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Title: Mode Poset Probability Polytopes, AS2015 Special Issue articles: This issue includes a series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics Conference held in Genoa, Italy, in June 2015. Special issue guest editors: Piotr Zwiernik and Fabio Rapallo.
Creator: Montúfar, Guido, Rauh, Johannes
Date: 2016, 2016-07-12
Description: A mode of a probability distribution is an elementary event that has more probability mass than each of its direct neighbors, with respect to...
Show moreA mode of a probability distribution is an elementary event that has more probability mass than each of its direct neighbors, with respect to some vicinity structure on the set of elementary events. The mode inequalities cut out a polytope from the simplex of probability distributions. Related to this is the concept of strong modes. A strong mode is an elementary event that has more probability mass than all its direct neighbors together. The set of probability distributions with a given set of strong modes is again a polytope. We study the vertices, the facets, and the volume of such polytopes depending on the sets of (strong) modes and the vicinity structures.
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Collection: Journal of Algebraic Statistics

Title: L-cumulants, L-cumulant embeddings and algebraic statistics, AS2012 Special Volume, part 1: 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.
Creator: Zwiernik, Piotr, AS2012 Special Volume, part 1: This issue includes a second series of papers from talks, posters and collaborations resulting from and
Description: Focusing on the discrete probabilistic setting we generalize the combinatorial definition of cumulants to L-cumulants. This generalization...
Show moreFocusing on the discrete probabilistic setting we generalize the combinatorial definition of cumulants to L-cumulants. This generalization keeps all the desired properties of the classical cumulants like semi-invariance and vanishing for independent blocks of random variables. These properties make L-cumulants useful for the algebraic analysis of statistical models. We illustrate this for general Markov models and hidden Markov processes in the case when the hidden process is binary. The main motivation of this work is to understand cumulant-like coordinates in alge- braic statistics and to give a more insightful explanation why tree cumulants give such an elegant description of binary hidden tree models. Moreover, we argue that L-cumulants can be used in the analysis of certain classical algebraic varieties.
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Collection: Journal of Algebraic Statistics

Title: Generalized Fréchet Bounds for Cell Entries in Multidimensional Contingency Tables, Special Volume in honor of memory of S.E.Fienberg
Creator: Richards, Donald, Uhler, Caroline
Description: We consider the lattice, L, of all subsets of a multidimensional contingency table and establish the properties of monotonicity and...
Show moreWe consider the lattice, L, of all subsets of a multidimensional contingency table and establish the properties of monotonicity and supermodularity for the marginalization function, n(·), on L. We derive from the supermodularity of n(·) some generalized Fr ́echet inequalities comple- menting and extending inequalities of Dobra and Fienberg. Further, we construct new monotonic and supermodular functions from n(·), and we remark on the connection between supermodularity and some correlation inequalities for probability distributions on lattices. We also apply an inequal- ity of Ky Fan to derive a new approach to Fr ́echet inequalities for multidimensional contingency tables.
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Collection: Journal of Algebraic Statistics

Title: Maximal Length Projections in Group Algebras with Applications to Linear Rank Tests of Uniformity
Creator: Bargagliotti, Anna E., Orrison, Michael
Description: Let G be a finite group, let CG be the complex group algebra of G, and let p ∈ CG. In this paper, we show how to construct submodules S of CG...
Show moreLet G be a finite group, let CG be the complex group algebra of G, and let p ∈ CG. In this paper, we show how to construct submodules S of CG of a fixed dimension with the property that the orthogonal projection of p onto S has maximal length. We then provide an example of how such submodules for the symmetric group Sn can be used to create new linear rank tests of uniformity in statistics for survey data that arises when respondents are asked to give a complete ranking of n items.
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Collection: Journal of Algebraic Statistics

Title: Connectivity for 3 x 3 x K contingency tables
Creator: Sumi, Toshio, 2012
Description: We consider an exact sequential conditional test for three-way conditional test of no interaction. At each time τ, the test uses as the...
Show moreWe consider an exact sequential conditional test for three-way conditional test of no interaction. At each time τ, the test uses as the conditional inference frame the set F(Hτ) of all tables with the same three two-way marginal tables as the obtained table Hτ . For 3 × 3 × K tables, we propose a method to construct F(Hτ) from F(Hτ−1). This enables us to perform efficiently the sequential exact conditional test. The subset Sτ of F (Hτ ) consisting of s + Hτ − Hτ −1 for s ∈ F(Hτ−1) contains Hτ , where the operations + and − are defined elementwise. Our argument is based on the minimal Markov basis for 3 × 3 × K contingency tables and we give a minimal subset M of some Markov basis which has the property that F (Hτ ) = {s − m | s ∈ Sτ , m ∈ M}.
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Collection: Journal of Algebraic Statistics

