1,014 research outputs found

    Identifying Graphs from Noisy Observational Data

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    There is a growing amount of data describing networks -- examples include social networks, communication networks, and biological networks. As the amount of available data increases, so does our interest in analyzing the properties and characteristics of these networks. However, in most cases the data is noisy, incomplete, and the result of passively acquired observational data; naively analyzing these networks without taking these errors into account can result in inaccurate and misleading conclusions. In my dissertation, I study the tasks of entity resolution, link prediction, and collective classification to address these deficiencies. I describe these tasks in detail and discuss my own work on each of these tasks. For entity resolution, I develop a method for resolving the identities of name mentions in email communications. For link prediction, I develop a method for inferring subordinate-manager relationships between individuals in an email communication network. For collective classification, I propose an adaptive active surveying method to address node labeling in a query-driven setting on network data. In many real-world settings, however, these deficiencies are not found in isolation and all need to be addressed to infer the desired complete and accurate network. Furthermore, because of the dependencies typically found in these tasks, the tasks are inherently inter-related and must be performed jointly. I define the general problem of graph identification which simultaneously performs these tasks; removing the noise and missing values in the observed input network and inferring the complete and accurate output network. I present a novel approach to graph identification using a collection of Coupled Collective Classifiers, C3, which, in addition to capturing the variety of features typically used for each task, can capture the intra- and inter-dependencies required to correctly infer nodes, edges, and labels in the output network. I discuss variants of C3 using different learning and inference paradigms and show the superior performance of C3, in terms of both prediction quality and runtime performance, over various previous approaches. I then conclude by presenting the Graph Alignment, Identification, and Analysis (GAIA) open-source software library which not only provides an implementation of C3 but also algorithms for various tasks in network data such as entity resolution, link prediction, collective classification, clustering, active learning, data generation, and analysis

    Improving resilience in Critical Infrastructures through learning from past events

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    Modern societies are increasingly dependent on the proper functioning of Critical Infrastructures (CIs). CIs produce and distribute essential goods or services, as for power transmission systems, water treatment and distribution infrastructures, transportation systems, communication networks, nuclear power plants, and information technologies. Being resilient, where resilience denotes the capacity of a system to recover from challenges or disruptive events, becomes a key property for CIs, which are constantly exposed to threats that can undermine safety, security, and business continuity. Nowadays, a variety of approaches exists in the context of CIs’ resilience research. This dissertation starts with a systematic review based on PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) on the approaches that have a complete qualitative dimension, or that can be used as entry points for semi-quantitative analyses. The review identifies four principal dimensions of resilience referred to CIs (i.e., techno-centric, organizational, community, and urban) and discusses the related qualitative or semi-quantitative methods. The scope of the thesis emphasizes the organizational dimension, as a socio-technical construct. Accordingly, the following research question has been posed: how can learning improve resilience in an organization? Firstly, the benefits of learning in a particular CI, i.e. the supply chain in reverse logistics related to the small arms utilized by Italian Armed Forces, have been studied. Following the theory of Learning From Incidents, the theoretical model helped to elaborate a centralized information management system for the Supply Chain Management of small arms within a Business Intelligence (BI) framework, which can be the basis for an effective decision-making process, capable of increasing the systemic resilience of the supply chain itself. Secondly, the research question has been extended to another extremely topical context, i.e. the Emergency Management (EM), exploring the crisis induced learning where single-loop and double-loop learning cycles can be established regarding the behavioral perspective. Specifically, the former refers to the correction of practices within organizational plans without changing core beliefs and fundamental rules of the organization, while the latter aims at resolving incompatible organizational behavior by restructuring the norms themselves together with the associated practices or assumptions. Consequently, with the aim of ensuring high EM systems resilience, and effective single-loop and double-loop crisis induced learning at organizational level, the study examined learning opportunities that emerge through the exploration of adaptive practices necessary to face the complexity of a socio-technical work domain as the EM of Covid-19 outbreaks on Oil & Gas platforms. Both qualitative and quantitative approaches have been adopted to analyze the resilience of this specific socio-technical system. On this consciousness, with the intention to explore systems theoretic possibilities to model the EM system, the Functional Resonance Analysis Method (FRAM) has been proposed as a qualitative method for developing a systematic understanding of adaptive practices, modelling planning and resilient behaviors and ultimately supporting crisis induced learning. After the FRAM analysis, the same EM system has also been studied adopting a Bayesian Network (BN) to quantify resilience potentials of an EM procedure resulting from the adaptive practices and lessons learned by an EM organization. While the study of CIs is still an open and challenging topic, this dissertation provides methodologies and running examples on how systemic approaches may support data-driven learning to ultimately improve organizational resilience. These results, possibly extended with future research drivers, are expected to support decision-makers in their tactical and operational endeavors

    An Integrated, Module-based Biomarker Discovery Framework

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    Identification of biomarkers that contribute to complex human disorders is a principal and challenging task in computational biology. Prognostic biomarkers are useful for risk assessment of disease progression and patient stratification. Since treatment plans often hinge on patient stratification, better disease subtyping has the potential to significantly improve survival for patients. Additionally, a thorough understanding of the roles of biomarkers in cancer pathways facilitates insights into complex disease formation, and provides potential druggable targets in the pathways. Many statistical methods have been applied toward biomarker discovery, often combining feature selection with classification methods. Traditional approaches are mainly concerned with statistical significance and fail to consider the clinical relevance of the selected biomarkers. Two additional problems impede meaningful biomarker discovery: gene multiplicity (several maximally predictive solutions exist) and instability (inconsistent gene sets from different experiments or cross validation runs). Motivated by a need for more biologically informed, stable biomarker discovery method, I introduce an integrated module-based biomarker discovery framework for analyzing high- throughput genomic disease data. The proposed framework addresses the aforementioned challenges in three components. First, a recursive spectral clustering algorithm specifically 4 tailored toward high-dimensional, heterogeneous data (ReKS) is developed to partition genes into clusters that are treated as single entities for subsequent analysis. Next, the problems of gene multiplicity and instability are addressed through a group variable selection algorithm (T-ReCS) based on local causal discovery methods. Guided by the tree-like partition created from the clustering algorithm, this algorithm selects gene clusters that are predictive of a clinical outcome. We demonstrate that the group feature selection method facilitate the discovery of biologically relevant genes through their association with a statistically predictive driver. Finally, we elucidate the biological relevance of the biomarkers by leveraging available prior information to identify regulatory relationships between genes and between clusters, and deliver the information in the form of a user-friendly web server, mirConnX

    Pacific Symposium on Biocomputing 2023

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    The Pacific Symposium on Biocomputing (PSB) 2023 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2023 will be held on January 3-7, 2023 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2023 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field

    Mining Behavior of Citizen Sensor Communities to Improve Cooperation with Organizational Actors

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    Web 2.0 (social media) provides a natural platform for dynamic emergence of citizen (as) sensor communities, where the citizens generate content for sharing information and engaging in discussions. Such a citizen sensor community (CSC) has stated or implied goals that are helpful in the work of formal organizations, such as an emergency management unit, for prioritizing their response needs. This research addresses questions related to design of a cooperative system of organizations and citizens in CSC. Prior research by social scientists in a limited offline and online environment has provided a foundation for research on cooperative behavior challenges, including \u27articulation\u27 and \u27awareness\u27, but Web 2.0 supported CSC offers new challenges as well as opportunities. A CSC presents information overload for the organizational actors, especially in finding reliable information providers (for awareness), and finding actionable information from the data generated by citizens (for articulation). Also, we note three data level challenges: ambiguity in interpreting unconstrained natural language text, sparsity of user behaviors, and diversity of user demographics. Interdisciplinary research involving social and computer sciences is essential to address these socio-technical issues. I present a novel web information-processing framework, called the Identify-Match- Engage (IME) framework. IME allows operationalizing computation in design problems of awareness and articulation of the cooperative system between citizens and organizations, by addressing data problems of group engagement modeling and intent mining. The IME framework includes: a.) Identification of cooperation-assistive intent (seeking-offering) from short, unstructured messages using a classification model with declarative, social and contrast pattern knowledge, b.) Facilitation of coordination modeling using bipartite matching of complementary intent (seeking-offering), and c.) Identification of user groups to prioritize for engagement by defining a content-driven measure of \u27group discussion divergence\u27. The use of prior knowledge and interplay of features of users, content, and network structures efficiently captures context for computing cooperation-assistive behavior (intent and engagement) from unstructured social data in the online socio-technical systems. Our evaluation of a use-case of the crisis response domain shows improvement in performance for both intent classification and group engagement prioritization. Real world applications of this work include use of the engagement interface tool during various recent crises including the 2014 Jammu and Kashmir floods, and intent classification as a service integrated by the crisis mapping pioneer Ushahidi\u27s CrisisNET project for broader impact

    Operationalizing fairness for responsible machine learning

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    As machine learning (ML) is increasingly used for decision making in scenarios that impact humans, there is a growing awareness of its potential for unfairness. A large body of recent work has focused on proposing formal notions of fairness in ML, as well as approaches to mitigate unfairness. However, there is a growing disconnect between the ML fairness literature and the needs to operationalize fairness in practice. This thesis addresses the need for responsible ML by developing new models and methods to address challenges in operationalizing fairness in practice. Specifically, it makes the following contributions. First, we tackle a key assumption in the group fairness literature that sensitive demographic attributes such as race and gender are known upfront, and can be readily used in model training to mitigate unfairness. In practice, factors like privacy and regulation often prohibit ML models from collecting or using protected attributes in decision making. To address this challenge we introduce the novel notion of computationally-identifiable errors and propose Adversarially Reweighted Learning (ARL), an optimization method that seeks to improve the worst-case performance over unobserved groups, without requiring access to the protected attributes in the dataset. Second, we argue that while group fairness notions are a desirable fairness criterion, they are fundamentally limited as they reduce fairness to an average statistic over pre-identified protected groups. In practice, automated decisions are made at an individual level, and can adversely impact individual people irrespective of the group statistic. We advance the paradigm of individual fairness by proposing iFair (individually fair representations), an optimization approach for learning a low dimensional latent representation of the data with two goals: to encode the data as well as possible, while removing any information about protected attributes in the transformed representation. Third, we advance the individual fairness paradigm, which requires that similar individuals receive similar outcomes. However, similarity metrics computed over observed feature space can be brittle, and inherently limited in their ability to accurately capture similarity between individuals. To address this, we introduce a novel notion of fairness graphs, wherein pairs of individuals can be identified as deemed similar with respect to the ML objective. We cast the problem of individual fairness into graph embedding, and propose PFR (pairwise fair representations), a method to learn a unified pairwise fair representation of the data. Fourth, we tackle the challenge that production data after model deployment is constantly evolving. As a consequence, in spite of the best efforts in training a fair model, ML systems can be prone to failure risks due to a variety of unforeseen reasons. To ensure responsible model deployment, potential failure risks need to be predicted, and mitigation actions need to be devised, for example, deferring to a human expert when uncertain or collecting additional data to address model’s blind-spots. We propose Risk Advisor, a model-agnostic meta-learner to predict potential failure risks and to give guidance on the sources of uncertainty inducing the risks, by leveraging information theoretic notions of aleatoric and epistemic uncertainty. This dissertation brings ML fairness closer to real-world applications by developing methods that address key practical challenges. Extensive experiments on a variety of real-world and synthetic datasets show that our proposed methods are viable in practice.Mit der zunehmenden Verwendung von Maschinellem Lernen (ML) in Situationen, die Auswirkungen auf Menschen haben, nimmt das Bewusstsein über das Potenzial für Unfair- ness zu. Ein großer Teil der jüngeren Forschung hat den Fokus auf das formale Verständnis von Fairness im Zusammenhang mit ML sowie auf Ansätze zur Überwindung von Unfairness gelegt. Jedoch driften die Literatur zu Fairness in ML und die Anforderungen zur Implementierung in der Praxis zunehmend auseinander. Diese Arbeit beschäftigt sich mit der Notwendigkeit für verantwortungsvolles ML, wofür neue Modelle und Methoden entwickelt werden, um die Herausforderungen im Fairness-Bereich in der Praxis zu bewältigen. Ihr wissenschaftlicher Beitrag ist im Folgenden dargestellt. In Kapitel 3 behandeln wir die Schlüsselprämisse in der Gruppenfairnessliteratur, dass sensible demografische Merkmale wie etwa die ethnische Zugehörigkeit oder das Geschlecht im Vorhinein bekannt sind und während des Trainings eines Modells zur Reduzierung der Unfairness genutzt werden können. In der Praxis hindern häufig Einschränkungen zum Schutz der Privatsphäre oder gesetzliche Regelungen ML-Modelle daran, geschützte Merkmale für die Entscheidungsfindung zu sammeln oder zu verwenden. Um diese Herausforderung zu überwinden, führen wir das Konzept der Komputational-identifizierbaren Fehler ein und stellen Adversarially Reweighted Learning (ARL) vor, ein Optimierungsverfahren, das die Worst-Case-Performance bei unbekannter Gruppenzugehörigkeit ohne Wissen über die geschützten Merkmale verbessert. In Kapitel 4 stellen wir dar, dass Konzepte für Gruppenfairness trotz ihrer Eignung als Fairnesskriterium grundsätzlich beschränkt sind, da Fairness auf eine gemittelte statistische Größe für zuvor identifizierte geschützte Gruppen reduziert wird. In der Praxis werden automatisierte Entscheidungen auf einer individuellen Ebene gefällt, und können unabhängig von der gruppenbezogenen Statistik Nachteile für Individuen haben. Wir erweitern das Konzept der individuellen Fairness um unsere Methode iFair (individually fair representations), ein Optimierungsverfahren zum Erlernen einer niedrigdimensionalen Darstellung der Daten mit zwei Zielen: die Daten so akkurat wie möglich zu enkodieren und gleichzeitig jegliche Information über die geschützten Merkmale in der transformierten Darstellung zu entfernen. In Kapitel 5 entwickeln wir das Paradigma der individuellen Fairness weiter, das ein ähnliches Ergebnis für ähnliche Individuen erfordert. Ähnlichkeitsmetriken im beobachteten Featureraum können jedoch unzuverlässig und inhärent beschränkt darin sein, Ähnlichkeit zwischen Individuen korrekt abzubilden. Um diese Herausforderung anzugehen, führen wir den neue Konzept der Fairnessgraphen ein, in denen Paare (oder Sets) von Individuen als ähnlich im Bezug auf die ML-Aufgabe identifiziert werden. Wir übersetzen das Problem der individuellen Fairness in eine Grapheinbindung und stellen PFR (pairwise fair representations) vor, eine Methode zum Erlernen einer vereinheitlichten paarweisen fairen Abbildung der Daten. In Kapitel 6 gehen wir die Herausforderung an, dass sich die Daten im Feld nach der Inbetriebnahme des Modells fortlaufend ändern. In der Konsequenz können ML-Systeme trotz größter Bemühungen, ein faires Modell zu trainieren, aufgrund einer Vielzahl an unvorhergesehenen Gründen scheitern. Um eine verantwortungsvolle Implementierung sicherzustellen, gilt es, Risiken für ein potenzielles Versagen vorherzusehen und Gegenmaßnahmen zu entwickeln,z.B. die Übertragung der Entscheidung an einen menschlichen Experten bei Unsicherheit oder das Sammeln weiterer Daten, um die blinden Flecken des Modells abzudecken. Wir stellen mit Risk Advisor einen modell-agnostischen Meta-Learner vor, der Risiken für potenzielles Versagen vorhersagt und Anhaltspunkte für die Ursache der zugrundeliegenden Unsicherheit basierend auf informationstheoretischen Konzepten der aleatorischen und epistemischen Unsicherheit liefert. Diese Dissertation bringt Fairness für verantwortungsvolles ML durch die Entwicklung von Ansätzen für die Lösung von praktischen Kernproblemen näher an die Anwendungen im Feld. Umfassende Experimente mit einer Vielzahl von synthetischen und realen Datensätzen zeigen, dass unsere Ansätze in der Praxis umsetzbar sind.The International Max Planck Research School for Computer Science (IMPRS-CS

    Exploiting Latent Features of Text and Graphs

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    As the size and scope of online data continues to grow, new machine learning techniques become necessary to best capitalize on the wealth of available information. However, the models that help convert data into knowledge require nontrivial processes to make sense of large collections of text and massive online graphs. In both scenarios, modern machine learning pipelines produce embeddings --- semantically rich vectors of latent features --- to convert human constructs for machine understanding. In this dissertation we focus on information available within biomedical science, including human-written abstracts of scientific papers, as well as machine-generated graphs of biomedical entity relationships. We present the Moliere system, and our method for identifying new discoveries through the use of natural language processing and graph mining algorithms. We propose heuristically-based ranking criteria to augment Moliere, and leverage this ranking to identify a new gene-treatment target for HIV-associated Neurodegenerative Disorders. We additionally focus on the latent features of graphs, and propose a new bipartite graph embedding technique. Using our graph embedding, we advance the state-of-the-art in hypergraph partitioning quality. Having newfound intuition of graph embeddings, we present Agatha, a deep-learning approach to hypothesis generation. This system learns a data-driven ranking criteria derived from the embeddings of our large proposed biomedical semantic graph. To produce human-readable results, we additionally propose CBAG, a technique for conditional biomedical abstract generation
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