Exponential sensitivity of noise-driven switching in genetic networks

Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and translation rates. However, provided mRNA lifetimes are short, switching can still be accurately simulated using protein-only models of gene expression. Exponential sensitivity limits the robustness of noise-driven switching, suggesting cells may use other mechanisms in order to switch reliably.

User-Level Sandboxing: a Safe and Efficient Mechanism for Extensibility

Extensible systems allow services to be configured and deployed for the specific needs of individual applications. This paper describes a safe and efficient method for user-level extensibility that requires only minimal changes to the kernel. A sandboxing technique is described that supports multiple logical protection domains within the same address space at user-level. This approach allows applications to register sandboxed code with the system, that may be executed in the context of any process. Our approach differs from other implementations that require special hardware support, such as segmentation or tagged translation look-aside buffers (TLBs), to either implement multiple protection domains in a single address space, or to support fast switching between address spaces. Likewise, we do not require the entire system to be written in a type-safe language, to provide fine-grained protection domains. Instead, our user-level sandboxing technique requires only paged-based virtual memory support, and the requirement that extension code is written either in a type-safe language, or by a trusted source. Using a fast method of upcalls, we show how our sandboxing technique for implementing logical protection domains provides significant performance improvements over traditional methods of invoking user-level services. Experimental results show our approach to be an efficient method for extensibility, with inter-protection domain communication costs close to those of hardware-based solutions leveraging segmentation.

Lightweight Formal Verification in Classroom Instruction of Reasoning about Functional Code

In college courses dealing with material that requires mathematical rigor, the adoption of a machine-readable representation for formal arguments can be advantageous. Students can focus on a specific collection of constructs that are represented consistently. Examples and counterexamples can be evaluated. Assignments can be assembled and checked with the help of an automated formal reasoning system. However, usability and accessibility do not have a high priority and are not addressed sufficiently well in the design of many existing machine-readable representations and corresponding formal reasoning systems. In earlier work [Lap09], we attempt to address this broad problem by proposing several specific design criteria organized around the notion of a natural context: the sphere of awareness a working human user maintains of the relevant constructs, arguments, experiences, and background materials necessary to accomplish the task at hand. We report on our attempt to evaluate our proposed design criteria by deploying within the classroom a lightweight formal verification system designed according to these criteria. The lightweight formal verification system was used within the instruction of a common application of formal reasoning: proving by induction formal propositions about functional code. We present all of the formal reasoning examples and assignments considered during this deployment, most of which are drawn directly from an introductory text on functional programming. We demonstrate how the design of the system improves the effectiveness and understandability of the examples, and how it aids in the instruction of basic formal reasoning techniques. We make brief remarks about the practical and administrative implications of the system’s design from the perspectives of the student, the instructor, and the grader.

An Efficient User-Level Shared Memory Mechanism for Application-Specific Extensions

This paper focuses on an efficient user-level method for the deployment of application-specific extensions, using commodity operating systems and hardware. A sandboxing technique is described that supports multiple extensions within a shared virtual address space. Applications can register sandboxed code with the system, so that it may be executed in the context of any process. Such code may be used to implement generic routines and handlers for a class of applications, or system service extensions that complement the functionality of the core kernel. Using our approach, application-specific extensions can be written like conventional user-level code, utilizing libraries and system calls, with the advantage that they may be executed without the traditional costs of scheduling and context-switching between process-level protection domains. No special hardware support such as segmentation or tagged translation look-aside buffers (TLBs) is required. Instead, our ``user-level sandboxing'' mechanism requires only paged-based virtual memory support, given that sandboxed extensions are either written by a trusted source or are guaranteed to be memory-safe (e.g., using type-safe languages). Using a fast method of upcalls, we show how our mechanism provides significant performance improvements over traditional methods of invoking user-level services. As an application of our approach, we have implemented a user-level network subsystem that avoids data copying via the kernel and, in many cases, yields far greater network throughput than kernel-level approaches.

Construction of Neural Network Classification Expert Systems Using Switching Theory Algorithms

A new family of neural network architectures is presented. This family of architectures solves the problem of constructing and training minimal neural network classification expert systems by using switching theory. The primary insight that leads to the use of switching theory is that the problem of minimizing the number of rules and the number of IF statements (antecedents) per rule in a neural network expert system can be recast into the problem of minimizing the number of digital gates and the number of connections between digital gates in a Very Large Scale Integrated (VLSI) circuit. The rules that the neural network generates to perform a task are readily extractable from the network's weights and topology. Analysis and simulations on the Mushroom database illustrate the system's performance.