Boosting t-SNE Efficiency for Sequencing Data: Insights from Kernel Selection

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Jan, Avais, Chourasia, Prakash, Ali, Sarwan, Patterson, Murray
Format:	Preprint
Published:	2025
Subjects:	Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting
by: Ali, Sarwan, et al.
Published: (2024)

Nearest Neighbor CCP-Based Molecular Sequence Analysis
by: Ali, Sarwan, et al.
Published: (2024)

A Universal Non-Parametric Approach For Improved Molecular Sequence Analysis
by: Ali, Sarwan, et al.
Published: (2024)

EPIC: Enhancing Privacy through Iterative Collaboration
by: Chourasia, Prakash, et al.
Published: (2024)

DANCE: Deep Learning-Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images
by: Murad, Taslim, et al.
Published: (2024)

Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences
by: Murad, Taslim, et al.
Published: (2024)

Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
by: Ali, Sarwan, et al.
Published: (2024)

DWFL: Enhancing Federated Learning through Dynamic Weighted Averaging
by: Chourasia, Prakash, et al.
Published: (2024)

Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks
by: Ali, Sarwan, et al.
Published: (2024)

Breaking the Euclidean Barrier: Hyperboloid-Based Biological Sequence Analysis
by: Ali, Sarwan, et al.
Published: (2025)

Sequence Analysis Using the Bezier Curve
by: Murad, Taslim, et al.
Published: (2025)

Uncovering Hierarchical Structure in LLM Embeddings with $δ$-Hyperbolicity, Ultrametricity, and Neighbor Joining
by: Chourasia, Prakash, et al.
Published: (2025)

Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based Computed Tomography Scan Analysis
by: Jan, Avais, et al.
Published: (2025)

Hilbert Curve Based Molecular Sequence Analysis
by: Ali, Sarwan, et al.
Published: (2024)

Converting Time Series Data to Numeric Representations Using Alphabetic Mapping and k-mer strategy
by: Ali, Sarwan, et al.
Published: (2024)

Explicit Path CGR: Maintaining Sequence Fidelity in Geometric Representations
by: Ali, Sarwan
Published: (2025)

EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
by: Zia, Qasim, et al.
Published: (2025)

Multi-Scale Reversible Chaos Game Representation: A Unified Framework for Sequence Classification
by: Ali, Sarwan, et al.
Published: (2026)

Sequence-to-Image Transformation for Sequence Classification Using Rips Complex Construction and Chaos Game Representation
by: Ali, Sarwan, et al.
Published: (2025)

Murmur2Vec: A Hashing Based Solution For Embedding Generation Of COVID-19 Spike Sequences
by: Ali, Sarwan, et al.
Published: (2025)

Robust Gradient Descent via Heavy-Ball Momentum with Predictive Extrapolation
by: Ali, Sarwan
Published: (2025)

DPSR: Differentially Private Sparse Reconstruction via Multi-Stage Denoising for Recommender Systems
by: Ali, Sarwan
Published: (2025)

Critical Windows of Complexity Control: When Transformers Decide to Reason or Memorize
by: Ali, Sarwan
Published: (2026)

On the continuum limit of t-SNE for data visualization
by: Calder, Jeff, et al.
Published: (2026)

t-viSNE: Interactive Assessment and Interpretation of t-SNE Projections
by: Chatzimparmpas, Angelos, et al.
Published: (2020)

Federated t-SNE and UMAP for Distributed Data Visualization
by: Qiao, Dong, et al.
Published: (2024)

Wasserstein t-SNE
by: Bachmann, Fynn, et al.
Published: (2022)

From $t$-SNE to UMAP with contrastive learning
by: Damrich, Sebastian, et al.
Published: (2022)

t-SNE Exaggerates Clusters, Provably
by: Bergam, Noah, et al.
Published: (2025)

ENS-t-SNE: Embedding Neighborhoods Simultaneously t-SNE
by: Miller, Jacob, et al.
Published: (2022)

Some Theoretical Limitations of t-SNE
by: Li, Rupert, et al.
Published: (2026)

The Tree-SNE Tree Exists
by: Kendrick, Jack
Published: (2025)

Class-constrained t-SNE: Combining Data Features and Class Probabilities
by: Meng, Linhao, et al.
Published: (2023)

Large data limits and scaling laws for tSNE
by: Murray, Ryan, et al.
Published: (2024)

DR-SNE: Density-Regularized Stochastic Neighbor Embedding
by: Kazanskii, Maksim
Published: (2026)

Accelerating hyperbolic t-SNE
by: Skrodzki, Martin, et al.
Published: (2024)

Selecting Hyperparameters for Tree-Boosting
by: Koster, Floris Jan, et al.
Published: (2026)

Stop Misusing t-SNE and UMAP for Visual Analytics
by: Jeon, Hyeon, et al.
Published: (2025)

Relating tSNE and UMAP to Classical Dimensionality Reduction
by: Draganov, Andrew, et al.
Published: (2023)

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	"8e1741ca7afee52a8446facb70b9a3b6"
language	"en"
ui	"standard"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1791214529.1038 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "8e1741ca7afee52a8446facb70b9a3b6" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1759}

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=8e1741ca7afee52a8446facb70b9a3b6; 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	"216.73.217.58"
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	"40291"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2512_15900/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2512_15900/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1791214529.0989
REQUEST_TIME	1791214529

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"8e1741ca7afee52a8446facb70b9a3b6"
language	"en"
ui	"standard"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1791214529.1038 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "8e1741ca7afee52a8446facb70b9a3b6" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1759}

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=8e1741ca7afee52a8446facb70b9a3b6; 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	"216.73.217.58"
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	"40291"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2512_15900/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2512_15900/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1791214529.0989
REQUEST_TIME	1791214529

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Similar Items

Similar Items

Environment & details:

Environment & details: