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Processing-in-memory for genomics workloads
Authors:
William Andrew Simon,
Leonid Yavits,
Konstantina Koliogeorgi,
Yann Falevoz,
Yoshihiro Shibuya,
Dominique Lavenier,
Irem Boybat,
Klea Zambaku,
Berkan Şahin,
Mohammad Sadrosadati,
Onur Mutlu,
Abu Sebastian,
Rayan Chikhi,
The BioPIM Consortium,
Can Alkan
Abstract:
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. The…
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Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. Therefore, there is a need for fast, energy-efficient, and cost-efficient technologies that enable genomics research without requiring data centers and cloud platforms. We recently launched the BioPIM Project to leverage emerging processing-in-memory (PIM) technologies to enable energy- and cost-efficient analysis of bioinformatics workloads. The BioPIM Project focuses on co-designing algorithms and data structures commonly used in genomics with several PIM architectures to achieve the highest cost, energy, and time savings.
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Submitted 4 February, 2026; v1 submitted 31 May, 2025;
originally announced June 2025.
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Asynchronous Batch Bayesian Optimization with Pipelining Evaluations for Experimental Resource$\unicode{x2013}$constrained Conditions
Authors:
Yujin Taguchi,
Yusuke Shibuya,
Yusuke Hiki,
Takashi Morikura,
Takahiro G. Yamada,
Akira Funahashi
Abstract:
Bayesian optimization is efficient even with a small amount of data and is used in engineering and in science, including biology and chemistry. In Bayesian optimization, a parameterized model with an uncertainty is fitted to explain the experimental data, and then the model suggests parameters that would most likely improve the results. Batch Bayesian optimization reduces the processing time of op…
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Bayesian optimization is efficient even with a small amount of data and is used in engineering and in science, including biology and chemistry. In Bayesian optimization, a parameterized model with an uncertainty is fitted to explain the experimental data, and then the model suggests parameters that would most likely improve the results. Batch Bayesian optimization reduces the processing time of optimization by parallelizing experiments. However, batch Bayesian optimization cannot be applied if the number of parallelized experiments is limited by the cost or scarcity of equipment; in such cases, sequential methods require an unrealistic amount of time. In this study, we developed pipelining Bayesian optimization (PipeBO) to reduce the processing time of optimization even with a limited number of parallel experiments. PipeBO was inspired by the pipelining of central processing unit architecture, which divides computational tasks into multiple processes. PipeBO was designed to achieve experiment parallelization by overlapping various processes of the experiments. PipeBO uses the results of completed experiments to update the parameters of running parallelized experiments. Using the Black-Box Optimization Benchmarking, which consists of 24 benchmark functions, we compared PipeBO with the sequential Bayesian optimization methods. PipeBO reduced the average processing time of optimization to about 56% for the experiments that consisted of two processes or even less for those with more processes for 20 out of the 24 functions. Overall, PipeBO parallelizes Bayesian optimization in the resource-constrained settings so that efficient optimization can be achieved.
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Submitted 5 December, 2024;
originally announced December 2024.
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Locality-Preserving Minimal Perfect Hashing of k-mers
Authors:
Giulio Ermanno Pibiri,
Yoshihiro Shibuya,
Antoine Limasset
Abstract:
Minimal perfect hashing is the problem of mapping a static set of $n$ distinct keys into the address space $\{1,\ldots,n\}$ bijectively. It is well-known that $n\log_2(e)$ bits are necessary to specify a minimal perfect hash function (MPHF) $f$, when no additional knowledge of the input keys is to be used. However, it is often the case in practice that the input keys have intrinsic relationships t…
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Minimal perfect hashing is the problem of mapping a static set of $n$ distinct keys into the address space $\{1,\ldots,n\}$ bijectively. It is well-known that $n\log_2(e)$ bits are necessary to specify a minimal perfect hash function (MPHF) $f$, when no additional knowledge of the input keys is to be used. However, it is often the case in practice that the input keys have intrinsic relationships that we can exploit to lower the bit complexity of $f$. For example, consider a string and the set of all its distinct $k$-mers as input keys: since two consecutive $k$-mers share an overlap of $k-1$ symbols, it seems possible to beat the classic $\log_2(e)$ bits/key barrier in this case. Moreover, we would like $f$ to map consecutive $k$-mers to consecutive addresses, as to also preserve as much as possible their relationship in the codomain. This is a useful feature in practice as it guarantees a certain degree of locality of reference for $f$, resulting in a better evaluation time when querying consecutive $k$-mers. Motivated by these premises, we initiate the study of a new type of locality-preserving MPHF designed for $k$-mers extracted consecutively from a collection of strings. We design a construction whose space usage decreases for growing $k$ and discuss experiments with a practical implementation of the method: in practice, the functions built with our method can be several times smaller and even faster to query than the most efficient MPHFs in the literature.
