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Title: Markov degree of configurations defined by fibers of a configuration
Date: 2015, 2015-11-09
Description: We consider a series of configurations defined by fibers of a given base configuration. We prove that Markov degree of the configurations is...
Show moreWe consider a series of configurations defined by fibers of a given base configuration. We prove that Markov degree of the configurations is bounded from above by the Markov complexity of the base configuration. As important examples of base configurations we consider incidence matrices of graphs and study the maximum Markov degree of configurations defined by fibers of the incidence matrices. In particular we give a proof that the Markov degree for two-way transportation polytopes is three.
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Collection: Journal of Algebraic Statistics

Title: On Polyhedral Approximations of Polytopes for Learning Bayesian Networks, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: The motivation for this paper is the geometric approach to statistical learning Bayesiannetwork (BN) structures. We review three vector...
Show moreThe motivation for this paper is the geometric approach to statistical learning Bayesiannetwork (BN) structures. We review three vector encodings of BN structures. The first one has been used by Jaakkola et al. [9] and also by Cussens [4], the other two use special integral vectors formerly introduced, called imsets [18, 20]. The topic is the comparison of outer polyhedral approximations of the corresponding polytopes. We show how to transform the inequalities suggested by Jaakkola et al. [9] into the framework of imsets. The result of our comparison is the observation that the implicit polyhedral approximation of the standard imset polytope suggested in [21] gives a tighter approximation than the (transformed) explicit polyhedral approximation from [9]. As a consequence, we confirm a conjecture from [21] that the above-mentioned implicit polyhedral approximation of the standard imset polytope is an LP relaxation of that polytope. In the end, we review recent attempts to apply the methods of integer programming to learning BN structures and discuss the task of finding suitable explicit LP relaxation in the imset-based approach.
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Collection: Journal of Algebraic Statistics

Title: Higher Connectivity of Fiber Graphs of Gröbner Bases, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: Fiber graphs of Gröbner bases from contingency tables are important in statistical hypothesis testing, where one studies random walks on these...
Show moreFiber graphs of Gröbner bases from contingency tables are important in statistical hypothesis testing, where one studies random walks on these graphs using the Metropolis-Hastings algorithm. The connectivity of the graphs has implications on how fast the algorithm converges. In this paper, we study a class of ber graphs with elementary combinatorial techniques and provide results that support a recent conjecture of Engström: the connectivity is given by the minimum vertex degree.
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Collection: Journal of Algebraic Statistics

Title: Betti Numbers of Cut Ideals of Trees, AS2012 Special Volume, part 2: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Date: 2013, 2013
Description: Cut ideals, introduced by Sturmfels and Sullivant, are used in phylogenetics and algebraic statistics. We study the minimal free resolutions...
Show moreCut ideals, introduced by Sturmfels and Sullivant, are used in phylogenetics and algebraic statistics. We study the minimal free resolutions of cut ideals of tree graphs. By employing basic methods from topological combinatorics, we obtain upper bounds for the Betti numbers of this type of ideals. These take the form of simple formulas on the number of vertices, which arise from the enumeration of induced subgraphs of certain incomparability graphs associated to the edge sets of trees.
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Collection: Journal of Algebraic Statistics

Title: Tying Up Loose Strands: Defining Equations of the Strand Symmetric Model
Date: 2015, 2015-06-11
Description: The strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show...
Show moreThe strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show that the set of known phylogenetic invariants for the general strand symmetric model of the three leaf claw tree entirely defines the ideal. This knowledge allows one to determine the vanishing ideal of the general strand symmetric model of any trivalent tree. Our proof of the main result is computational. We use the fact that the Zariski closure of the strand symmetric model is the secant variety of a toric variety to compute the dimension of the variety. We then show that the known equations generate a prime ideal of the correct dimension using elimination theory.
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Collection: Journal of Algebraic Statistics

