From the article: Abstract: An overview of neural network architectures is presented. Some of these architectures have been created in recent years, whereas others originate from many decades ago. Apart from providing a practical tool for comparing deep learning models, the Neural Network Zoo also uncovers a taxonomy of network architectures, their chronology, and traces back lineages and inspirations for these neural information processing systems.
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To study the ways in which compounds can induce adverse effects, toxicologists have been constructing Adverse Outcome Pathways (AOPs). An AOP can be considered as a pragmatic tool to capture and visualize mechanisms underlying different types of toxicity inflicted by any kind of stressor, and describes the interactions between key entities that lead to the adverse outcome on multiple biological levels of organization. The construction or optimization of an AOP is a labor intensive process, which currently depends on the manual search, collection, reviewing and synthesis of available scientific literature. This process could however be largely facilitated using Natural Language Processing (NLP) to extract information contained in scientific literature in a systematic, objective, and rapid manner that would lead to greater accuracy and reproducibility. This would support researchers to invest their expertise in the substantive assessment of the AOPs by replacing the time spent on evidence gathering by a critical review of the data extracted by NLP. As case examples, we selected two frequent adversities observed in the liver: namely, cholestasis and steatosis denoting accumulation of bile and lipid, respectively. We used deep learning language models to recognize entities of interest in text and establish causal relationships between them. We demonstrate how an NLP pipeline combining Named Entity Recognition and a simple rules-based relationship extraction model helps screen compounds related to liver adversities in the literature, but also extract mechanistic information for how such adversities develop, from the molecular to the organismal level. Finally, we provide some perspectives opened by the recent progress in Large Language Models and how these could be used in the future. We propose this work brings two main contributions: 1) a proof-of-concept that NLP can support the extraction of information from text for modern toxicology and 2) a template open-source model for recognition of toxicological entities and extraction of their relationships. All resources are openly accessible via GitHub (https://github.com/ontox-project/en-tox).
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We present a novel architecture for an AI system that allows a priori knowledge to combine with deep learning. In traditional neural networks, all available data is pooled at the input layer. Our alternative neural network is constructed so that partial representations (invariants) are learned in the intermediate layers, which can then be combined with a priori knowledge or with other predictive analyses of the same data. This leads to smaller training datasets due to more efficient learning. In addition, because this architecture allows inclusion of a priori knowledge and interpretable predictive models, the interpretability of the entire system increases while the data can still be used in a black box neural network. Our system makes use of networks of neurons rather than single neurons to enable the representation of approximations (invariants) of the output.
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There is a growing literature investigating the relationship between oscillatory neural dynamics measured using electroencephalography (EEG) and/or magnetoencephalography (MEG), and sentence-level language comprehension. Recent proposals have suggested a strong link between predictive coding accounts of the hierarchical flow of information in the brain, and oscillatory neural dynamics in the beta and gamma frequency ranges. We propose that findings relating beta and gamma oscillations to sentence-level language comprehension might be unified under such a predictive coding account. Our suggestion is that oscillatory activity in the beta frequency range may reflect both the active maintenance of the current network configuration responsible for representing the sentence-level meaning under construction, and the top-down propagation of predictions to hierarchically lower processing levels based on that representation. In addition, we suggest that oscillatory activity in the low and middle gamma range reflect the matching of top-down predictions with bottom-up linguistic input, while evoked high gamma might reflect the propagation of bottom-up prediction errors to higher levels of the processing hierarchy. We also discuss some of the implications of this predictive coding framework, and we outline ideas for how these might be tested experimentally.
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Adverse Outcome Pathways (AOPs) are conceptual frameworks that tie an initial perturbation (molecular initiat- ing event) to a phenotypic toxicological manifestation (adverse outcome), through a series of steps (key events). They provide therefore a standardized way to map and organize toxicological mechanistic information. As such, AOPs inform on key events underlying toxicity, thus supporting the development of New Approach Methodologies (NAMs), which aim to reduce the use of animal testing for toxicology purposes. However, the establishment of a novel AOP relies on the gathering of multiple streams of evidence and infor- mation, from available literature to knowledge databases. Often, this information is in the form of free text, also called unstructured text, which is not immediately digestible by a computer. This information is thus both tedious and increasingly time-consuming to process manually with the growing volume of data available. The advance- ment of machine learning provides alternative solutions to this challenge. To extract and organize information from relevant sources, it seems valuable to employ deep learning Natural Language Processing techniques. We review here some of the recent progress in the NLP field, and show how these techniques have already demonstrated value in the biomedical and toxicology areas. We also propose an approach to efficiently and reliably extract and combine relevant toxicological information from text. This data can be used to map underlying mechanisms that lead to toxicological effects and start building quantitative models, in particular AOPs, ultimately allowing animal-free human-based hazard and risk assessment.
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Machine learning models have proven to be reliable methods in classification tasks. However, little research has been done on classifying dwelling characteristics based on smart meter & weather data before. Gaining insights into dwelling characteristics can be helpful to create/improve the policies for creating new dwellings at NZEB standard. This paper compares the different machine learning algorithms and the methods used to correctly implement the models. These methods include the data pre-processing, model validation and evaluation. Smart meter data was provided by Groene Mient, which was used to train several machine learning algorithms. The models that were generated by the algorithms were compared on their performance. The results showed that Recurrent Neural Network (RNN) 2performed the best with 96% of accuracy. Cross Validation was used to validate the models, where 80% of the data was used for training purposes and 20% was used for testing purposes. Evaluation metrices were used to produce classification reports, which can indicate which of the models work the best for this specific problem. The models were programmed in Python.
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Het doel van dit onderzoek is te onderzoeken onder welke omstandigheden en onder welke condities relatief moderne modelleringstechnieken zoals support vector machines, neural networks en random forests voordelen zouden kunnen hebben in medisch-wetenschappelijk onderzoek en in de medische praktijk in vergelijking met meer traditionele modelleringstechnieken, zoals lineaire regressie, logistische regressie en Cox regressie.
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This investigation explores relations between 1) a theory of human cognition, called Embodied Cognition, 2) the design of interactive systems and 3) the practice of ‘creative group meetings’ (of which the so-called ‘brainstorm’ is perhaps the best-known example). The investigation is one of Research-through-Design (Overbeeke et al., 2006). This means that, together with students and external stakeholders, I designed two interactive prototypes. Both systems contain a ‘mix’ of both physical and digital forms. Both are designed to be tools in creative meeting sessions, or brainstorms. The tools are meant to form a natural, element in the physical meeting space. The function of these devices is to support the formation of shared insight: that is, the tools should support the process by which participants together, during the activity, get a better grip on the design challenge that they are faced with. Over a series of iterations I reflected on the design process and outcome, and investigated how users interacted with the prototypes.
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In recent years, drones have increasingly supported First Responders (FRs) in monitoring incidents and providing additional information. However, analysing drone footage is time-intensive and cognitively demanding. In this research, we investigate the use of AI models for the detection of humans in drone footage to aid FRs in tasks such as locating victims. Detecting small-scale objects, particularly humans from high altitudes, poses a challenge for AI systems. We present first steps of introducing and evaluating a series of YOLOv8 Convolutional Neural Networks (CNNs) for human detection from drone images. The models are fine-tuned on a created drone image dataset of the Dutch Fire Services and were able to achieve a 53.1% F1-Score, identifying 439 out of 825 humans in the test dataset. These preliminary findings, validated by an incident commander, highlight the promising utility of these models. Ongoing efforts aim to further refine the models and explore additional technologies.
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The event-related potential (ERP) approach has provided a wealth of fine-grained information about the time course and the neural basis of cognitive processing events. However, in the 1980s and 1990s, an increasing number of researchers began to realize that an ERP only represents a certain part of the event-related electroencephalographic (EEG) signal. This chapter focuses on another aspect of event-related EEG activity: oscillatory EEG activity. There exists a meaningful relationship between oscillatory neuronal dynamics, on the one hand, and a wide range of cognitive processes, on the other hand. Given that the analysis of oscillatory dynamics extracts information from the EEG/magnetoencephalographic (EEG/MEG) signal that is largely lost with the traditional time-locked averaging of single trials used in the ERP approach, studying the dynamic oscillatory patterns in the EEG/MEG is at least a useful addition to the traditional ERP approach.
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