:: Library Catalog

Saved in:

Bibliographic Details
Main Authors:	Ghiasi, Nika Mansouri, Güloglu, Talu, Mustafa, Harun, Firtina, Can, Koliogeorgi, Konstantina, Kanellopoulos, Konstantinos, Mao, Haiyu, Nadig, Rakesh, Sadrosadati, Mohammad, Park, Jisung, Mutlu, Onur
Format:	Preprint
Published:	2025
Subjects:	Hardware Architecture Distributed, Parallel, and Cluster Computing Genomics
Online Access:	https://arxiv.org/abs/2504.03732
Tags:	Add Tag No Tags, Be the first to tag this record!

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
by: Lindegger, Joël, et al.
Published: (2023)

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
by: Ghiasi, Nika Mansouri, et al.
Published: (2024)

GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
by: Eudine, Julien, et al.
Published: (2026)

Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
by: Firtina, Can, et al.
Published: (2024)

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
by: Cavlak, Meryem Banu, et al.
Published: (2022)

RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization
by: Firtina, Can, et al.
Published: (2023)

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
by: Eris, Furkan, et al.
Published: (2025)

Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques
by: Firtina, Can
Published: (2025)

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
by: Kim, Jeremie S., et al.
Published: (2019)

REIS: A High-Performance and Energy-Efficient Retrieval System with In-Storage Processing
by: Chen, Kangqi, et al.
Published: (2025)

Processing-in-memory for genomics workloads
by: Simon, William Andrew, et al.
Published: (2025)

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
by: Rumpf, Maximilian-David, et al.
Published: (2023)

RUBICON: A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
by: Singh, Gagandeep, et al.
Published: (2022)

Genome-on-Diet: Taming Large-Scale Genomic Analyses via Sparsified Genomics
by: Alser, Mohammed, et al.
Published: (2022)

MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
by: Gollwitzer, Arvid E., et al.
Published: (2023)

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
by: Bingöl, Zülal, et al.
Published: (2021)

Ariadne: A Hotness-Aware and Size-Adaptive Compressed Swap Technique for Fast Application Relaunch and Reduced CPU Usage on Mobile Devices
by: Liang, Yu, et al.
Published: (2025)

Deciphering Pleiotropic Single‐Nucleotide Polymorphisms Governing Fertility–Milk Yield Trade‐Offs in Dairy Cattle: A Genome‐Wide Chromosomal Landscape Analysis
by: Heydar Ghiasi, et al.
Published: (2026)

CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models
by: Ambrozak, Simon, et al.
Published: (2026)

CiMBA: Accelerating Genome Sequencing through On-Device Basecalling via Compute-in-Memory
by: Simon, William Andrew, et al.
Published: (2025)

RevaMp3D: Architecting the Processor Core and Cache Hierarchy for Systems with Monolithically-Integrated Logic and Memory
by: Ghiasi, Nika Mansouri, et al.
Published: (2022)

Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory
by: Bostanci, F. Nisa, et al.
Published: (2024)

Multiple Genome Analytics Framework: The Case of All SARS-CoV-2 Complete Variants
by: Xylogiannopoulos, Konstantinos
Published: (2022)

A Chromosome-level Assembly and Functional Genomic Resources for the Model Annelid Capitella teleta.
by: Davies, Billie E, et al.
Published: (2026)

Conduit: Programmer-Transparent Near-Data Processing Using Multiple Compute-Capable Resources in Solid State Drives
by: Nadig, Rakesh, et al.
Published: (2026)

Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii).
by: Tracy, Claire B, et al.
Published: (2026)

The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.
by: May, Samuel A, et al.
Published: (2025)

AtSubP‐2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning
by: Naveen Duhan, et al.
Published: (2025)

MBGD: Microbial Genome Database for Comparative Analysis Featuring Enhanced Functionality to Characterize Gene and Genome Functions Through Large-scale Orthology Analysis.
by: Uchiyama, Ikuo, et al.
Published: (2025)

Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies.
by: Hsu, Po-Cheng, et al.
Published: (2025)

Genomic signatures of speciation and adaptation in the ctenophore Mnemiopsis.
by: Ketchum, Remi N, et al.
Published: (2026)

Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.
by: Giles, Emily C, et al.
Published: (2025)

