Dynamic Display of Changing Posterior in Bayesian Survival Analysis: The Software

We consider the problem of estimating an unknown distribution function in the presence of censoring under the conditions that a parametric model is believed to hold approximately. We use a Bayesian approach, in which the prior on is a mixture of Dirichlet distributions. A hyperparameter of the prior determines the extent to which this prior concentrates its mass around the parametric family. A Gibbs sampling algorithm to estimate the posterior distributions of the parameters of interest is reviewed. An importance sampling scheme enables us to use the output of the Gibbs sampler to very quickly recalculate the posterior when we change the hyperparameters of the prior. The calculations can be done sufficiently fast to enable the dynamic display of the changing posterior as the prior hyperparameters are varied. This paper provides a literate program completely documenting the code for performing the dynamic graphics.

Parallel processing and expert systems

Whether it be monitoring the thermal subsystem of Space Station Freedom, or controlling the navigation of the autonomous rover on Mars, NASA missions in the 1990s cannot enjoy an increased level of autonomy without the efficient implementation of expert systems. Merely increasing the computational speed of uniprocessors may not be able to guarantee that real-time demands are met for larger systems. Speedup via parallel processing must be pursued alongside the optimization of sequential implementations. Prototypes of parallel expert systems have been built at universities and industrial laboratories in the U.S. and Japan. The state-of-the-art research in progress related to parallel execution of expert systems is surveyed. The survey discusses multiprocessors for expert systems, parallel languages for symbolic computations, and mapping expert systems to multiprocessors. Results to date indicate that the parallelism achieved for these systems is small. The main reasons are (1) the body of knowledge applicable in any given situation and the amount of computation executed by each rule firing are small, (2) dividing the problem solving process into relatively independent partitions is difficult, and (3) implementation decisions that enable expert systems to be incrementally refined hamper compile-time optimization. In order to obtain greater speedups, data parallelism and application parallelism must be exploited

Simulating futures in extended common LISP

Stack-groups comprise the mechanism underlying implementation of multiprocessing in Extended Common LISP, i.e., running multiple quasi-simultaneous processes within a single LISP address space. On the other hand, the future construct of MULTILISP, an extension of the LISP dialect scheme, deals with parallel execution. The source of concurrency that future exploits is the overlap between computation of a value and use of the value. Described is a simulation of the future construct by an interpreter utilizing stack-group extensions to common LISP

Lisp, Jazz, Aikido -- Three Expressions of a Single Essence

The relation between Science (what we can explain) and Art (what we can't) has long been acknowledged and while every science contains an artistic part, every art form also needs a bit of science. Among all scientific disciplines, programming holds a special place for two reasons. First, the artistic part is not only undeniable but also essential. Second, and much like in a purely artistic discipline, the act of programming is driven partly by the notion of aesthetics: the pleasure we have in creating beautiful things. Even though the importance of aesthetics in the act of programming is now unquestioned, more could still be written on the subject. The field called "psychology of programming" focuses on the cognitive aspects of the activity, with the goal of improving the productivity of programmers. While many scientists have emphasized their concern for aesthetics and the impact it has on their activity, few computer scientists have actually written about their thought process while programming. What makes us like or dislike such and such language or paradigm? Why do we shape our programs the way we do? By answering these questions from the angle of aesthetics, we may be able to shed some new light on the art of programming. Starting from the assumption that aesthetics is an inherently transversal dimension, it should be possible for every programmer to find the same aesthetic driving force in every creative activity they undertake, not just programming, and in doing so, get deeper insight on why and how they do things the way they do. On the other hand, because our aesthetic sensitivities are so personal, all we can really do is relate our own experiences and share it with others, in the hope that it will inspire them to do the same. My personal life has been revolving around three major creative activities, of equal importance: programming in Lisp, playing Jazz music, and practicing Aikido. But why so many of them, why so different ones, and why these specifically? By introspecting my personal aesthetic sensitivities, I eventually realized that my tastes in the scientific, artistic, and physical domains are all motivated by the same driving forces, hence unifying Lisp, Jazz, and Aikido as three expressions of a single essence, not so different after all. Lisp, Jazz, and Aikido are governed by a limited set of rules which remain simple and unobtrusive. Conforming to them is a pleasure. Because Lisp, Jazz, and Aikido are inherently introspective disciplines, they also invite you to transgress the rules in order to find your own. Breaking the rules is fun. Finally, if Lisp, Jazz, and Aikido unify so many paradigms, styles, or techniques, it is not by mere accumulation but because they live at the meta-level and let you reinvent them. Working at the meta-level is an enlightening experience. Understand your aesthetic sensitivities and you may gain considerable insight on your own psychology of programming. Mine is perhaps common to most lispers. Perhaps also common to other programming communities, but that, is for the reader to decide..

Cobweb/3: A portable implementation

An algorithm is examined for data clustering and incremental concept formation. An overview is given of the Cobweb/3 system and the algorithm on which it is based, as well as the practical details of obtaining and running the system code. The implementation features a flexible user interface which includes a graphical display of the concept hierarchies that the system constructs

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape