9,265 research outputs found
Spatial adaptive settlement systems in archaeology. Modelling long-term settlement formation from spatial micro interactions
Despite research history spanning more than a century, settlement patterns still hold a promise to contribute to the theories of large-scale processes in human history. Mostly they have been presented as passive imprints of past human activities and spatial interactions they shape have not been studied as the driving force of historical processes. While archaeological knowledge has been used to construct geographical theories of evolution of settlement there still exist gaps in this knowledge. Currently no theoretical framework has been adopted to explore them as spatial systems emerging from micro-choices of small population units.
The goal of this thesis is to propose a conceptual model of adaptive settlement systems based on complex adaptive systems framework. The model frames settlement system formation processes as an adaptive system containing spatial features, information flows, decision making population units (agents) and forming cross scale feedback loops between location choices of individuals and space modified by their aggregated choices. The goal of the model is to find new ways of interpretation of archaeological locational data as well as closer theoretical integration of micro-level choices and meso-level settlement structures.
The thesis is divided into five chapters, the first chapter is dedicated to conceptualisation of the general model based on existing literature and shows that settlement systems are inherently complex adaptive systems and therefore require tools of complexity science for causal explanations. The following chapters explore both empirical and theoretical simulated settlement patterns based dedicated to studying selected information flows and feedbacks in the context of the whole system.
Second and third chapters explore the case study of the Stone Age settlement in Estonia comparing residential location choice principles of different periods. In chapter 2 the relation between environmental conditions and residential choice is explored statistically. The results confirm that the relation is significant but varies between different archaeological phenomena. In the third chapter hunter-fisher-gatherer and early agrarian Corded Ware settlement systems were compared spatially using inductive models. The results indicated a large difference in their perception of landscape regarding suitability for habitation. It led to conclusions that early agrarian land use significantly extended land use potential and provided a competitive spatial benefit. In addition to spatial differences, model performance was compared and the difference was discussed in the context of proposed adaptive settlement system model. Last two chapters present theoretical agent-based simulation experiments intended to study effects discussed in relation to environmental model performance and environmental determinism in general. In the fourth chapter the central place foragingmodel was embedded in the proposed model and resource depletion, as an environmental modification mechanism, was explored. The study excluded the possibility that mobility itself would lead to modelling effects discussed in the previous chapter.
The purpose of the last chapter is the disentanglement of the complex relations between social versus human-environment interactions. The study exposed non-linear spatial effects expected population density can have on the system and the general robustness of environmental inductive models in archaeology to randomness and social effect. The model indicates that social interactions between individuals lead to formation of a group agency which is determined by the environment even if individual cognitions consider the environment insignificant. It also indicates that spatial configuration of the environment has a certain influence towards population clustering therefore providing a potential pathway to population aggregation. Those empirical and theoretical results showed the new insights provided by the complex adaptive systems framework. Some of the results, including the explanation of empirical results, required the conceptual model to provide a framework of interpretation
Transaction Fraud Detection via Spatial-Temporal-Aware Graph Transformer
How to obtain informative representations of transactions and then perform
the identification of fraudulent transactions is a crucial part of ensuring
financial security. Recent studies apply Graph Neural Networks (GNNs) to the
transaction fraud detection problem. Nevertheless, they encounter challenges in
effectively learning spatial-temporal information due to structural
limitations. Moreover, few prior GNN-based detectors have recognized the
significance of incorporating global information, which encompasses similar
behavioral patterns and offers valuable insights for discriminative
representation learning. Therefore, we propose a novel heterogeneous graph
neural network called Spatial-Temporal-Aware Graph Transformer (STA-GT) for
transaction fraud detection problems. Specifically, we design a temporal
encoding strategy to capture temporal dependencies and incorporate it into the
graph neural network framework, enhancing spatial-temporal information modeling
and improving expressive ability. Furthermore, we introduce a transformer
module to learn local and global information. Pairwise node-node interactions
overcome the limitation of the GNN structure and build up the interactions with
the target node and long-distance ones. Experimental results on two financial
datasets compared to general GNN models and GNN-based fraud detectors
demonstrate that our proposed method STA-GT is effective on the transaction
fraud detection task
MolFM: A Multimodal Molecular Foundation Model
Molecular knowledge resides within three different modalities of information
sources: molecular structures, biomedical documents, and knowledge bases.
