A Benchmark Analysis of Graph and Non-Graph Methods for Caenorhabditis Elegans Neuron Classification

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Lu, Jingqi, Han, Keqi, Wang, Yun, Mi, Lu, Yang, Carl
Format:	Preprint
Published:	2026
Subjects:	Neurons and Cognition Artificial Intelligence
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

_version_	1866914364398764032
author	Lu, Jingqi Han, Keqi Wang, Yun Mi, Lu Yang, Carl
author_facet	Lu, Jingqi Han, Keqi Wang, Yun Mi, Lu Yang, Carl
contents	This study establishes a benchmark for Caenorhabditis elegans neuron classification, comparing four graph methods (GCN, GraphSAGE, GAT, GraphTransformer) against four non-graph methods (Logistic Regression, MLP, LOLCAT, NeuPRINT). Using the functional connectome, we classified Sensory, Interneuron, and Motor neurons based on Spatial, Connection, and Neuronal Activity features. Results show that attention-based GNNs significantly outperform baselines on the Spatial and Connection features. The Neuronal Activity features yielded poor performance, likely due to the low temporal resolution of the underlying neuronal activity data. Our benchmark validates the use of GNNs and highlights that Spatial and Connection features are key predictors for Caenorhabditis elegans neuron classes. Code is available at: https://github.com/JingqiLuu/neuronclf-gnn-benchmark.
format	Preprint
id	arxiv_https___arxiv_org_abs_2603_02241
institution	arXiv
publishDate	2026
record_format	arxiv
spellingShingle	A Benchmark Analysis of Graph and Non-Graph Methods for Caenorhabditis Elegans Neuron Classification Lu, Jingqi Han, Keqi Wang, Yun Mi, Lu Yang, Carl Neurons and Cognition Artificial Intelligence This study establishes a benchmark for Caenorhabditis elegans neuron classification, comparing four graph methods (GCN, GraphSAGE, GAT, GraphTransformer) against four non-graph methods (Logistic Regression, MLP, LOLCAT, NeuPRINT). Using the functional connectome, we classified Sensory, Interneuron, and Motor neurons based on Spatial, Connection, and Neuronal Activity features. Results show that attention-based GNNs significantly outperform baselines on the Spatial and Connection features. The Neuronal Activity features yielded poor performance, likely due to the low temporal resolution of the underlying neuronal activity data. Our benchmark validates the use of GNNs and highlights that Spatial and Connection features are key predictors for Caenorhabditis elegans neuron classes. Code is available at: https://github.com/JingqiLuu/neuronclf-gnn-benchmark.
title	A Benchmark Analysis of Graph and Non-Graph Methods for Caenorhabditis Elegans Neuron Classification
topic	Neurons and Cognition Artificial Intelligence
url	https://arxiv.org/abs/2603.02241

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	"55c61787f4d709bb7faf8c0c8c32fe99"
ui	"standard"
language	"en"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790971091.3178 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "55c61787f4d709bb7faf8c0c8c32fe99" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1762}

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=55c61787f4d709bb7faf8c0c8c32fe99; ui=standard; language=en"
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	"216.73.217.142"
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	"51717"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2603_02241/Details """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2603_02241/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790971091.3137
REQUEST_TIME	1790971091

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"55c61787f4d709bb7faf8c0c8c32fe99"
ui	"standard"
language	"en"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790971091.3178 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "55c61787f4d709bb7faf8c0c8c32fe99" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1762}

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=55c61787f4d709bb7faf8c0c8c32fe99; ui=standard; language=en"
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	"216.73.217.142"
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	"51717"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2603_02241/Details """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2603_02241/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790971091.3137
REQUEST_TIME	1790971091

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Similar Items

Environment & details:

Environment & details: