5,611 research outputs found

    The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

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    Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch\u27s APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch\u27s data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch\u27s analytic tools by developing a customized plugin for OpenAI\u27s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app

    An embodied approach to informational interventions: using conceptual metaphors to promote sustainable healthy diets

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    Poor diet quality and environmental degradation are two major challenges of our times. Unhealthy and unsustainable dietary practices, such as the overconsumption of meat and consumer food waste behaviour, contribute greatly to both issues. Across seventeen online and field experiments, in two different cultures (US and China), this thesis investigates if the embodied cognition approach, and more specifically, research on conceptual metaphors, can be used to develop interventions to promote sustainable healthy diets. Interventions relying on conceptual metaphors have been shown to stimulate attitudinal and behavioural changes in other fields (e.g., marketing and political communications), but are rarely adopted to encourage sustainable healthy diets. To fill in this gap in the literature, I conducted five sets of experimental studies examining the effects of different metaphors on specific sustainable healthy dietary practices, each of which forms an independent empirical paper (Chapters 2-6 of the thesis). After introducing the current perspectives on embodied cognition and conceptual metaphors in the context of this research (Chapter 1), Chapter 2 looks into the conceptual metaphor “Healthy is Up”, demonstrating that US people implicitly associate healthiness with verticality, and offering recommendations for healthy eating guidelines. Chapter 3 extends this research to Chinese samples and partially replicates the results. Chapter 4 shows that the anthropomorphic metaphor “Animals are Friends” discourages meat consumption by inducing anticipatory guilt among US omnivores, whereas Chapter 5 reveals that Chinese omnivores are more responsive to another anthropomorphic metaphor, namely, “Animals are Family”. Bringing lab insights 6 to the real world, Chapter 6 demonstrates with a longitudinal field experiment that anthropomorphic metaphors together with environmental feedback result in a higher reduction in food waste as compared to other feedback interventions. The strengths, limitations and implications of those empirical papers are discussed in the conclusive part of the thesis

    Planetary Hinterlands:Extraction, Abandonment and Care

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    This open access book considers the concept of the hinterland as a crucial tool for understanding the global and planetary present as a time defined by the lasting legacies of colonialism, increasing labor precarity under late capitalist regimes, and looming climate disasters. Traditionally seen to serve a (colonial) port or market town, the hinterland here becomes a lens to attend to the times and spaces shaped and experienced across the received categories of the urban, rural, wilderness or nature. In straddling these categories, the concept of the hinterland foregrounds the human and more-than-human lively processes and forms of care that go on even in sites defined by capitalist extraction and political abandonment. Bringing together scholars from the humanities and social sciences, the book rethinks hinterland materialities, affectivities, and ecologies across places and cultural imaginations, Global North and South, urban and rural, and land and water

    Location Reference Recognition from Texts: A Survey and Comparison

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    A vast amount of location information exists in unstructured texts, such as social media posts, news stories, scientific articles, web pages, travel blogs, and historical archives. Geoparsing refers to recognizing location references from texts and identifying their geospatial representations. While geoparsing can benefit many domains, a summary of its specific applications is still missing. Further, there is a lack of a comprehensive review and comparison of existing approaches for location reference recognition, which is the first and core step of geoparsing. To fill these research gaps, this review first summarizes seven typical application domains of geoparsing: geographic information retrieval, disaster management, disease surveillance, traffic management, spatial humanities, tourism management, and crime management. We then review existing approaches for location reference recognition by categorizing these approaches into four groups based on their underlying functional principle: rule-based, gazetteer matching–based, statistical learning-–based, and hybrid approaches. Next, we thoroughly evaluate the correctness and computational efficiency of the 27 most widely used approaches for location reference recognition based on 26 public datasets with different types of texts (e.g., social media posts and news stories) containing 39,736 location references worldwide. Results from this thorough evaluation can help inform future methodological developments and can help guide the selection of proper approaches based on application needs

    Multidisciplinary perspectives on Artificial Intelligence and the law

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    This open access book presents an interdisciplinary, multi-authored, edited collection of chapters on Artificial Intelligence (‘AI’) and the Law. AI technology has come to play a central role in the modern data economy. Through a combination of increased computing power, the growing availability of data and the advancement of algorithms, AI has now become an umbrella term for some of the most transformational technological breakthroughs of this age. The importance of AI stems from both the opportunities that it offers and the challenges that it entails. While AI applications hold the promise of economic growth and efficiency gains, they also create significant risks and uncertainty. The potential and perils of AI have thus come to dominate modern discussions of technology and ethics – and although AI was initially allowed to largely develop without guidelines or rules, few would deny that the law is set to play a fundamental role in shaping the future of AI. As the debate over AI is far from over, the need for rigorous analysis has never been greater. This book thus brings together contributors from different fields and backgrounds to explore how the law might provide answers to some of the most pressing questions raised by AI. An outcome of the Católica Research Centre for the Future of Law and its interdisciplinary working group on Law and Artificial Intelligence, it includes contributions by leading scholars in the fields of technology, ethics and the law.info:eu-repo/semantics/publishedVersio

    Sound Event Detection by Exploring Audio Sequence Modelling

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    Everyday sounds in real-world environments are a powerful source of information by which humans can interact with their environments. Humans can infer what is happening around them by listening to everyday sounds. At the same time, it is a challenging task for a computer algorithm in a smart device to automatically recognise, understand, and interpret everyday sounds. Sound event detection (SED) is the process of transcribing an audio recording into sound event tags with onset and offset time values. This involves classification and segmentation of sound events in the given audio recording. SED has numerous applications in everyday life which include security and surveillance, automation, healthcare monitoring, multimedia information retrieval, and assisted living technologies. SED is to everyday sounds what automatic speech recognition (ASR) is to speech and automatic music transcription (AMT) is to music. The fundamental questions in designing a sound recognition system are, which portion of a sound event should the system analyse, and what proportion of a sound event should the system process in order to claim a confident detection of that particular sound event. While the classification of sound events has improved a lot in recent years, it is considered that the temporal-segmentation of sound events has not improved in the same extent. The aim of this thesis is to propose and develop methods to improve the segmentation and classification of everyday sound events in SED models. In particular, this thesis explores the segmentation of sound events by investigating audio sequence encoding-based and audio sequence modelling-based methods, in an effort to improve the overall sound event detection performance. In the first phase of this thesis, efforts are put towards improving sound event detection by explicitly conditioning the audio sequence representations of an SED model using sound activity detection (SAD) and onset detection. To achieve this, we propose multi-task learning-based SED models in which SAD and onset detection are used as auxiliary tasks for the SED task. The next part of this thesis explores self-attention-based audio sequence modelling, which aggregates audio representations based on temporal relations within and between sound events, scored on the basis of the similarity of sound event portions in audio event sequences. We propose SED models that include memory-controlled, adaptive, dynamic, and source separation-induced self-attention variants, with the aim to improve overall sound recognition

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Universal Self-adaptive Prompting

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    A hallmark of modern large language models (LLMs) is their impressive general zero-shot and few-shot abilities, often elicited through prompt-based and/or in-context learning. However, while highly coveted and being the most general, zero-shot performances in LLMs are still typically weaker due to the lack of guidance and the difficulty of applying existing automatic prompt design methods in general tasks when ground-truth labels are unavailable. In this study, we address this by presenting Universal Self-adaptive Prompting (USP), an automatic prompt design approach specifically tailored for zero-shot learning (while compatible with few-shot). Requiring only a small amount of unlabeled data & an inference-only LLM, USP is highly versatile: to achieve universal prompting, USP categorizes a possible NLP task into one of the three possible task types, and then uses a corresponding selector to select the most suitable queries & zero-shot model-generated responses as pseudo-demonstrations, thereby generalizing ICL to the zero-shot setup in a fully automated way. We evaluate zero-shot USP with two PaLM models, and demonstrate performances that are considerably stronger than standard zero-shot baselines and are comparable to or even superior than few-shot baselines across more than 20 natural language understanding (NLU) and natural language generation (NLG) tasks.Comment: 10 pages, 3 figures, 4 tables (19 pages, 5 figures and 9 tables including references and appendices

    VNHSGE: VietNamese High School Graduation Examination Dataset for Large Language Models

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    The VNHSGE (VietNamese High School Graduation Examination) dataset, developed exclusively for evaluating large language models (LLMs), is introduced in this article. The dataset, which covers nine subjects, was generated from the Vietnamese National High School Graduation Examination and comparable tests. 300 literary essays have been included, and there are over 19,000 multiple-choice questions on a range of topics. The dataset assesses LLMs in multitasking situations such as question answering, text generation, reading comprehension, visual question answering, and more by including both textual data and accompanying images. Using ChatGPT and BingChat, we evaluated LLMs on the VNHSGE dataset and contrasted their performance with that of Vietnamese students to see how well they performed. The results show that ChatGPT and BingChat both perform at a human level in a number of areas, including literature, English, history, geography, and civics education. They still have space to grow, though, especially in the areas of mathematics, physics, chemistry, and biology. The VNHSGE dataset seeks to provide an adequate benchmark for assessing the abilities of LLMs with its wide-ranging coverage and variety of activities. We intend to promote future developments in the creation of LLMs by making this dataset available to the scientific community, especially in resolving LLMs' limits in disciplines involving mathematics and the natural sciences.Comment: 74 pages, 44 figure

    Automated identification and behaviour classification for modelling social dynamics in group-housed mice

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    Mice are often used in biology as exploratory models of human conditions, due to their similar genetics and physiology. Unfortunately, research on behaviour has traditionally been limited to studying individuals in isolated environments and over short periods of time. This can miss critical time-effects, and, since mice are social creatures, bias results. This work addresses this gap in research by developing tools to analyse the individual behaviour of group-housed mice in the home-cage over several days and with minimal disruption. Using data provided by the Mary Lyon Centre at MRC Harwell we designed an end-to-end system that (a) tracks and identifies mice in a cage, (b) infers their behaviour, and subsequently (c) models the group dynamics as functions of individual activities. In support of the above, we also curated and made available a large dataset of mouse localisation and behaviour classifications (IMADGE), as well as two smaller annotated datasets for training/evaluating the identification (TIDe) and behaviour inference (ABODe) systems. This research constitutes the first of its kind in terms of the scale and challenges addressed. The data source (side-view single-channel video with clutter and no identification markers for mice) presents challenging conditions for analysis, but has the potential to give richer information while using industry standard housing. A Tracking and Identification module was developed to automatically detect, track and identify the (visually similar) mice in the cluttered home-cage using only single-channel IR video and coarse position from RFID readings. Existing detectors and trackers were combined with a novel Integer Linear Programming formulation to assign anonymous tracks to mouse identities. This utilised a probabilistic weight model of affinity between detections and RFID pickups. The next task necessitated the implementation of the Activity Labelling module that classifies the behaviour of each mouse, handling occlusion to avoid giving unreliable classifications when the mice cannot be observed. Two key aspects of this were (a) careful feature-selection, and (b) judicious balancing of the errors of the system in line with the repercussions for our setup. Given these sequences of individual behaviours, we analysed the interaction dynamics between mice in the same cage by collapsing the group behaviour into a sequence of interpretable latent regimes using both static and temporal (Markov) models. Using a permutation matrix, we were able to automatically assign mice to roles in the HMM, fit a global model to a group of cages and analyse abnormalities in data from a different demographic
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