Crowdsource Annotation and Automatic Reconstruction of Online Discussion Threads

Modern communication relies on electronic messages organized in the form of discussion threads. Emails, IMs, SMS, website comments, and forums are all composed of threads, which consist of individual user messages connected by metadata and discourse coherence to messages from other users. Threads are used to display user messages effectively in a GUI such as an email client, providing a background context for understanding a single message. Many messages are meaningless without the context provided by their thread. However, a number of factors may result in missing thread structure, ranging from user mistake (replying to the wrong message), to missing metadata (some email clients do not produce/save headers that fully encapsulate thread structure; and, conversion of archived threads from over repository to another may also result in lost metadata), to covert use (users may avoid metadata to render discussions difficult for third parties to understand). In the field of security, law enforcement agencies may obtain vast collections of discussion turns that require automatic thread reconstruction to understand. For example, the Enron Email Corpus, obtained by the Federal Energy Regulatory Commission during its investigation of the Enron Corporation, has no inherent thread structure. In this thesis, we will use natural language processing approaches to reconstruct threads from message content. Reconstruction based on message content sidesteps the problem of missing metadata, permitting post hoc reorganization and discussion understanding. We will investigate corpora of email threads and Wikipedia discussions. However, there is a scarcity of annotated corpora for this task. For example, the Enron Emails Corpus contains no inherent thread structure. Therefore, we also investigate issues faced when creating crowdsourced datasets and learning statistical models of them. Several of our findings are applicable for other natural language machine classification tasks, beyond thread reconstruction. We will divide our investigation of discussion thread reconstruction into two parts. First, we explore techniques needed to create a corpus for our thread reconstruction research. Like other NLP pairwise classification tasks such as Wikipedia discussion turn/edit alignment and sentence pair text similarity rating, email thread disentanglement is a heavily class-imbalanced problem, and although the advent of crowdsourcing has reduced annotation costs, the common practice of crowdsourcing redundancy is too expensive for class-imbalanced tasks. As the first contribution of this thesis, we evaluate alternative strategies for reducing crowdsourcing annotation redundancy for class-imbalanced NLP tasks. We also examine techniques to learn the best machine classifier from our crowdsourced labels. In order to reduce noise in training data, most natural language crowdsourcing annotation tasks gather redundant labels and aggregate them into an integrated label, which is provided to the classifier. However, aggregation discards potentially useful information from linguistically ambiguous instances. For the second contribution of this thesis, we show that, for four of five natural language tasks, filtering of the training dataset based on crowdsource annotation item agreement improves task performance, while soft labeling based on crowdsource annotations does not improve task performance. Second, we investigate thread reconstruction as divided into the tasks of thread disentanglement and adjacency recognition. We present the Enron Threads Corpus, a newly-extracted corpus of 70,178 multi-email threads with emails from the Enron Email Corpus. In the original Enron Emails Corpus, emails are not sorted by thread. To disentangle these threads, and as the third contribution of this thesis, we perform pairwise classification, using text similarity measures on non-quoted texts in emails. We show that i) content text similarity metrics outperform style and structure text similarity metrics in both a class-balanced and class-imbalanced setting, and ii) although feature performance is dependent on the semantic similarity of the corpus, content features are still effective even when controlling for semantic similarity. To reconstruct threads, it is also necessary to identify adjacency relations among pairs. For the forum of Wikipedia discussions, metadata is not available, and dialogue act typologies, helpful for other domains, are inapplicable. As our fourth contribution, via our experiments, we show that adjacency pair recognition can be performed using lexical pair features, without a dialogue act typology or metadata, and that this is robust to controlling for topic bias of the discussions. Yet, lexical pair features do not effectively model the lexical semantic relations between adjacency pairs. To model lexical semantic relations, and as our fifth contribution, we perform adjacency recognition using extracted keyphrases enhanced with semantically related terms. While this technique outperforms a most frequent class baseline, it fails to outperform lexical pair features or tf-idf weighted cosine similarity. Our investigation shows that this is the result of poor word sense disambiguation and poor keyphrase extraction causing spurious false positive semantic connections. In concluding this thesis, we also reflect on open issues and unanswered questions remaining after our research contributions, discuss applications for thread reconstruction, and suggest some directions for future work

Chronic Health Conditions Among US Veterans Discharged From Military Service for Misconduct

