DADO: A Parallel Processor for Expert Systems

DADO is a parallel, tree-structured machine designed to provide significant performance improvements in the execution of large expert systems implemented in production system form. A full-scale version of the DADO machine would comprise a large (on the order of a hundred thousand) set of processing elements (PE's), each containing its own processor, a small amount (16K bytes, in the current prototype design) of local random access memory, and a specialized I/O switch. The PE's are introduced to form a complete binary tree. This paper describes the application domain of the DADO machine and the rationale for its design. We then focus on the machine architecture and detail the hardware design of a moderately large prototype comprising 1023 microprocessors currently under development at Columbia University. We conclude with very encouraging performance statistics recently calculated from an analysis of extensive simulations of the system

DADO: A Parallel Processor for Expert Systems

DADO is a parallel, tree-structured machine designed to provide significant performance improvements in the execution of large expert systems implemented in production system form. A full-scale version of the DADO machine would comprise a large (on the order of a hundred thousand) set of processing elements (PE's), each containing its own processor, a small amount (16K bytes, in the current prototype design) of local random access memory, and a specialized I/O switch. The PE's are introduced to form a complete binary tree. This paper describes the application domain of the DADO machine and the rationale for its design. We then focus on the machine architecture and detail the hardware design of a moderately large prototype comprising 1023 microprocessors currently under development at Columbia University. We conclude with very encouraging performance statistics recently calculated from an analysis of extensive simulations of the system

Predicting Combinatorial Binding of Transcription Factors to Regulatory Elements in the Human Genome by Association Rule Mining

Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cisregulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regulate gene expression in concert by identifying over-represented combinations of sequence motifs that occur together in the genome. In order to detect combinations of transcription factor binding motifs, we developed a data mining approach based on the use of association rules, which are typically used in market basket analysis. We scored each segment of the genome for the presence or absence of each of 83 transcription factor binding motifs, then used association rule mining algorithms to mine this dataset, thus identifying frequently occurring pairs of distinct motifs within a segment. Results: Support for most pairs of transcription factor binding motifs was highly correlated across different chromosomes although pair significance varied. Known true positive motif pairs showed higher association rule support, confidence, and significance than background. Our subsets of high-confidence, high-significance mined pairs of transcription factors showed enrichment for co-citation in PubMed abstracts relative to all pairs, and the predicted associations were often readily verifiable in the literature. Conclusion: Functional elements in the genome where transcription factors bind to regulate expression in a combinatorial manner are more likely to be predicted by identifying statistically and biologically significant combinations of transcription factor binding motifs than by simply scanning the genome for the occurrence of binding sites for a single transcription factor.NIAAA Alcohol Training GrantNational Science FoundationCellular and Molecular Biolog

Performance Analysis of Two Competing DADO PE Designs

In parallel processing, useful computation is performed by having a number or processors computing values and communicating these results to neighboring processors. It is a crucial design issue in any parallel processing architecture to determine the optimal balance or resources for competing requirements of typical problems to be solved by the device, i.e. computation versus communication. For example, in a highly parallel machine consisting of many individual processing elements (PE's), there is a trade ofr between the complexity of the constituent PE's and the number of such elements which may be embedded in a fixed silicon area. Part or the PE's circuitry must be dedicated to communication processing. Increasing the ability and the speed at which a PE can perform communication can be done, but only at the expense or the number of processors on a chip. DADO is a large scale VLSI computer designed for the rapid execution of AI production systems. This paper analyses the nature of the instruction stream expected to be executed on DADO for production system applications, with emphasis placed on the number or processors in the machine and the size of the problem. We describe four different proposed methods of handling I/O and their queueing network models. The models were carefully simulated to determine which I/O scheme and its resulting circuit complexity is best suited (most efficient) with respect to the DADO instruction stream

More Rules May Mean Faster Parallel Execution

In this brief paper we report a simple scheme to extract implicit parallelism in the low-level match phase of the parallel execution of production system programs. The essence of the approach is to replicate rules while introducing new constraints within each copy to restrict each individual rule to match a potentially smaller set of data elements. Speed up is achieved by matching each copy of a rule in parallel. Variations of this approach may be applicable to logic-based programming systems, such as PROLOG, executed in a parallel environment. Indeed, sequential implementations of OPS-style production systems based on the RETE match algorithm may enjoy performance advantages as well. This scheme may be implemented by a simple preprocessing stage which requires no modification to the underlying match algorithms

The Do-loop Considered Harmful in Production System Programming

In this paper we focus on some aspects of Expert System programming. In particular we consider some of the language constructs which from part of a new production system language known as Herbal that we are developing at Columbia University. These language constructs greatly increase the expressiveness of a typical production system language and can be efficiently executed on a para11el machine. We briefly describe the DADO machine under development at Columbia University and J basic algorithm for production system execution for that machine. We conclude with a discussion of some performance Statistics recently calculated from m _analysis of production systems simulations and describe the expected effects of our added language constructs on these statistics

Programming the DADO Machine: An Introduction to PPL/M

DADO (Stolfo and Shaw, 1982) is a highly parallel, tree-structured machine designed to provide significant performance improvements in the execution of Artificial Intelligence software. The DADO prototype, currently being constructed at Columbia University, comprises 1023 processing elements (PE's) each consisting of an Intel 8751 microcomputer chip and an Intel 2186 8K by 8 RAM chip. The PE's are interconnected in a complete binary tree. A full version of DADO would comprise on the order of a hundred thousand PE's each consisting ot a much smaller amount ot local memory, roughly 2K bytes of RAM. (The 8K RAM employed in the DADO prototype was chosen to allow a modest amount of flexibility in designing and implementing the software base for the full version of DADO.) In addition, a specialized combinatorial I/O switch is incorporated in the full DADO design to perform the most basic communication primitives at much higher speeds than is possible with sequential logic, as it is implemented on the prototype machine