Title: Matrix Completion for the Independence Model
Creator: Kubjas, Kaie, Rosen, Zvi
Description: We investigate the problem of completing partial matrices to rank-one matrices in the standard simplex ∆mn−1. The motivation for studying this...
Show moreWe investigate the problem of completing partial matrices to rank-one matrices in the standard simplex ∆mn−1. The motivation for studying this problem comes from statistics: A lack of eligible completion can provide a falsification test for partial observations to come from the independence model. For each pattern of specified entries, we give equations and inequalities which are satisfied if and only if an eligible completion exists. We also describe the set of valid completions, and we optimize over this set.
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Collection: Journal of Algebraic Statistics

Title: One example of general unidentifiable tensors
Creator: Chiantini, Luca, Mella, Massimiliano, Ottaviani, Giorgio
Description: Abstract. Theidentifiabilityofparametersinaprobabilisticmodelisacrucialnotioninstatistical inference. We prove that a general tensor of rank 8...
Show moreAbstract. Theidentifiabilityofparametersinaprobabilisticmodelisacrucialnotioninstatistical inference. We prove that a general tensor of rank 8 in C3 ⊗ C6 ⊗ C6 has at least 6 decompositions as sum of simple tensors, so it is not 8-identifiable. This is the highest known example of balanced tensors of dimension 3, which are not k-identifiable, when k is smaller than the generic rank.
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Collection: Journal of Algebraic Statistics

Title: Hilbert Polynomial of the Kimura 3-Parameter Model, AS2012 Special Volume, part 1: 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.
Creator: Kubjas, Kaie, inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July
Description: In [2] Buczyn ́ska and Wi ́sniewski showed that the Hilbert polynomial of the algebraic variety associated to the Jukes-Cantor binary model on...
Show moreIn [2] Buczyn ́ska and Wi ́sniewski showed that the Hilbert polynomial of the algebraic variety associated to the Jukes-Cantor binary model on a trivalent tree depends only on the number of leaves of the tree and not on its shape. We ask if this can be generalized to other group-based models. The Jukes-Cantor binary model has Z2 as the underlying group. We consider the Kimura 3-parameter model with Z2 × Z2 as the underlying group. We show that the generalization of the statement about the Hilbert polynomials to the Kimura 3-parameter model is not possible as the Hilbert polynomial depends on the shape of a trivalent tree.
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Collection: Journal of Algebraic Statistics

Title: Assessing Graduate Student Progress in Engineering Ethics
Creator: Davis, Michael, Feinerman, Alan
Date: 2010-11-10, 2011
Publisher: Springer
Description: Under a grant from the National Science Foundation, the authors (and others) undertook to integrate ethics into graduate engineering classes...
Show moreUnder a grant from the National Science Foundation, the authors (and others) undertook to integrate ethics into graduate engineering classes at three universities—and to assess success in a way allowing comparison across classes (and institutions). This paper describes the attempt to carry out that assessment. Standard methods of assessment turned out to demand too much class time. Under pressure from instructors, the authors developed an alternative method that is both specific in content to individual classes and allows comparison across classes. Results are statistically significant for ethical sensitivity and knowledge. They show measurable improvement in a single semester.
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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, society, or the system. For...
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: A Case of "Gray Plagiarism" from the History of the History of Computing
Creator: Davis, Michael
Date: 2006, 2006
Publisher: Plagiary : Cross-Disciplinary Studies in Plagiarism, Fabrication, and Falsfication
Description: Claiming as one's own what one knows to be the discovery of another is certainly plagiarism. But what about merely failing to acknowledge the...
Show moreClaiming as one's own what one knows to be the discovery of another is certainly plagiarism. But what about merely failing to acknowledge the work of another where one does not give the impression that the discovery is one's own? Does it matter how easy it was to make the discovery? This paper analyzes a case in this gray area in academic ethics. The focus is not on the failure to attribute itself but on the attempt of an independent scholar who, believing himself to be the victim of "gray plagiarism”, sought a forum in which to make his complaint. The story could be told from several perspectives. I shall tell it primarily from the perspective of the complainant, an outsider, because I believe that way of telling it best reveals the need to think more deeply about how we (acting for the universities to which we belong) assign credit, especially to scholars outside, and about how we respond when someone complains of a failure to assign credit. My purpose is not to indict individuals but to change a system. This paper updates a case I first described in 1993.
Davis, M. (2006). “Gray Plagiarism”: A Case from the History of the History of Computing. Plagiary: Cross‐Disciplinary Studies in Plagiarism, Fabrication, and Falsification, 1 (7): 1‐18.
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Title: Do the Professional Ethics of Chemists and Engineers Differ ?
Creator: Davis, Michael
Date: 2011, 2002
Publisher: HYLE - International Journal for Philosophy of Chemistry
Description: This paper provides a sketch of my general way of understanding professions and then applies that sketch to a specific question, how to...
Show moreThis paper provides a sketch of my general way of understanding professions and then applies that sketch to a specific question, how to distinguish between two very similar professions, chemistry and engineering. I argue that the professional ethics of chemists do differ from the professional ethics of engineers and that the differences are important. The argument requires definition of both ‘ethics’ and ‘profession’ – as well delving into the details of chemistry and engineering.
HYLE – International Journal for Philosophy of Chemistry Vol. 8, No . 1 (2002) http://www.hyle.org/journal/issues/8-1/davis.htm
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Title: Ethics in the Details : Communicating Engineering Ethics via Micro-Insertion
Creator: Davis, Michael, Riley, Kathryn, Cox, Apryl, Maciukenas, James
Date: 2009, 2009
Publisher: IEEE
Description: Work is described on a National Science Foundation grant that supports the development, assessment, and dissemination of “micro-insertion”...
Show moreWork is described on a National Science Foundation grant that supports the development, assessment, and dissemination of “micro-insertion” problems designed to integrate ethics into the graduate engineering curriculum. In contrast to traditional modular approaches to ethics pedagogy, micro-insertions introduce ethical issues by means of a “low-dose” approach. Following a description of the micro-insertion approach, we outline the workshop structure being used to teach engineering faculty and graduate students how to write micro-insertions for graduate engineering courses, with particular attention to how the grant develops engineering students’ (and faculty members’) ability to communicate across disciplinary boundaries. We also describe previous and planned methods for assessing the effectiveness of micro-insertions. Finally, we explain the role that technical communication faculty and graduate students are playing as part of the grant team, speciﬁcally in developing an Ethics In-Basket that will disseminate micro-insertions developed during the grant.
IEEE Transactions on Professional Communications Vol. 52, Issue 1, pp. 95-108.
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Title: IIT's Workshops for Integrating Ethics into Technical Courses : Some Lessons Learned
Creator: Davis, Michael
Date: 2006, 2006
Publisher: Philosophy Documentation Center
Description: In 1990, IIT's Center for the Study of Ethics in the Professions received a grant of more than $210,000 from the National Science Foundation...
Show moreIn 1990, IIT's Center for the Study of Ethics in the Professions received a grant of more than $210,000 from the National Science Foundation to try a campus-wide approach to integrating professional ethics into its technical curriculum; in 1996, the Center received another $100,000 to continue the project, with the emphasis on passing along to other institutions what was learned at IIT; and, in 2000, the Center received a third grant for three years, with the same emphasis, for $244,000. Between 1990 and 2004, more than 160 faculty “graduated” from the workshop and another dozen or so attended as unofficial volunteers. I was the principal investigator under all three grants, but shared the work with three co-PIs, the “we” in what follows. Though I generally prefer to emphasize what we did right, emphasizing what I now think we should have done differently should be more helpful here. There are at least three reasons why that should be so. First, I have already made many presentations, including several in Japan, arguing the (very real) merits of what we did. While repetition can help to make a point, sooner or later, though usually sooner, the effect of repetition ceases to repay the effort. I fear I may have reached that point. Second, I have nowhere before said much about what now seem mistakes —or, at least, lost opportunities. Discussing them here should add to what is known about ethics workshops. Adding to that knowledge seems worthy in itself. Third, you are already committed to ethics across the curriculum. The question before you now is how to carry out that commitment. I believe there is much to learn from our mistakes. We certainly learned much from the mistakes of those whose workshops we studied before undertaking our own. Running that workshop included the following activities: recruiting, scheduling, content, and research. For each activity, I will first briefly explain what we did and then what I now think we should have done.
