3 code implementations • 3 Nov 2023 • Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joel Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
This dual comparison positions MetaTrinity as a broadly applicable solution for metagenomic classification, combining advantages of both ends of the spectrum: speed and accuracy.
1 code implementation • 25 Oct 2023 • Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joel Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses.
1 code implementation • 8 Oct 2023 • Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
mean) while improving accuracy by 1. 35$\times$ (1. 34$\times$) in terms of F-1 score on average (geo.
1 code implementation • 9 Dec 2022 • Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu
However, for many applications, the majority of reads do no match the reference genome of interest (i. e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.
1 code implementation • 20 Jul 2022 • Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie Kim, Taha Shahroodi, Meryem Banu Cavlak, Joel Lindegger, Mohammed Alser, Juan Gómez Luna, Sreenivas Subramoney, Onur Mutlu
We identify an urgent need for a flexible, high-performance, and energy-efficient HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs.
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 • 16 May 2022 • Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gomez-Luna, Onur Mutlu
We hope that these efforts and the challenges we discuss provide a foundation for future work in making genome analysis more intelligent.
no code implementations • 30 Mar 2022 • Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do, Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research.
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 • 27 Mar 2021 • Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms.
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.
no code implementations • 22 Dec 2020 • Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, João Dinis Ferreira, Nika Mansouri Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gómez-Luna, Onur Mutlu
Compared to a CPU and a high-end GPU, SIMDRAM is 257x and 31x more energy-efficient, while providing 93x and 6x higher operation throughput, respectively.
Hardware Architecture Distributed, Parallel, and Cluster Computing Emerging Technologies
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
2 code implementations • 28 Feb 2020 • Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul
We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques.
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).
1 code implementation • 20 Oct 2019 • Mohammed Alser, Taha Shahroodi, Juan Gomez-Luna, Can Alkan, Onur Mutlu
The key idea of SneakySnake is to reduce the approximate string matching (ASM) problem to the single net routing (SNR) problem in VLSI chip layout.
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.
1 code implementation • 6 Apr 2016 • Mohammed Alser, Hasan Hassan, Hongyi Xin, Oğuz Ergin, Onur Mutlu, Can Alkan
The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10.