1 code implementation • 14 Jun 2022 • Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, Onur Mutlu
We introduce COVIDHunter, a flexible and accurate COVID-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region, predicts COVID-19 statistics (the daily number of cases, hospitalizations, and deaths), and provides suggestions on what strength the upcoming mitigation measure should be.
1 code implementation • 17 Jan 2022 • Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
Also available in Bioconda at: https://anaconda. org/bioconda/fastremap-bio.
1 code implementation • 16 Dec 2021 • Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu
We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches.
1 code implementation • 6 Feb 2021 • Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, Onur Mutlu
The key idea of COVIDHunter is to quantify the spread of COVID-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e. g., climate, temperature, humidity) and mitigation measures.
1 code implementation • 17 Sep 2020 • Minesh Patel, Jeremie S. Kim, Taha Shahroodi, Hasan Hassan, Onur Mutlu
As a concrete example, we introduce and evaluate BEEP, the first error profiling methodology that uses the known on-die ECC function to recover the number and bit-exact locations of unobservable raw bit errors responsible for observable post-correction errors.
Hardware Architecture
2 code implementations • 16 Sep 2020 • Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
Unfortunately, it is currently bottlenecked by the computational power and memory bandwidth limitations of existing systems, as many of the steps in genome sequence analysis must process a large amount of data.
Hardware Architecture Genomics
1 code implementation • 18 Dec 2019 • Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
There are several tools that attempt to accelerate the process of updating a read data set from one reference to another (i. e., remapping).
no code implementations • 26 Jul 2019 • Saugata Ghose, Amirali Boroumand, Jeremie S. Kim, Juan Gómez-Luna, Onur Mutlu
First, we describe our work on systematically identifying opportunities for PIM in real applications, and quantify potential gains for popular emerging applications (e. g., machine learning, data analytics, genome analysis).
Distributed, Parallel, and Cluster Computing Hardware Architecture
1 code implementation • 12 Feb 2019 • Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, Onur Mutlu
Our experiments with real read sets demonstrate that Apollo is the only algorithm that 1) uses reads from any sequencing technology within a single run and 2) scales well to polish large assemblies without splitting the assembly into multiple parts.
1 code implementation • 2 Nov 2017 • Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i. e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i. e., sequence alignment) to determine the origin of the read.