Teaching Ethics, Vol. 7, Issue 2, 1-14
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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 issues inherent in...
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: University Research and the Wages of Commerce.
Creator: Davis, Michael
Date: 2006, 1991
Publisher: Notre Dame Law School
Description: This is a response to a talk given by Ralph Nader on "The Relationship Between the University and Business and Industry." The author...
Show moreThis is a response to a talk given by Ralph Nader on "The Relationship Between the University and Business and Industry." The author acknowledges that a problems do come up when universities have close ties with industry. However, the author explores the reality of these partnerships through some examples of his own experience at the Illinois Institute of Technology.
Journal of College and University Law, Vol. 19, No. 2, 1991. pp. 29-38.
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Title: The Usefulness of Moral Theory in Practical Ethics: A Question of Comparative Cost (A Response to Harris)
Creator: Davis, Michael
Date: 2009, 2009
Publisher: Philosophy Documentation Center
Description: I find myself agreeing with almost everything in Harris’s defense of moral theory except the end: moral theories can often be useful in...
Show moreI find myself agreeing with almost everything in Harris’s defense of moral theory except the end: moral theories can often be useful in resolving moral dilemmas. Both students and practitioners of practical ethics should be constantly reminded of this, because in practical ethics we need all of the help we can get. If (as it seems) these two sentences state the conclusion, Harris has committed a non sequitur. While making a good argument for the general usefulness of moral theory in practical ethics, he has not made any argument for its usefulness to students or practitioners as such. He has simply assumed that what is true of some who engage in practical ethics is true of students and practitioners in particular. In theory, of course, moral theory should be useful even to students and practitioners, helping them to identify issues they might have overlooked, to seek information they might otherwise not have thought relevant, and to formulate courses of action that might not otherwise have occurred to them. In practice, however, moral theory will seldom, if ever, be useful (or, at least, useful enough). We do not (as Harris claims) need all the help we can get in practical ethics. What we need is all the help we can get at reasonable cost. We should only invest the time and effort needed to learn and use moral theory when the investment is no greater than for an otherwise equally useful alternative. Since there is at least one equally useful alternative requiring much less investment, the time and effort students and practitioners would have to invest in moral theory will (in general) be much greater than necessary for their purposes. So, neither students nor practitioners need moral theory.
Teaching Ethics Vol. 10, Issue 1, pp. 69-78
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Title: Professionalism Means Putting Your Profession First
Creator: Davis, Michael
Date: 2007, 1988
Publisher: Georgetown School of Law
Description: Ask a lawyer what "professionalism" means and you are likely to hear that professionalism means putting your client first or acting as an...
Show moreAsk a lawyer what "professionalism" means and you are likely to hear that professionalism means putting your client first or acting as an officer of the court. Only rarely will a lawyer say that professionalism means putting justice first. Never, I think, will a lawyer even suggest that professionalism means putting your profession first. Yet this is the thesis of this paper. The paper has three parts. Section I makes certain distinctions necessary to prevent misunderstanding my thesis. Section II and III develop the thesis into a conception of professionalism. Sections IV and V use that conception to help with the most difficult of undertakings, justifying professional discipline to someone convicted of professional misconduct which harmed neither her client nor an identifiable third party.
Georgetown Journal of Legal Ethics. Vol. 2, Issue 1. Summer 1988. pp.341-357.
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Title: Optimizing Cell-Free Protein Synthesis for Increased Yield and Activity of Colicins
Creator: Jin, Xing, Kightlinger, Weston, Hong, Seok Hoon
Date: 2019
Publisher: MDPI
Description: Colicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics....
Show moreColicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics. Cell-free protein synthesis (CFPS) is a useful production platform for toxic proteins because it eliminates the need to maintain cell viability, a common problem in cell-based production. Previously, we demonstrated that colicins produced by CFPS based on crude Escherichia coli lysates are e?ective in eradicating antibiotic-tolerant bacteria known as persisters. However, we also found that some colicins have poor solubility or low cell-killing activity. In this study, we improved the solubility of colicin M from 16% to nearly 100% by producing it in chaperone-enriched E. coli extracts, resulting in enhanced cell-killing activity. We also improved the cytotoxicity of colicin E3 by adding or co-expressing the E3 immunity protein during the CFPS reaction, suggesting that the E3 immunity protein enhances colicin E3 activity in addition to protecting the host strain. Finally, we con?rmed our previous ?nding that active colicins can be rapidly synthesized by observing colicin E1 production over time in CFPS. Within three hours of CFPS incubation, colicin E1 reached its maximum production yield and maintained high cytotoxicity during longer incubations up to 20 h. Taken together, our ?ndings indicate that colicin production can be easily optimized for improved solubility and activity using the CFPS platform.
Sponsorship: NIH R15AI130988
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Title: Controlling biofilms using synthetic biology approaches
Creator: Fang, Kuili, Park, Oh-Jin, Hong, Seok Hoon
Date: 2020
Description: Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene...
Show moreBacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of bio?lms due to the non-growing nature of bio?lm bacteria and the physical barrier provided by the extracellular matrix, eradicating bio?lms is a very di?cult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling bio?lms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate bio?lms via protein engineering of bio?lm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables bene?cial applications of bio?lms through the production of biomaterials and patterning bio?lms with speci?c temporal and spatial structures. Advances in synthetic biology will add novel bio?lm functionalities for future therapeutic, biomanufacturing, and environmental applications.
Sponsorship: NIH-R15AI130988, NSF CBET-1917130
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