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Submitted 12 April, 2023; v1 submitted 24 October, 2022;
originally announced October 2022.
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Selfish Mining Attacks Exacerbated by Elastic Hash Supply
Authors:
Yoko Shibuya,
Go Yamamoto,
Fuhito Kojima,
Elaine Shi,
Shin'ichiro Matsuo,
Aron Laszka
Abstract:
Several attacks have been proposed against Proof-of-Work blockchains, which may increase the attacker's share of mining rewards (e.g., selfish mining, block withholding). A further impact of such attacks, which has not been considered in prior work, is that decreasing the profitability of mining for honest nodes incentivizes them to stop mining or to leave the attacked chain for a more profitable…
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Several attacks have been proposed against Proof-of-Work blockchains, which may increase the attacker's share of mining rewards (e.g., selfish mining, block withholding). A further impact of such attacks, which has not been considered in prior work, is that decreasing the profitability of mining for honest nodes incentivizes them to stop mining or to leave the attacked chain for a more profitable one. The departure of honest nodes exacerbates the attack and may further decrease profitability and incentivize more honest nodes to leave. In this paper, we first present an empirical analysis showing that there is a statistically significant correlation between the profitability of mining and the total hash rate, confirming that miners indeed respond to changing profitability. Second, we present a theoretical analysis showing that selfish mining under such elastic hash supply leads either to the collapse of a chain, i.e., all honest nodes leaving, or to a stable equilibrium depending on the attacker's initial share.
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Submitted 14 March, 2021;
originally announced March 2021.
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Public Sentiment and Demand for Used Cars after A Large-Scale Disaster: Social Media Sentiment Analysis with Facebook Pages
Authors:
Yuya Shibuya,
Hideyuki Tanaka
Abstract:
There have been various studies analyzing public sentiment after a large-scale disaster. However, few studies have focused on the relationship between public sentiment on social media and its results on people's activities in the real world. In this paper, we conduct a long-term sentiment analysis after the Great East Japan Earthquake and Tsunami of 2011 using Facebook Pages with the aim of invest…
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There have been various studies analyzing public sentiment after a large-scale disaster. However, few studies have focused on the relationship between public sentiment on social media and its results on people's activities in the real world. In this paper, we conduct a long-term sentiment analysis after the Great East Japan Earthquake and Tsunami of 2011 using Facebook Pages with the aim of investigating the correlation between public sentiment and people's actual needs in areas damaged by water disasters. In addition, we try to analyze whether different types of disaster-related communication created different kinds of relationships on people's activities in the physical world. Our analysis reveals that sentiment of geo-info-related communication, which might be affected by sentiment inside a damaged area, had a positive correlation with the prices of used cars in the damaged area. On the other hand, the sentiment of disaster-interest-based-communication, which might be affected more by people who were interested in the disaster, but were outside the damaged area, had a negative correlation with the prices of used cars. The result could be interpreted to mean that when people begin to recover, used-car prices rise because they become more positive in their sentiment. This study suggests that, for long-term disaster-recovery analysis, we need to consider the different characteristics of online communication posted by locals directly affected by the disaster and non-locals not directly affected by the disaster.
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Submitted 22 January, 2018;
originally announced January 2018.