Marty J. Wolf

TrExML: a maximum-likelihood approach for extensive tree-space exploration

MOTIVATION Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified. RESULTS This paper presents the Advanced Stepwise Addition Algorithm for exploring tree-space and two algorithms for generating all binary trees on a set of sequences. The Advanced Stepwise Addition Algorithm has been implemented in TrExML, a phylogenetic program for maximum-likelihood analysis of nucleotide sequences. TrExML is shown to be more effective at finding near optimal trees than a similar program, fastDNAml, implying that TrExML offers a better approach to account for phylogenetic uncertainty than has previously been possible. A program, TreeGen, is also described; it generates binary trees on a set of sequences allowing for extensive exploration of tree-space using other programs. AVAILABILITY TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html.

AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method

Heuristics for the NP-complete problem of calculating the optimal phylogenetic tree for a set of aligned rRNA sequences based on the maximum likelihood method are computationally expensive. In most existing algorithms, the tree evaluation and branch length optimization functions, calculating the likelihood value for each tree topology examined in the search space, account for the greatest part of the overall computation time. This paper introduces AxML, a program derived from fastDNAml, incorporating a fast topology evaluation junction. The algorithmic optimizations introduced, represent a general approach for accelerating this function and are applicable to both sequential and parallel phylogeny programs, irrespective of their search space strategy. Therefore, their integration into three existing phylogeny programs rendered encouraging results. Experimental results on conventional processor architectures show a global run time improvement of 35% up to 47% for the various test sets and program versions we used.

The ethics of designing artificial agents

In their important paper “Autonomous Agents”, Floridi and Sanders use “levels of abstraction” to argue that computers are or may soon be moral agents. In this paper we use the same levels of abstraction to illuminate differences between human moral agents and computers. In their paper, Floridi and Sanders contributed definitions of autonomy, moral accountability and responsibility, but they have not explored deeply some essential questions that need to be answered by computer scientists who design artificial agents. One such question is, “Can an artificial agent that changes its own programming become so autonomous that the original designer is no longer responsible for the behavior of the artificial agent?” To explore this question, we distinguish between LoA1 (the user view) and LoA2 (the designer view) by exploring the concepts of unmodifiable, modifiable and fully modifiable tables that control artificial agents. We demonstrate that an agent with an unmodifiable table, when viewed at LoA2, distinguishes an artificial agent from a human one. This distinction supports our first counter-claim to Floridi and Sanders, namely, that such an agent is not a moral agent, and the designer bears full responsibility for its behavior. We also demonstrate that even if there is an artificial agent with a fully modifiable table capable of learning* and intentionality* that meets the conditions set by Floridi and Sanders for ascribing moral agency to an artificial agent, the designer retains strong moral responsibility.

Developing artificial agents worthy of trust: Would you buy a used car from this artificial agent?

There is a growing literature on the concept of e-trust and on the feasibility and advisability of “trusting” artificial agents. In this paper we present an object-oriented model for thinking about trust in both face-to-face and digitally mediated environments. We review important recent contributions to this literature regarding e-trust in conjunction with presenting our model. We identify three important types of trust interactions and examine trust from the perspective of a software developer. Too often, the primary focus of research in this area has been on the artificial agents and the humans they may encounter after they are deployed. We contend that the humans who design, implement, and deploy the artificial agents are crucial to any discussion of e-trust and to understanding the distinctions among the concepts of trust, e-trust and face-to-face trust.

Accelerating Parallel Maximum Likelihood-Based Phylogenetic Tree Calculations Using Subtree Equality Vectors

Heuristics for calculating phylogenetic trees for a large sets of aligned rRNA sequences based on the maximum likelihood method are computationally expensive. The core of most parallel algorithms, which accounts for the greatest part of computation time, is the tree evaluation function, that calculates the likelihood value for each tree topology. This paper describes and uses Subtree Equality Vectors (SEVs) to reduce the number of required floating point operations during topology evaluation. We integrated our optimizations into various sequential programs and into parallel fastDNAml, one of the most common and efficient parallel programs for calculating large phylogenetic trees. Experimental results for our parallel program, which renders exactly the same output as parallel fastDNAml show global runtime improvements of 26% to 65%. The optimization scales best on clusters of PCs, which also implies a substantial cost saving factor for the determination of large trees.

On two-path convexity in multipartite tournaments

In the context of two-path convexity, we study the rank, Helly number, Radon number, Caratheodory number, and hull number for multipartite tournaments. We show the maximum Caratheodory number of a multipartite tournament is 3. We then derive tight upper bounds for rank in both general multipartite tournaments and clone-free multipartite tournaments. We show that these same tight upper bounds hold for the Helly number, Radon number, and hull number. We classify all clone-free multipartite tournaments of maximum Helly number, Radon number, hull number, and rank.

On the meaning of free software

To many who develop and use free software, the GNU General Public License represents an embodiment of the meaning of free software. In this paper we examine the definition and meaning of free software in the context of three events surrounding the GNU General Public License. We use a case involving the GPU software project to establish the importance of Freedom 0 in the meaning of free software. We analyze version 3 of the GNU General Public License and conclude that although a credible case can be made that the added restrictions are consistent with the definition of free software, the case requires subtle arguments. Strong arguments against the added restrictions are less subtle, and may therefore be more convincing to many users and developers. We also analyze the Affero General Public License and conclude that it is inconsistent with the definition of free software.

Ethical issues in open source software

In this essay we argue that the current social and ethical structure in the Open Source Software (OSS) Community stem from its roots in academia. The individual developers experience a level of autonomy similar to that of a faculty member. Furthermore, we assert that the Open Source Software Community’s social structure demands benevolent leadership. We argue that it is difficult to pass off low quality open source software as high quality software and that the Open Source development model offers strong accountability. Finally, we argue that Open Source Software introduces ethical challenges for universities and the software development community.

Artificial Agents, Cloud Computing, and Quantum Computing: Applying Floridi’s Method of Levels of Abstraction

In his paper “On the Intrinsic Value of Information Objects and the Infosphere,” Luciano Floridi asserts that the goal of Information Ethics (IE) “is to fill an ‘ethical vacuum’ brought to light by the ICT revolution, to paraphrase Moor” (1985). He claims “IE will prove its value only if its applications bear fruit. This is the work that needs to be done in the near future” (Floridi 2002). Our chapter proposes to do part of that work. Initially we focus on Floridi’s Method of Levels of Abstraction (LoA). We begin by examining his methodology as it was first developed with J. W. Sanders in “The Method of Abstraction” (Floridi and Sanders 2004) and expanded in “The Method of Levels of Abstraction” (Floridi 2008a, b). Then we will demonstrate the general applicability and ethical utility of the method of levels of abstraction by considering three different computational paradigms: artificial agents, cloud computing, and quantum computing. In particular, we examine artificial agents as systems that embody the traditional digital computer (modeled as a single Turing machine). This builds on previous work by Floridi and Sanders (2004) and Grodzinsky et al. (2008). New contributions of this chapter include the application of the method of levels of abstraction to the developing paradigm of cloud computing and to the nascent paradigm of quantum computing. In all three paradigms, we emphasize aspects that highlight ethical issues.

The instructional information processing account of digital computation

What is nontrivial digital computation? It is the processing of discrete data through discrete state transitions in accordance with finite instructional information. The motivation for our account is that many previous attempts to answer this question are inadequate, and also that this account accords with the common intuition that digital computation is a type of information processing. We use the notion of reachability in a graph to defend this characterization in memory-based systems and underscore the importance of instructional information for digital computation. We argue that our account evaluates positively against adequacy criteria for accounts of computation.