Safe and Verifiable Design of Concurrent Java Programs

The design of concurrent programs has a reputation for being difficult, and thus potentially dangerous in safetycritical real-time and embedded systems. The recent appearance of Java, whilst cleaning up many insecure aspects of OO programming endemic in C++, suffers from a deceptively simple threads model that is an insecure variant of ideas that are over 25 years old [1]. Consequently, we cannot directly exploit a range of new CASE tools -- based upon modern developments in parallel computing theory -- that can verify and check the design of concurrent systems for a variety of dangers\ud such as deadlock and livelock that otherwise plague us during testing and maintenance and, more seriously, cause catastrophic failure in service. \ud Our approach uses recently developed Java class\ud libraries based on Hoare's Communicating Sequential Processes (CSP); the use of CSP greatly simplifies the design of concurrent systems and, in many cases, a parallel approach often significantly simplifies systems originally approached sequentially. New CSP CASE tools permit designs to be verified against formal specifications\ud and checked for deadlock and livelock. Below we introduce CSP and its implementation in Java and develop a small concurrent application. The formal CSP description of the application is provided, as well as that of an equivalent sequential version. FDR is used to verify the correctness of both implementations, their\ud equivalence, and their freedom from deadlock and livelock

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

Approximate Bayesian computation methods can be used to evaluate posterior distributions without having to calculate likelihoods. In this paper we discuss and apply an approximate Bayesian computation (ABC) method based on sequential Monte Carlo (SMC) to estimate parameters of dynamical models. We show that ABC SMC gives information about the inferability of parameters and model sensitivity to changes in parameters, and tends to perform better than other ABC approaches. The algorithm is applied to several well known biological systems, for which parameters and their credible intervals are inferred. Moreover, we develop ABC SMC as a tool for model selection; given a range of different mathematical descriptions, ABC SMC is able to choose the best model using the standard Bayesian model selection apparatus.Comment: 26 pages, 9 figure

Automatic generation of scheduling and communication code in real-time parallel programs

Inter-process communication and scheduling are notorious problem areas in the design of real-time systems. Using CASE tools, the system design phase will in general result in a system description in the form of parallel processes. Manual allocation of these processes to processors may result in error prone and/or slow communication code. Scheduling of the processes, necessary to meet timing constraints, is also a tedious task that takes many iterations. The described design tools result in code that is comparable in quality and performance with expert manual realization. Many network layers have been implemented to relieve the user from the low-level programming of communication software. However, the increase in user-friendliness is usually paid with performance degradation. The proposed approach combines user-friendliness with high performance by generating communication software that is tailor-made for the application. A similar approach is followed with the scheduling software. Schedulers in the form of a built-in a kernel are available all the time and cause overhead all the time. The proposed preprocessor tool generates scheduling software after analyzing the timing requirements of the particular application. This results in simple code for simple timing requirements and more complicated code for complex timing requirements. The tools have been implemented in Occam for use on a transputer. However, the results are valid for any distributed memory machine

Chromosomal location of human genes encoding major heat-shock protein HSP70

The HSP70 family of heat-shock proteins constitutes the major proteins synthesized in response to elevated temperatures and other forms of stress. In eukaryotes members of the HSP70 family also include a protein similar if not identical to bovine brain uncoating ATPase and glucose-regulated proteins. An intriguing relation has been established between expression of heat-shock proteins and transformation in mammalian cells. Elevated levels of HSP70 are found in some transformed cell lines, and viral and cellular gene products that are capable of transforming cells in vitro can also stimulate transcription of HSP70 genes. To determine the organization of this complex multigene family in the human genome, we used complementary approaches: Southern analysis and protein gels of Chinese hamster-human somatic cell hybrids, and in situ hybridization to human chromosomes. We demonstrate that functional genes encoding HSP70 proteins map to human chromosomes 6, 14, 21, and at least one other chromosome .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45535/1/11188_2005_Article_BF01534692.pd

Fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin with gemtuzumab ozogamicin improves event-free survival in younger patients with newly diagnosed aml and overall survival in patients with npm1 and flt3 mutations

Purpose To determine the optimal induction chemotherapy regimen for younger adults with newly diagnosed AML without known adverse risk cytogenetics. Patients and Methods One thousand thirty-three patients were randomly assigned to intensified (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin [FLAG-Ida]) or standard (daunorubicin and Ara-C [DA]) induction chemotherapy, with one or two doses of gemtuzumab ozogamicin (GO). The primary end point was overall survival (OS). Results There was no difference in remission rate after two courses between FLAG-Ida + GO and DA + GO (complete remission [CR] + CR with incomplete hematologic recovery 93% v 91%) or in day 60 mortality (4.3% v 4.6%). There was no difference in OS (66% v 63%; P = .41); however, the risk of relapse was lower with FLAG-Ida + GO (24% v 41%; P < .001) and 3-year event-free survival was higher (57% v 45%; P < .001). In patients with an NPM1 mutation (30%), 3-year OS was significantly higher with FLAG-Ida + GO (82% v 64%; P = .005). NPM1 measurable residual disease (MRD) clearance was also greater, with 88% versus 77% becoming MRD-negative in peripheral blood after cycle 2 (P = .02). Three-year OS was also higher in patients with a FLT3 mutation (64% v 54%; P = .047). Fewer transplants were performed in patients receiving FLAG-Ida + GO (238 v 278; P = .02). There was no difference in outcome according to the number of GO doses, although NPM1 MRD clearance was higher with two doses in the DA arm. Patients with core binding factor AML treated with DA and one dose of GO had a 3-year OS of 96% with no survival benefit from FLAG-Ida + GO. Conclusion Overall, FLAG-Ida + GO significantly reduced relapse without improving OS. However, exploratory analyses show that patients with NPM1 and FLT3 mutations had substantial improvements in OS. By contrast, in patients with core binding factor AML, outcomes were excellent with DA + GO with no FLAG-Ida benefit

Parallel and Distributed Computing in Education (Invited Talk)

The natural world is certainly not organised through a central thread of control. Things happen as the result of the actions and interactions of unimaginably large numbers of independent agents, operating at all levels of scale from nuclear to astronomic. Computer systems aiming to be of real use in this real world need to model, at the appropriate level of abstraction, that part of it for which it is to be of service. If that modelling can reflect the natural concurrency in the system, it ought to be much simpler Yet, traditionally, concurrent programming is considered to be an advanced and difficult topic - certainly much harder than serial computing which, therefore, needs to be mastered first. But this tradition is wrong. This talk presents an intuitive, sound and practical model of parallel computing that can be mastered by undergraduate students in the first year of a computing (major) degree. It is based upon Hoare's mathematical theory of Communicating Sequential Processes (CSP), but does not require mathematical maturity from the students - that maturity is pre-engineered in the model. Fluency can be quickly developed in both message-passing and shared-memory concurrency, whilst learning to cope with key issues such as race hazards, deadlock, livelock, process starvation and the efficient use of resources. Practical work can be hosted on commodity PCs or UNIX workstations using either Java or the Occam multiprocessing language. Armed with this maturity, students are well-prepared for coping with real problems on real parallel architectures that have, possibly, less robust mathematical foundations

An Architecture for Modelling Emergence in CA-Like Systems

We consider models of emergence, adding downward causation to conventional models where causation permeates from low-level elements to high-level behaviour. We describe an architecture and prototype simulation medium for tagging and modelling emergent features in CA-like systems. This is part of ongoing work on engineering emergence