Inferring Energy Bounds via Static Program Analysis and Evolutionary Modeling of Basic Blocks

The ever increasing number and complexity of energy-bound devices (such as the ones used in Internet of Things applications, smart phones, and mission critical systems) pose an important challenge on techniques to optimize their energy consumption and to verify that they will perform their function within the available energy budget. In this work we address this challenge from the software point of view and propose a novel parametric approach to estimating tight bounds on the energy consumed by program executions that are practical for their application to energy verification and optimization. Our approach divides a program into basic (branchless) blocks and estimates the maximal and minimal energy consumption for each block using an evolutionary algorithm. Then it combines the obtained values according to the program control flow, using static analysis, to infer functions that give both upper and lower bounds on the energy consumption of the whole program and its procedures as functions on input data sizes. We have tested our approach on (C-like) embedded programs running on the XMOS hardware platform. However, our method is general enough to be applied to other microprocessor architectures and programming languages. The bounds obtained by our prototype implementation can be tight while remaining on the safe side of budgets in practice, as shown by our experimental evaluation.Comment: Pre-proceedings paper presented at the 27th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2017), Namur, Belgium, 10-12 October 2017 (arXiv:1708.07854). Improved version of the one presented at the HIP3ES 2016 workshop (v1): more experimental results (added benchmark to Table 1, added figure for new benchmark, added Table 3), improved Fig. 1, added Fig.

Bio-inspired call-stack reconstruction for performance analysis

The correlation of performance bottlenecks and their associated source code has become a cornerstone of performance analysis. It allows understanding why the efficiency of an application falls behind the computer's peak performance and enabling optimizations on the code ultimately. To this end, performance analysis tools collect the processor call-stack and then combine this information with measurements to allow the analyst comprehend the application behavior. Some tools modify the call-stack during run-time to diminish the collection expense but at the cost of resulting in non-portable solutions. In this paper, we present a novel portable approach to associate performance issues with their source code counterpart. To address it, we capture a reduced segment of the call-stack (up to three levels) and then process the segments using an algorithm inspired by multi-sequence alignment techniques. The results of our approach are easily mapped to detailed performance views, enabling the analyst to unveil the application behavior and its corresponding region of code. To demonstrate the usefulness of our approach, we have applied the algorithm to several first-time seen in-production applications to describe them finely, and optimize them by using tiny modifications based on the analyses.We thankfully acknowledge Mathis Bode for giving us access to the Arts CF binaries, and Miguel Castrillo and Kim Serradell for their valuable insight regarding Nemo. We would like to thank Forschungszentrum Jülich for the computation time on their Blue Gene/Q system. This research has been partially funded by the CICYT under contracts No. TIN2012-34557 and TIN2015-65316-P.Peer ReviewedPostprint (author's final draft

PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.

Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions

An Empirical Study on Android for Saving Non-shared Data on Public Storage

With millions of apps that can be downloaded from official or third-party market, Android has become one of the most popular mobile platforms today. These apps help people in all kinds of ways and thus have access to lots of user's data that in general fall into three categories: sensitive data, data to be shared with other apps, and non-sensitive data not to be shared with others. For the first and second type of data, Android has provided very good storage models: an app's private sensitive data are saved to its private folder that can only be access by the app itself, and the data to be shared are saved to public storage (either the external SD card or the emulated SD card area on internal FLASH memory). But for the last type, i.e., an app's non-sensitive and non-shared data, there is a big problem in Android's current storage model which essentially encourages an app to save its non-sensitive data to shared public storage that can be accessed by other apps. At first glance, it seems no problem to do so, as those data are non-sensitive after all, but it implicitly assumes that app developers could correctly identify all sensitive data and prevent all possible information leakage from private-but-non-sensitive data. In this paper, we will demonstrate that this is an invalid assumption with a thorough survey on information leaks of those apps that had followed Android's recommended storage model for non-sensitive data. Our studies showed that highly sensitive information from billions of users can be easily hacked by exploiting the mentioned problematic storage model. Although our empirical studies are based on a limited set of apps, the identified problems are never isolated or accidental bugs of those apps being investigated. On the contrary, the problem is rooted from the vulnerable storage model recommended by Android. To mitigate the threat, we also propose a defense framework