Good spaced seeds for homology search
Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. 
 
 Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.

title: Palindromes in SARS and Other Coronaviruses
abstract: With the identification of a novel coronavirus associated with the severe acute respiratory syndrome (SARS), computational analysis of its RNA genome sequence is expected to give useful clues to help elucidate the origin, evolution, and pathogenicity of the virus. In this paper, we study the collective counts of palindromes in the SARS genome along with all the completely sequenced coronaviruses. Based on a Markov-chain model for the genome sequence, the mean and standard deviation for the number of palindromes at or above a given length are derived. These theoretical results are complemented by extensive simulations to provide empirical estimates. Using a z score obtained from these mathematical and empirical means and standard deviations, we have observed that palindromes of length four are significantly underrepresented in all the coronaviruses in our data set. In contrast, length-six palindromes are significantly underrepresented only in the SARS coronavirus. Two other features are unique to the SARS sequence. First, there is a length-22 palindrome TCTTTAACAAGCTTGTTAAAGA spanning positions 25962-25983. Second, there are two repeating length-12 palindromes TTATAATTATAA spanning positions 22712-22723 and 22796-22807. Some further investigations into possible biological implications of these palindrome features are proposed.

title: Dynamic voltage and frequency scaling based on workload decomposition
abstract: This paper presents a technique called "workload decomposition" in which the CPU workload is decomposed in two parts: on-chip and off-chip. The on-chip workload signifies the CPU clock cycles that are required to execute instructions in the CPU whereas the off-chip workload captures the number of external memory access clock cycles that are required to perform external memory transactions. When combined with a dynamic voltage and frequency scaling (DVFS) technique to minimize the energy consumption, this workload decomposition method results in higher energy savings. The workload decomposition itself is performed at run time based on statistics reported by a performance monitoring unit (PMU) without a need for application profiling or compiler support. We have implemented the proposed DVFS with workload decomposition technique on the BitsyX platform, an Intel PXA255-based platform manufactured by ADS Inc., and performed detailed energy measurements. These measurements show that, for a number of widely used software applications, a CPU energy saving of 80% can be achieved for memory-bound programs while satisfying the user-specified timing constraints.

title: PA-ZSA (Power-Aware Zero-Slack Algorithm): A Graph-Based Timing Analysis for Ultra-Low Power CMOS VLSI
abstract: This paper describes a slack budget distribution algorithm for ultra-low power CMOS logic circuits in a VLSI design environment. We introduce Power-Aware Zero-Slack Algorithm (PA-ZSA), which distributes the surplus time slacks into the most power-hungry modules. The PA-ZSA ensures that the total slack budget is near-maximal and the total power is minimal as a power-aware version of the well-known zero-slack algorithm (ZSA). Based on these time slacks, we have conducted the low-power optimization at gate level by using technology scaling technique. The experimental results show that our strategy reduces average 36% of the total (static and dynamic) power over the conventional slack budget distribution algorithms.

title: Knowledge Seeking Activities for Content Intelligence
abstract: This paper proposes a problem on the knowledge seeking activities compared with information seeking and knowledge discovery from text. A knowledge seeking activity is accomplished by a dynamic linkage of contents that is called “content intelligence.” An algorithm called “crossover” of knowledge units is proposed.

title: A Korean-Japanese-Chinese Aligned Wordnet with Shared Semantic Hierarchy
abstract: A Korean-Japanese-Chinese aligned wordnet, “CoreNet” is introduced. For the purpose of this paper, the term “wordnet” refers to a network of words. It is constructed based on a shared semantic hierarchy that is originated from NTT Goidaikei (Lexical Hierarchical System). Korean wordnet was constructed through the semantic category assignment to every meaning of Korean words in a dictionary. Verbs and adjectives’ word senses are assigned to the same semantic hierarchy as that of nouns. Each sense of verbs is investigated from corpora for their usage, and compared with Japanese translation. Chinese wordnet with the same semantic hierarchy was built up based on the comparison with Korean wordnet. Each sense of Chinese verb corresponds to Korean with its argument structure. The use of the same semantic hierarchy for nouns and predicates has several advantages. First, the surface forms of nouns and predicates share the similar one, especially in Chinese words. In case of Korean and Japanese, the typical formation is like “do+Noun” in English like “Noun+suru” in Japanese and “Noun+hada” in Korean. Second, the language generation from conceptual structures takes freedom to choose the surface form whether it chooses noun phrases or verb phrases. CoreNet has been constructed by the following principles: word sense mapping to concept, corpus-based, multi-lingualism, and single concept system for multi-languages. The overall flow of construction is based on dictionary-based bootstrapping, incremental similarity-based classification and manual post-editing. Among consideration points, the followings are introduced: multiple concept mapping, verbal noun, and concept splitting. For multiple concept mapping, a word is mapped into numerous concepts that comprise respective meanings of the word. For example, school is an “institution for the instruction of students.” The word school is mapped into three concepts such as location, organization, and facility. For verbal noun, a word that is a verb is assigned to concepts after it is transformed to a noun. For example, “write” is transformed to its noun form “writing” that is mapped into a concept writing falling under event. For concept splitting, every time inconsistency among nodes of concepts is discovered, a node may be added. What differs between CoreNet and NTT Goidaikei is that CoreNet features mapping between word senses (not just words) and concepts. These works have lasted since 1994.

title: Frame-Based Dynamic Voltage and Frequency Scaling for an MPEG Player
abstract: This paper describes a dynamic voltage and frequency scaling (DVFS) technique for MPEG decoding to reduce the energy consumption while maintaining a quality of service (QoS) constraint. The computational workload for an incoming frame is predicted by using a frame-based history so that the processor voltage and frequency can be scaled to provide the exact amount of computing power needed to decode the frame. More precisely, the required decoding time for each frame is separated into two parts: a frame-dependent (FD) part and a frame-independent (FI) part. The FD part varies greatly according to the type of the incoming frame whereas the FI part remains constant regardless of the frame type. Separation of the FI part from the overall decoding sequence provides two key benefits depending on the hardware platform: better compensation of the error due to workload prediction and higher level of energy saving when given a QoS degradation level. The proposed DVFS scheme has been implemented on two platforms, a low performance StrongArm-1110-based evaluation board from Intel and a high performance XScale-based testbed designed at USC. In the StrongArm-1110-based system, the FI part is used to compensate for the prediction error that may occur during the FD part, whereas in the XScale-based system, the FI part is used to reduce energy consumption by employing the lowest CPU frequency during the corresponding time intervals. Detailed current measurements in these two platforms demonstrate larger than 87 % and 80 % CPU energy saving while maintaining a user-provided frame rate, respectively. Index Terms — Dynamic voltage and frequency scaling, MPEG decoding, workload decomposition.