The Mitochondrial Genome of Cathaya argyrophylla Reaches 18.99 Mb: Analysis of Super-Large Mitochondrial Genomes in Pinaceae
by: Huang, Kerui, et al.
Published: (2024)

Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet.
by: Au, Eric H, et al.
Published: (2025)

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.
by: Kosch, Tiffany A, et al.
Published: (2024)

Machine Learning-Driven Intelligent Memory System Design: From On-Chip Caches to Storage
by: Bera, Rahul, et al.
Published: (2026)

Athena: Synergizing Data Prefetching and Off-Chip Prediction via Online Reinforcement Learning
by: Bera, Rahul, et al.
Published: (2026)

Toward Interpretable and Generalizable AI in Regulatory Genomics
by: Nagai, Masayuki, et al.
Published: (2026)

Metadata-guided Feature Disentanglement for Functional Genomics
by: Rakowski, Alexander, et al.
Published: (2024)

if (filemtime($filename) + $maxlifetime < time()) { unlink($filename); $count++; } } return $count; } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ protected function saveSession($sessId, $data): bool { $sessFile = $this->path . '/sess_' . $sessId; if ($handle = fopen($sessFile, 'w')) { $return = false; // Lock the file for exclusive access to avoid issues with multiple // processes writing session simultaneously: if (flock($handle, LOCK_EX)) { $return = fwrite($handle, $data); // Make sure that there's no trailing data by truncating the file to // the correct length: ftruncate($handle, strlen($data)); fflush($handle); flock($handle, LOCK_UN); } fclose($handle); if ($return !== false) { return true; } } // If we got this far, something went wrong with the file output... // It is tempting to throw an exception here, but this code is called // outside of the context of exception handling, so all we can do is // echo a message.

// Anecdotal testing Today and Yesterday seems to indicate destroy() // is called by the garbage collector and everything is good. // Something to keep in mind though. return 0; } /** * Write function that is called when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ public function write($sessId, $data): bool { if ($this->writesDisabled) { return true; } return $this->saveSession($sessId, $data); } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ abstract protected function saveSession($sessId, $data): bool; }

* * @return void */ public function writeClose() { // The assumption is that we're using PHP's ext/session. // session_write_close() will actually overwrite $_SESSION with an // empty array on completion -- which leads to a mismatch between what // is in the storage object and $_SESSION. To get around this, we // temporarily reset $_SESSION to an array, and then re-link it to // the storage object. // // Additionally, while you _can_ write to $_SESSION following a // session_write_close() operation, no changes made to it will be // flushed to the session handler. As such, we now mark the storage // object isImmutable. $storage = $this->getStorage(); if (! $storage->isImmutable()) { $_SESSION = $storage->toArray(true); session_write_close(); $storage->fromArray($_SESSION); $storage->markImmutable(); } } /** * Attempt to set the session name * * If the session has already been started, or if the name provided fails * validation, an exception will be raised. * * @param string $name * @return SessionManager * @throws Exception\InvalidArgumentException */ public function setName($name) { if ($this->sessionExists()) { throw new Exception\InvalidArgumentException( 'Cannot set session name after a session has already started'

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"46e0edc9a51c07e01bbd92e481f4421a"
language	"en"
ui	"standard"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1784681115.7843 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "46e0edc9a51c07e01bbd92e481f4421a" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1583}
SessionHelper	Laminas\Stdlib\ArrayObject {#1772}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"VUFIND_SESSION=46e0edc9a51c07e01bbd92e481f4421a; language=en; ui=standard"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.216.85"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"43246"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2504_03732/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2504_03732/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1784681115.78
REQUEST_TIME	1784681115

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"46e0edc9a51c07e01bbd92e481f4421a"
language	"en"
ui	"standard"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1784681115.7843 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "46e0edc9a51c07e01bbd92e481f4421a" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1583}
SessionHelper	Laminas\Stdlib\ArrayObject {#1772}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"VUFIND_SESSION=46e0edc9a51c07e01bbd92e481f4421a; language=en; ui=standard"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.216.85"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"43246"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2504_03732/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2504_03732/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1784681115.78
REQUEST_TIME	1784681115

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Similar Items

Similar Items

Environment & details:

Environment & details: