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Reconfigurable hardware accelerators: Opportunities, trends, and challenges
With the emerging big data applications of Machine Learning, Speech Recognition, Artificial
Intelligence, and DNA Sequencing in recent years, computer architecture research …
Intelligence, and DNA Sequencing in recent years, computer architecture research …
[PDF][PDF] A scored non-deterministic finite automata processor for sequence alignment
R Karbowniczak, R Karakchi - arxiv preprint arxiv …, 2024 - sc24.supercomputing.org
1 Extended Abstract With the rapid expansion of symbolic data in fields such as internet
data, biological data, and financial data, the need for efficient pattern matching and regular …
data, biological data, and financial data, the need for efficient pattern matching and regular …
Optimizing Sequence Alignment with Scored NFAs
R Karbowniczak, R Karakchi - arxiv preprint arxiv:2501.02162, 2025 - arxiv.org
The rapid increase in symbolic data has underscored the significance of pattern matching
and regular expression processing. While nondeterministic finite automata (NFA) are …
and regular expression processing. While nondeterministic finite automata (NFA) are …
A Scored Non-Deterministic Finite Automata Processor for Sequence Alignment
RKR Karakchi - arxiv preprint arxiv:2410.19758, 2024 - arxiv.org
The rapid growth of symbolic data in areas like internet, biological, and financial data has
increased the demand for efficient pattern matching and regular expression processing. Non …
increased the demand for efficient pattern matching and regular expression processing. Non …
High-level synthesis of a genomic database search engine
R Karakchi, JA Bradshaw… - … Computing and FPGAs …, 2016 - ieeexplore.ieee.org
Genomic database search is an I/O-bound problem, so avoiding unnecessary I/O
transactions is a key consideration for improving search throughput. Many approximate …
transactions is a key consideration for improving search throughput. Many approximate …