine learning models are often constructed taking into account multiple objectives, e.g., to minimize inference time while also maximizing accuracy. Multi-objective hyperparameter optimization (MHPO) algorithms return such candidate models and the approximation of the Pareto front is used to assess their performance. However, when estimating generalization performance of an approximation of a Pareto front found on a validation set by computing the performance of the individual models on the test set, models might no longer be Pareto-optimal. This makes it unclear how to measure performance. To resolve this, we provide a novel evaluation protocol that allows measuring the generalization performance of MHPO methods and to study its capabilities for comparing two optimization experiments.

The field of natural language processing (NLP) has grown over the last few years: conferences have become larger, we have published an incredible amount of papers, and state-of-the-art research has been implemented in a large variety of customer-facing products. However, this paper argues that we have been less successful than we should have been and reflects on where and how the field fails to tap its full potential. Specifically, we demonstrate that, in recent years, subpar time allocation has been a major obstacle for NLP research. We outline multiple concrete problems together with their negative consequences and, importantly, suggest remedies to improve the status quo. We hope that this paper will be a starting point for discussions around which common practices are -- or are not -- beneficial for NLP research.

In many unmanned aerial vehicle (UAV) applications for surveillance and data collection, it is not possible to reach all requested locations due to the given maximum flight time. Hence, the requested locations must be prioritized and the problem of selecting the most important locations is modeled as an Orienteering Problem (OP). To fully exploit the kinematic properties of the UAV in such scenarios, we combine the OP with the generation of time-optimal trajectories with bounds on velocity and acceleration. We define the resulting problem as the Kinematic Orienteering Problem (KOP) and propose an exact mixed-integer formulation together with a Large Neighborhood Search (LNS) as a heuristic solution method. We demonstrate the effectiveness of our approach based on Orienteering instances from the literature and benchmark against optimal solutions of the Dubins Orienteering Problem (DOP) as the state-of-the-art. Additionally, we show by simulation \color{black} that the resulting solutions can be tracked precisely by a modern MPC-based flight controller. Since we demonstrate that the state-of-the-art in generating time-optimal trajectories in multiple dimensions is not generally correct, we further present an improved analytical method for time-optimal trajectory generation.