Title: The maximum likelihood degree of Fermat hypersurfaces
Date: 2015, 2015-11-09
Description: We study the critical points of the likelihood function over the Fermat hypersurface. This problem is related to one of the main problems in...
Show moreWe study the critical points of the likelihood function over the Fermat hypersurface. This problem is related to one of the main problems in statistical optimization: maximum likelihood estimation. The number of critical points over a projective variety is a topological invariant of the variety and is called maximum likelihood degree. We provide closed formulas for the maximum likelihood degree of any Fermat curve in the projective plane and of Fermat hypersurfaces of degree 2 in any projective space. Algorithmic methods to compute the ML degree of a generic Fermat hypersurface are developed throughout the paper. Such algorithms heavily exploit the symmetries of the varieties we are considering. A computational comparison of the different methods and a list of the maximum likelihood degrees of several Fermat hypersurfaces are available in the last section.
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Collection: Journal of Algebraic Statistics

Title: On the Connectivity of Fiber Graphs
Date: 2015, 2015-06-11
Description: We consider the connectivity of fiber graphs with respect to Gröbner basis and Graver basis moves. First, we present a sequence of fiber...
Show moreWe consider the connectivity of fiber graphs with respect to Gröbner basis and Graver basis moves. First, we present a sequence of fiber graphs using moves from a Gröbner basis and prove that their edge-connectivity is lowest possible and can have an arbitrarily large distance from the minimal degree. We then show that graph-theoretic properties of fiber graphs do not depend on the size of the right-hand side. This provides a counterexample to a conjecture of Engström on the node-connectivity of fiber graphs. Our main result shows that the edge-connectivity in all fiber graphs of this counterexample is best possible if we use moves from Graver basis instead.
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Collection: Journal of Algebraic Statistics