Effective incorporation of molecular knowledge from these modalities holds
paramount significance in facilitating biomedical research. However, existing
multimodal molecular foundation models exhibit limitations in capturing
intricate connections between molecular structures and texts, and more
importantly, none of them attempt to leverage a wealth of molecular expertise
derived from knowledge graphs. In this study, we introduce MolFM, a multimodal
molecular foundation model designed to facilitate joint representation learning
from molecular structures, biomedical texts, and knowledge graphs. We propose
cross-modal attention between atoms of molecular structures, neighbors of
molecule entities and semantically related texts to facilitate cross-modal
comprehension. We provide theoretical analysis that our cross-modal
pre-training captures local and global molecular knowledge by minimizing the
distance in the feature space between different modalities of the same
molecule, as well as molecules sharing similar structures or functions. MolFM
achieves state-of-the-art performance on various downstream tasks. On
cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04%
absolute gains under the zero-shot and fine-tuning settings, respectively.
Furthermore, qualitative analysis showcases MolFM's implicit ability to provide
grounding from molecular substructures and knowledge graphs. Code and models
are available on https://github.com/BioFM/OpenBioMed.Comment: 31 pages, 15 figures, and 15 table
Automatic Intersection Management in Mixed Traffic Using Reinforcement Learning and Graph Neural Networks
Connected automated driving has the potential to significantly improve urban
traffic efficiency, e.g., by alleviating issues due to occlusion. Cooperative
behavior planning can be employed to jointly optimize the motion of multiple
vehicles. Most existing approaches to automatic intersection management,
however, only consider fully automated traffic. In practice, mixed traffic,
i.e., the simultaneous road usage by automated and human-driven vehicles, will
be prevalent. The present work proposes to leverage reinforcement learning and
a graph-based scene representation for cooperative multi-agent planning. We
build upon our previous works that showed the applicability of such machine
learning methods to fully automated traffic. The scene representation is
extended for mixed traffic and considers uncertainty in the human drivers'
intentions. In the simulation-based evaluation, we model measurement
uncertainties through noise processes that are tuned using real-world data. The
paper evaluates the proposed method against an enhanced first in - first out
scheme, our baseline for mixed traffic management. With increasing share of
automated vehicles, the learned planner significantly increases the vehicle
throughput and reduces the delay due to interaction. Non-automated vehicles
benefit virtually alike.Comment: 8 pages, 7 figures, 34th IEEE Intelligent Vehicles Symposium (IV),
updated to accepted versio
Using machine learning to predict pathogenicity of genomic variants throughout the human genome
Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität.
Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores.
Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt.
Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity.
Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants.
The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency.
In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org
Resilience and food security in a food systems context
This open access book compiles a series of chapters written by internationally recognized experts known for their in-depth but critical views on questions of resilience and food security. The book assesses rigorously and critically the contribution of the concept of resilience in advancing our understanding and ability to design and implement development interventions in relation to food security and humanitarian crises. For this, the book departs from the narrow beaten tracks of agriculture and trade, which have influenced the mainstream debate on food security for nearly 60 years, and adopts instead a wider, more holistic perspective, framed around food systems. The foundation for this new approach is the recognition that in the current post-globalization era, the food and nutritional security of the world’s population no longer depends just on the performance of agriculture and policies on trade, but rather on the capacity of the entire (food) system to produce, process, transport and distribute safe, affordable and nutritious food for all, in ways that remain environmentally sustainable. In that context, adopting a food system perspective provides a more appropriate frame as it incites to broaden the conventional thinking and to acknowledge the systemic nature of the different processes and actors involved. This book is written for a large audience, from academics to policymakers, students to practitioners
Knowledge Distillation and Continual Learning for Optimized Deep Neural Networks
Over the past few years, deep learning (DL) has been achieving state-of-theart performance on various human tasks such as speech generation, language translation, image segmentation, and object detection. While traditional machine learning models require hand-crafted features, deep learning algorithms can automatically extract discriminative features and learn complex knowledge from large datasets. This powerful learning ability makes deep learning models attractive to both academia and big corporations.
Despite their popularity, deep learning methods still have two main limitations: large memory consumption and catastrophic knowledge forgetting. First, DL algorithms use very deep neural networks (DNNs) with many billion parameters, which have a big model size and a slow inference speed. This restricts the application of DNNs in resource-constraint devices such as mobile phones and autonomous vehicles. Second, DNNs are known to suffer from catastrophic forgetting. When incrementally learning new tasks, the model performance on old tasks significantly drops. The ability to accommodate new knowledge while retaining previously learned knowledge is called continual learning. Since the realworld environments in which the model operates are always evolving, a robust neural network needs to have this continual learning ability for adapting to new changes
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Exploring third-party certification programmes in commodity value chains
This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonCertification programmes have become a widely adopted practice across commodity
industries and serve as a mechanism for encouraging sustainable agriculture aimed at
improving livelihoods, reducing poverty, and conserving the environment. Certification has
also become critical in shaping the value creation and capture potential of producers,
manufacturers, and consumers embedded in the value chains of many commodity industries.
However, recent years has seen commodity certification programmes struggling to yield the
expected benefits for which they were putatively established. Drawing on temporal myopia
(TM) as a theoretical lens, this study explores the existential challenges facing the loosely
coupled actors in CVCs, that has led to the floundering of these certification programmes.
Focusing on the Ghana cocoa industry, the study provides a fine-grained explication of how
the differential and competing organizing practices of these actors cumulatively contribute to
the near collapse of these certification programmes. Adopting an interpretive approach and
an exploratory qualitative research design, data for the empirical inquiry were chiefly
collected using semi-structured interviews with cocoa farmers (25), the Ghana Cocoa Board
(5), certification organisations (5), cooperatives (7) and produce buying companies (10). This
was supplemented with focus group discussions (44), and publicly available documents on
certification programmes. The study makes three main findings. First, the study unpacks the
state of the art of certification programmes to understand how loosely coupled actors respond
to certification practices, emphasizing how the activities of various loosely coupled actors
contribute to those structures and procedures, which provides understanding of the
organising practices required in certification programmes. Second, it highlights how TM
accounts for the floundering of certification programmes in CVCs. Third, it demonstrates how
environmental, social, and institutional factors may interact with the certification
requirements, rubrics, and standards, to precipitate a range of organising practices that may
operate in combination or serially to facilitate (or impede) certification programmes. The
contribution of the thesis is also three-fold. First, broadening our understanding of the state
of the art to certification in organising, this study extends our understanding of how loosely
coupled actors in CVCs frame, make meaning, and respond to certification practices. Second,
the study shows how taken for granted everyday organizing practices of the loosely coupled
actors could serially combine to precipitate the near collapse of the certification programmes which frequently seek to promote sustainable production and livelihoods. Third, the study
offers deeper insights into how temporal myopia serves as a blocking mechanism which
induces these loosely coupled actors’, to focus on short term gains within the contingencies of
the socio-economic environment in which they operate.Ghana Scholarship Secretaria
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Learning from Sequential User Data: Models and Sample-efficient Algorithms
Recent advances in deep learning have made learning representation from ever-growing datasets possible in the domain of vision, natural language processing (NLP), and robotics, among others. However, deep networks are notoriously data-hungry; for example, training language models with attention mechanisms sometimes requires trillions of parameters and tokens. In contrast, we can often access a limited number of samples in many tasks. It is crucial to learn models from these `limited\u27 datasets. Learning with limited datasets can take several forms. In this thesis, we study how to select data samples sequentially such that downstream task performance is maximized. Moreover, we study how to introduce prior knowledge in the deep networks to maximize prediction performance. We focus on four sequential tasks: computerized adaptive testing in psychometrics, sketching in recommender systems, knowledge tracing in computer-assisted education, and career path modeling in the labor market.
In the first two tasks, we devise novel sample-efficient algorithms to query a minimal number of sequential samples to improve future predictions. We propose a Bilevel Optimization-Based framework for computerized adaptive testing to learn a data-driven question selection algorithm that improves existing data selection policies. We also tackle the sketching problem in the recommender system, with the task of recommending the next item using a stored subset of prior data samples. In this setting, we develop a data-driven sequential selection algorithm that tackles evolving downstream task distribution. In the last two tasks, we devise novel neural models to introduce prior knowledge exploiting limited data samples. For knowledge tracing, we propose a novel neural architecture, inspired by cognitive and psychometric models, to improve the prediction of students\u27 future performance and utilize the labeled data samples efficiently. For career path modeling, we propose a novel and interpretable monotonic nonlinear state-space model to analyze online user professional profiles and provide actionable feedback and recommendations to users on how they can reach their career goals.
The data-driven differentiable data selection algorithms for the first two tasks open up future directions to query (a non-differentiable operation) a minimal number of samples optimally to maximize prediction performance. The structures, introduced in the neural architecture for the models in the last two tasks using prior knowledge, open up future directions to learn deep models augmented with prior knowledge using limited data samples
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