Veterans who are discharged from military service due to misconduct are vulnerable to negative health-related outcomes, including homelessness, incarceration, and suicide. We used national data from the Veterans Health Administration for 218,608 veterans of conflicts in Iraq and Afghanistan that took place after the events of September 11, 2001, to compare clinical diagnoses between routinely-discharged (n = 203,174) and misconduct-discharged (n = 15,433) veterans. Misconduct-discharged veterans had significantly higher risk for all mental health conditions (adjusted odds ratio [AOR] range, 2.5–8.0) and several behaviorally linked chronic health conditions (AOR range, 1.2–5.9). Misconduct-discharged veterans have serious and complex health care needs; prevention efforts should focus on behavioral risk factors to prevent the development and exacerbation of chronic health conditions among this vulnerable population

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

Crowdsource Annotation and Automatic Reconstruction of Online Discussion Threads

Modern communication relies on electronic messages organized in the form of discussion threads. Emails, IMs, SMS, website comments, and forums are all composed of threads, which consist of individual user messages connected by metadata and discourse coherence to messages from other users. Threads are used to display user messages effectively in a GUI such as an email client, providing a background context for understanding a single message. Many messages are meaningless without the context provided by their thread. However, a number of factors may result in missing thread structure, ranging from user mistake (replying to the wrong message), to missing metadata (some email clients do not produce/save headers that fully encapsulate thread structure; and, conversion of archived threads from over repository to another may also result in lost metadata), to covert use (users may avoid metadata to render discussions difficult for third parties to understand). In the field of security, law enforcement agencies may obtain vast collections of discussion turns that require automatic thread reconstruction to understand. For example, the Enron Email Corpus, obtained by the Federal Energy Regulatory Commission during its investigation of the Enron Corporation, has no inherent thread structure. In this thesis, we will use natural language processing approaches to reconstruct threads from message content. Reconstruction based on message content sidesteps the problem of missing metadata, permitting post hoc reorganization and discussion understanding. We will investigate corpora of email threads and Wikipedia discussions. However, there is a scarcity of annotated corpora for this task. For example, the Enron Emails Corpus contains no inherent thread structure. Therefore, we also investigate issues faced when creating crowdsourced datasets and learning statistical models of them. Several of our findings are applicable for other natural language machine classification tasks, beyond thread reconstruction. We will divide our investigation of discussion thread reconstruction into two parts. First, we explore techniques needed to create a corpus for our thread reconstruction research. Like other NLP pairwise classification tasks such as Wikipedia discussion turn/edit alignment and sentence pair text similarity rating, email thread disentanglement is a heavily class-imbalanced problem, and although the advent of crowdsourcing has reduced annotation costs, the common practice of crowdsourcing redundancy is too expensive for class-imbalanced tasks. As the first contribution of this thesis, we evaluate alternative strategies for reducing crowdsourcing annotation redundancy for class-imbalanced NLP tasks. We also examine techniques to learn the best machine classifier from our crowdsourced labels. In order to reduce noise in training data, most natural language crowdsourcing annotation tasks gather redundant labels and aggregate them into an integrated label, which is provided to the classifier. However, aggregation discards potentially useful information from linguistically ambiguous instances. For the second contribution of this thesis, we show that, for four of five natural language tasks, filtering of the training dataset based on crowdsource annotation item agreement improves task performance, while soft labeling based on crowdsource annotations does not improve task performance. Second, we investigate thread reconstruction as divided into the tasks of thread disentanglement and adjacency recognition. We present the Enron Threads Corpus, a newly-extracted corpus of 70,178 multi-email threads with emails from the Enron Email Corpus. In the original Enron Emails Corpus, emails are not sorted by thread. To disentangle these threads, and as the third contribution of this thesis, we perform pairwise classification, using text similarity measures on non-quoted texts in emails. We show that i) content text similarity metrics outperform style and structure text similarity metrics in both a class-balanced and class-imbalanced setting, and ii) although feature performance is dependent on the semantic similarity of the corpus, content features are still effective even when controlling for semantic similarity. To reconstruct threads, it is also necessary to identify adjacency relations among pairs. For the forum of Wikipedia discussions, metadata is not available, and dialogue act typologies, helpful for other domains, are inapplicable. As our fourth contribution, via our experiments, we show that adjacency pair recognition can be performed using lexical pair features, without a dialogue act typology or metadata, and that this is robust to controlling for topic bias of the discussions. Yet, lexical pair features do not effectively model the lexical semantic relations between adjacency pairs. To model lexical semantic relations, and as our fifth contribution, we perform adjacency recognition using extracted keyphrases enhanced with semantically related terms. While this technique outperforms a most frequent class baseline, it fails to outperform lexical pair features or tf-idf weighted cosine similarity. Our investigation shows that this is the result of poor word sense disambiguation and poor keyphrase extraction causing spurious false positive semantic connections. In concluding this thesis, we also reflect on open issues and unanswered questions remaining after our research contributions, discuss applications for thread reconstruction, and suggest some directions for future work