Title: Engineering Escherichia coli to produce and secrete colicins for rapid and selective biofilm cell killing
Date: 2021
Description: Bacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional...
Show moreBacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional antibiotics. Antimicrobial bacteriocins are alternatives to conventional antibiotics and are characterized by unique cell-killing mechanisms, including pore formation on cell membranes, nuclease activity, and cell wall synthesis inhibition. Here, we used cell-free protein synthesis to rapidly evaluate the antibiofilm activities of colicins E1, E2, and E3. We found that E2 (with DNase activity) most effectively killed target biofilm cells (i.e., the K361 strain) while leaving nontargeted biofilms intact. We then engineered probiotic Escherichia coli microorganisms with genetic circuits to controllably synthesize and secrete colicin E2, which successfully inhibited biofilms and killed preformed indicator biofilms. Our findings suggest that colicins rapidly and selectively kill target biofilm cells in multispecies biofilms and demonstrate the potential of using microorganisms engineered to produce antimicrobial colicin proteins as live therapeutic strategies to treat biofilm-associated infections.
Sponsorship: NIH-R15AI130988
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Title: Empirical Modeling of Public Safety to Voice Traffic to Aid Emergency Capacity
Creator: Taher, Tanim, Bacchus, Roger
Date: 2012-04-18, 2012-04-18
Description: An RF measurement system with high time resolution is implemented to determine the statistical characteristics of...
Show moreAn RF measurement system with high time resolution is implemented to determine the statistical characteristics of various channels in the Land Mobile Radio bands. The applicability of simple statistical models to the observed data is investigated, as well as their validity over short and long periods of time. The results show that the statistics of the idle and holding times of communication on these channels vary significantly over time and demonstrate daily periodicity, requiring non-stationary models to accurately represent them. Over short durations of time however, conventional distributions such as the exponential and lognormal may adequately characterize the properties of these quantities, allowing convenient and compact representations of the data. Results based on empirical data are presented to quantify the probability of stationarity for voice traffic within a time span of given length. The findings are useful for network planning or streamlining, network simulation and modeling, and investigation of dynamic spectrum access.
Sponsorship: National Science Foundation, Federal Communications Commission, Motorola, Cleversafe, Roberson & Associates LLC
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Title: Replacement as a Problem for Justification of Preventative Detention
Creator: Davis, Michael
Date: 2011, 2011-04
Publisher: John Jay College of Criminal Justice of The City University of New Yor
Description: What makes Don E. Scheid’s article on indefinite detention interesting is that he thinks through many of the moral...
Show moreWhat makes Don E. Scheid’s article on indefinite detention interesting is that he thinks through many of the moral issues inherent in attempting to prevent (or, rather, keep to a minimum) certain kinds of violent crime, an attempt we have come to call (however unwisely) ‘‘the war on terror.’’ Scheid takes ‘‘war’’ as literally as possible, while making the reasonable assumption that this war, unlike wars generally, is not a temporary expedient responding to a moral emergency but an institution that must operate at full power for a long time, decades at least. Scheid’s argument yields a long list of preconditions for justified indefinite preventive detention: a high standard of dangerousness (‘‘mega-terrorism’’), a reasonable standard of proof of dangerousness, as good an investigation as conditions will allow, adequate resources for the defense, a hearing before a fair and independent tribunal, detention under the most comfortable conditions practical, and periodic review of the detainee’s supposed dangerousness. To these preconditions one more should be added: that detaining the persons in question will reduce the danger posed. I take this additional precondition to follow from Scheid’s own defense of indefinite detention, not from an independent argument. Scheid limits his argument to megaterrorists because the scale of destruction they have already achieved (for example, destruction of the World Trade Center) shows them to be dangerous on a scale ordinary crime is not and so to invite measures of prevention beyond what seems necessary (or proper) for ordinary criminals. Scheid explicitly declines to consider the non-consequentialist argument that preventive detention is what a mega-terrorist deserves for his character or for what he has already done. Scheid’s argument for preventive detention is consequentialist throughout: we may, and should, detain to prevent (or at least substantially reduce the probability of) the large-scale destruction of life that mega-terrorists aim at. We may justifiably deny a few, including some innocent persons, their freedom because, and only because, it makes the rest of us, the great majority, considerably safer. My additional precondition can be defended in the same way: where there is no danger posed, any detention is (all else equal) a net loss in happiness, well being, or whatever reasonable measure of consequences we adopt. A precondition of preventative detention must be a net reduction in danger posed. Where what is proposed is an institution of preventative detention, the institution must have that effect overall. What I shall argue here is that preventive detention generally fails to satisfy this condition and Scheid’s indefinite preventive detention of mega-terrorists always does. An institution to prevent terrorism by detaining terrorists cannot, in practice, significantly reduce the danger terrorism poses.
Criminal Justice Ethics. Vol. 30, No. 1, April 2011, 90-97.
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Title: Learning the Lingo? Gender, Prestige and Linguistic Adaptation in Review Communities
Creator: Hemphill, Libby, Otterbacher, Jahna
Date: 2011-11-19, 2012-02
Publisher: ACM Press
Description: Women and men communicate differently in both face-to- face and computer-mediated environments. We study linguistic...
Show moreWomen and men communicate differently in both face-to- face and computer-mediated environments. We study linguistic patterns considered gendered in reviews contributed to the Internet Movie Database. IMDb has been described as a male-majority community, in which females contribute fewer reviews and enjoy less prestige than males. Analyzing reviews posted by prolific males and females, we hypothesize that females adjust their communication styles to be in sync with their male counterparts. We find evidence that while certain characteristics of “female language” persevere over time (e.g., frequent use of pronouns) others (e.g., hedging) decrease with time. Surprisingly, we also find that males often increase their use of “female” features. Our results indicate, that even when they resemble men’s reviews linguistically, women’s reviews still enjoy less prestige and smaller audiences.
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Title: Tweet Acts: How Constituents Lobby Congress via Twitter
Creator: Hemphill, Libby, Roback, Andrew
Date: 2014, 2014
Description: Twitter is increasingly becoming a medium through which constituents can lobby their elected representatives in...
Show moreTwitter is increasingly becoming a medium through which constituents can lobby their elected representatives in Congress about issues that matter to them. Past research has focused on how citizens communicate with each other or how members of Congress (MOCs) use social media in general; our research examines how citizens communicate with MOCs. We contribute to existing literature through the careful examination of hundreds of citizen-authored tweets and the development of a categorization scheme to describe common strategies of lobbying on Twitter. Our findings show that contrary to past research that assumed citizens used Twitter to merely shout out their opinions on issues, citizens utilize a variety of sophisticated techniques to impact political outcomes.
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Title: 'Ain't No One Here But Us Social Forces' : Constructing the Social Responsibility of Engineers.
Creator: Davis, Michael
Date: 2011-04, 2011-06
Publisher: Springer
Description: There are many ways to avoid responsibility, for example, explaining what happens as the work of the gods, fate,...
Show moreThere are many ways to avoid responsibility, for example, explaining what happens as the work of the gods, fate, society, or the system. For engineers, “technology” or “the organization” will serve this purpose quite well. We may distinguish at least nine (related) senses of “responsibility”, the most important of which are: (a) responsibility-as-causation (the storm is responsible for flooding), (b) responsibility-as-liability (he is the person responsible and will have to pay), (c) responsibility-as-competency (he’s a responsible person, that is, he’s rational), (d) responsibility-as-office (he’s the responsible person, that is, the person in charge), and (e) a responsibility-as-domain-of-tasks (these are her responsibilities, that is, the things she is supposed to do). For all but the causal sense of responsibility, responsibility may be taken (in a relatively straightforward sense)—and generally is. Why then would anyone want to claim that certain technologies make it impossible to attribute responsibility to engineers (or anyone else)? In this paper, I identify seven arguments for that claim and explain why each is fallacious. The most important are: (1) the argument from “many hands”, (2) the argument from individual ignorance, and (3) the argument from blind forces. Each of these arguments makes the same fundamental mistake, the assumption that a certain factual situation, being fixed, settles responsibility, that is, that individuals, either individually or by some group decision, cannot take responsibility. I conclude by pointing out the sort of decisions (and consequences) engineers have explicitly taken responsibility for and why taking responsibility for them is rational, all things considered. There is no technological bar to such responsibility.
Science and Engineering Ethics.
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Title: They Aren't Like Me, They are Bad, and They are to Blame: A Theoretically-Informed Study of Stigma of Hoarding Disorder and Obsessive-Compulsive Disorder
Date: 2018, 2018
Publisher: Elsevier

