Search Results for author: Mohammed Alser

Found 15 papers, 13 papers with code

ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis

1 code implementation20 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

When we analyze the state-of-the-art works, we find that there is a pressing need for a flexible, high-performant, and energy-efficient hardware-software co-design to efficiently and effectively solve all the major inefficiencies in the Baum-Welch algorithm for pHMMs.

Multiple Sequence Alignment

COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling

1 code implementation14 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.

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

1 code implementation16 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 seeds matches.

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping

1 code implementation27 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.

COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model

1 code implementation6 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.

SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM

no code implementations22 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

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

2 code implementations16 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

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes

1 code implementation18 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).

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

1 code implementation20 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.

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

1 code implementation12 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.

GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies

1 code implementation2 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.

GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping

1 code implementation6 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.

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