We consider the problem of reverse-engineering dynamic models of biochemical networks from experimental data using polynomial dynamic systems. In earlier work, we developed an algorithm to identify minimal wiring diagrams, that is, directed graphs that represent the causal relationships between network variables. Here we extend this algorithm to identify a most likely dynamic model from the set...

One of the greatest aspirations of the human mind has been to realize machines that surpass its cognitive intelligence. The rapid expansion in computing power, about to exceed the equivalent of the human brain, has yet to produce such a machine. The article by Neftci et al. in PNAS (1) offers a refreshing and humbling reminder that the brain’s cognition does not arise from exacting digital prec...

We propose a new design for inspection and reverse engineering environments. We have designed and experimented with such an environinent for capturing sense data of niechaniccil parts in an intelligent way. We construct a sensing -+ CAD interface for the automatic recoiistruction of parts from visual data. We briefly discuss the use of the dynamic recursive finite state machine (DRFSM) as a new...

Microarray technologies, which enable the simultaneous measurement of all RNA transcripts in a cell, have spawned the development of algorithms for reverse-engineering transcription control networks. In this article, we classify the algorithms into two general strategies: physical modeling and influence modeling. We discuss the biological and computational principles underlying each strategy, a...

Reverse engineering the variability of an existing system is a challenging activity. The architect knowledge is essential to identify variation points and explicit constraints between features, for instance in feature models (FMs), but the manual creation of FMs is both timeconsuming and error-prone. On a large scale, it is very difficult for an architect to guarantee that the resulting FM ensu...

In a review of existing reverse engineering literature, it became clear that there is no shared vision on key topics in reverse engineering. As a result, the many research contributions appear to lack uniformity with regard to the way results are reported. In this short paper, we present ”the Reverse Engineering wiki”1, an initiative started at ICPC 2006 in the working session on Experimental S...

INTRODUCTION: REVERSE ENGINEERING This paper motivates and describes a research program in the area of reverse engineering being conducted at the Georgia Institute of Technology. Reverse engineering is an emerging interest area within the software engineering eld. Software engineering itself is concerned with improving the productivity of the software development process and the quality of the ...

We propose a new design for inspection and reverse engineering environments In particular we investigate the use of discrete event dynamic systems DEDS to guide and control the active exploration and sensing of mechanical parts for industrial inspection and reverse engineering We introduce dynamic recursive nite state machines DRFSM as a new DEDS tool for utilizing the recursive nature of the m...

Communication protocols determine how network components interact with each other. Therefore, the ability to derive a speci cation of a protocol can be useful in various contexts, such as to support deeper black-box testing or e ective defense mechanisms. Unfortunately, it is often hard to obtain the speci cation because systems implement closed (i.e., undocumented) protocols, or because a time...

Advanced technologies and biology have extremely different physical implementations, but they are far more alike in systems-level organization than is widely appreciated. Convergent evolution in both domains produces modular architectures that are composed of elaborate hierarchies of protocols and layers of feedback regulation, are driven by demand for robustness to uncertain environments, and ...