Title: Transdiagnostic Emotional Vulnerabilities Linking Obsessive-Compulsive and Depressive Symptoms in a Community-Based Sample of Adolescents
Date: 2017, 2017
Publisher: Wiley Periodicals, Inc.
Description: Background: Transdiagnostic emotional vulnerabilities are suspected to underlie psychopathologic comorbidity but have received little...
Show moreBackground: Transdiagnostic emotional vulnerabilities are suspected to underlie psychopathologic comorbidity but have received little attention in adolescent emotional pathology literature. We examined distress tolerance, anxiety sensitivity, and anhedonia as concomitant transdiagnostic mechanisms that account for (i.e., statistically mediate) the covariance between adolescent obsessive-compulsive disorder (OCD) and major depressive disorder (MDD) symptoms. Method: Data on MDD, OCD, and the three aforementioned transdiagnostic vulnerabilities were collected from a community-based sample of 3,094 9th graders in a large metropolitan area and analyzed using mixed effects modeling to evaluate mediation effects. Results: Individually and when controlling for each other, all three transdiagnostic vulnerabilities mediated the relation between OCD and MDD symptoms both before and after adjusting for demographics. Conclusions: Distress tolerance, anxiety sensitivity, and anhedonia may be unique mechanisms accounting for comorbidity between OCD and MDD symptoms in youth. Longitudinal evaluation of these candidate transdiagnostic emotional vulnerabilities in adolescent OCD-MDD comorbidity is warranted.
Sponsorship: Grant sponsor: National Institute on Drug Abuse; Contract grant number: R01?DA033296.
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Title: Machine Learning at the Bureau of Labor Statistics
Date: 2019-11-21,
Description: Vinesh Kannan (CS '19) shares his experiences working as a...
Show moreVinesh Kannan (CS '19) shares his experiences working as a data science fellow at the Bureau of Labor Statistics (BLS). Vinesh worked on the team that produces occupation and wage data used by policymakers, hiring staff, job seekers, and researchers across the country. He helped improve machine learning systems at the BLS: automatically identifying problematic training data and classifying rare jobs. Vinesh offers advice for students who may be interested in applying for the 2020 Civic Digital Fellowship, a program that recruits university students at all levels to spend a summer working on civic technology projects with various federal agencies.
Sponsorship: College of Science, Department of Computer Science, Department of Applied Mathematics, Machine Learning at IIT
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Title: , From positivism to conventionalism: Comte, Renouvier, and Poincaré
Date: 2019, 2019
Publisher: Elsevier

Title: Examining Partnership-Health Associations Among Lesbian Women and Gay Men Using Population-Level Data
Date: 2019,
Description: Abstract...
Show moreAbstract Purpose: The aim was to provide the first broad assessment of partnership-health associations across partnership statuses among sexual minority individuals. Methods: Using population-level data from the 2016 U.S. Behavioral Risk Factor Surveillance System, specifically the 26 states/territories that assessed sexual orientation and gender identity, we ran analyses of covariance and logistic regressions to compare lesbian and gay individuals (N = 2963) of different partnership statuses in general health, physical health and health conditions, mental health, health behaviors, and healthcare access/utilization domains. Results: All omnibus and logistic regression models were significant (p < 0.001). Follow-up pairwise comparisons of mean differences across partnership groups revealed that in at least one variable in the general health, mental health, health behaviors, and healthcare access/utilization domains, married lesbian and gay individuals reported the best health, followed by partnered, single, and then divorced, separated, and widowed lesbian and gay individuals (p < 0.001). Exceptions included variables in the physical health and health conditions domain, the health behaviors of smoking and heavy drinking, and ever having an HIV test. When stratifying by sex, for both gay men and lesbian women being married or partnered related to the best health in at least one variable in each health domain, and in the majority of all outcome variables. Conclusion: This article provides the first evidence for partnership-health associations among gay and lesbian individuals based on a large-scale, multi-domain test of population-level data. Future research could examine temporal links between same-sex marriage legislation and health outcomes among sexual minority individuals.
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Title: Three agendas for changing the public stigma of mental illness.
Date: 2018, 2017
Publisher: American Psychological Association
Description: OBJECTIVE: Antistigma programs may be guided by 3 differing agendas: services (promote treatment engagement),...
Show moreOBJECTIVE: Antistigma programs may be guided by 3 differing agendas: services (promote treatment engagement), rights (help people achieve rightful goals), and self-worth (facilitate self-worth and efficacy). This study examined the construct validity of this perspective by examining the factor structure of importance ratings of the 3 agendas. The study examined how importance might be viewed differently by the population as a whole versus a subsample of people who reported previous experience with mental health services and hence could be directly harmed by stigma. METHODS: 373 individuals recruited using Mechanical Turk completed importance ratings for each of the 3 agendas. Measures of public stigma were completed to examine concurrent validity of importance ratings. Those who reported taking medications for a psychiatric disorder were divided into a separate group and completed a measure of self-stigma. RESULTS: Outcomes seemed to confirm the factor structure of the 3 agendas model thereby offering partial support for the framework. Group analyses showed the services agenda was viewed as more important than rights or self-worth. People with mental health experience viewed the services agenda as more important than the other 2. However, dividing the mental health group into low and high self-stigma revealed that those with low self-stigma rated the rights agenda as more important. Conclusions and Implication for Practice: Participants with lower self-stigma identify the harm brought by stigma and thus endorse rights and self-worth more than those with higher self-stigma. Implications of these findings are discussed to assist to prioritize agendas for public health campaigns.
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Title: Using Peer Navigators to Address the Integrated Healthcare Needs of African Americans with Serious Mental Illness
Date: 2017, 2017
Publisher: American Psychiatric Association
Description: Objective Impact of a peer navigator program (PNP) develop by a community based participatory research team was...
Show moreObjective Impact of a peer navigator program (PNP) develop by a community based participatory research team was examined on African Americans with serious mental illness who were homeless. Methods Research participants were randomized to PNP or a treatment-as-usual control group for one year. Data on physical and mental health, recovery, and quality of life were collected at baseline, 4, 8 and 12 months. Results Findings from group by trial ANOVAs of omnibus measures of the four constructs showed significant impact over the one year for participants in PNP compared to control described by small to moderate effect sizes. These differences emerged even though both groups showed significant improvements in reduced homelessness and insurance coverage. Conclusions Implications for improving in-the-field health care for this population are discussed. Whether these results occurred because navigators were peers per se needs to be examined in future research.
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