MS-BART: Unified Modeling of Mass Spectra and Molecules for Structure Elucidation

Fuente: arXiv

Gespeichert in:

Bibliographische Detailangaben
Hauptverfasser:	Han, Yang, Wang, Pengyu, Yu, Kai, Chen, Xin, Chen, Lu
Format:	Preprint
Veröffentlicht:	2025
Schlagworte:	Machine Learning
Online-Zugang:	Acceder al recurso
Tags:	Tag hinzufügen Keine Tags, Fügen Sie den ersten Tag hinzu!

Ähnliche Einträge

FlowMS: Flow Matching for De Novo Structure Elucidation from Mass Spectra
von: Nie, Jianan, et al.
Veröffentlicht: (2026)

DiffMS: Diffusion Generation of Molecules Conditioned on Mass Spectra
von: Bohde, Montgomery, et al.
Veröffentlicht: (2025)

Atomic Diffusion Models for Small Molecule Structure Elucidation from NMR Spectra
von: Xiong, Ziyu, et al.
Veröffentlicht: (2025)

DiffNMR: Diffusion Models for Nuclear Magnetic Resonance Spectra Elucidation
von: Yang, Qingsong, et al.
Veröffentlicht: (2025)

DiffSpectra: Molecular Structure Elucidation from Spectra using Diffusion Models
von: Wang, Liang, et al.
Veröffentlicht: (2025)

Breaking the Modality Barrier: Generative Modeling for Accurate Molecule Retrieval from Mass Spectra
von: Zhang, Yiwen, et al.
Veröffentlicht: (2025)

MSAlign: Aligning Molecule and Mass Spectra Foundation Models for Metabolite Identification
von: Krzakala, Paul, et al.
Veröffentlicht: (2026)

ChemBART: A Pre-trained BART Model Assisting Organic Chemistry Analysis
von: Li, Kenan, et al.
Veröffentlicht: (2026)

An Infinite BART model
von: Battiston, Marco, et al.
Veröffentlicht: (2025)

One Small Step with Fingerprints, One Giant Leap for De Novo Molecule Generation from Mass Spectra
von: Neo, Neng Kai Nigel, et al.
Veröffentlicht: (2025)

Spectra-to-Structure and Structure-to-Spectra Inference Across the Periodic Table
von: Wang, Yufeng, et al.
Veröffentlicht: (2025)

SCENT: Aligning Mass Spectra with Molecular Structure for Olfactory Perception
von: Zhang, Ziqi, et al.
Veröffentlicht: (2026)

Generative Regression with IQ-BART
von: O'Hagan, Sean, et al.
Veröffentlicht: (2025)

Cross-Modality Controlled Molecule Generation with Diffusion Language Model
von: Zhang, Yunzhe, et al.
Veröffentlicht: (2025)

From Generalist to Specialist: A Survey of Large Language Models for Chemistry
von: Han, Yang, et al.
Veröffentlicht: (2024)

K-Fold Causal BART for CATE Estimation
von: Souto, Hugo Gobato, et al.
Veröffentlicht: (2024)

Probit Monotone BART
von: Fisher, Jared D.
Veröffentlicht: (2025)

Test-Time Tuned Language Models Enable End-to-end De Novo Molecular Structure Generation from MS/MS Spectra
von: Mismetti, Laura, et al.
Veröffentlicht: (2025)

GoMS: Graph of Molecule Substructure Network for Molecule Property Prediction
von: Qu, Shuhui, et al.
Veröffentlicht: (2025)

NMIRacle: Multi-modal Generative Molecular Elucidation from IR and NMR Spectra
von: Ottomano, Federico, et al.
Veröffentlicht: (2025)

COMET:Combined Matrix for Elucidating Targets
von: Wang, Haojie, et al.
Veröffentlicht: (2024)

UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
von: Kong, Xiangzhe, et al.
Veröffentlicht: (2025)

Unifying Low Dimensional Spectra in Deep Learning
von: Garrod, Connall, et al.
Veröffentlicht: (2024)

flexBART: Flexible Bayesian regression trees with categorical predictors
von: Deshpande, Sameer K.
Veröffentlicht: (2022)

Elucidating Rectified Flow with Deterministic Sampler: Polynomial Discretization Complexity for Multi and One-step Models
von: Yang, Ruofeng, et al.
Veröffentlicht: (2025)

Distinguishable Deletion: Unifying Knowledge Erasure and Refusal for Large Language Model Unlearning
von: Yang, Puning, et al.
Veröffentlicht: (2026)

Weight Spectra Induced Efficient Model Adaptation
von: Si, Chongjie, et al.
Veröffentlicht: (2025)

Extracting Emotion Phrases from Tweets using BART
von: Rezapour, Mahdi
Veröffentlicht: (2024)

ChemDFM-X: Towards Large Multimodal Model for Chemistry
von: Zhao, Zihan, et al.
Veröffentlicht: (2024)

CIC-BART-SSA: Controllable Image Captioning with Structured Semantic Augmentation
von: Basioti, Kalliopi, et al.
Veröffentlicht: (2024)

Spectra: Rethinking Optimizers for LLMs Under Spectral Anisotropy
von: Huang, Zhendong, et al.
Veröffentlicht: (2026)

Elucidating Representation Degradation Problem in Diffusion Model Training
von: Yao, Zhipeng, et al.
Veröffentlicht: (2026)

Towards a General Time Series Forecasting Model with Unified Representation and Adaptive Transfer
von: Wang, Yihang, et al.
Veröffentlicht: (2024)

LMDM:Latent Molecular Diffusion Model For 3D Molecule Generation
von: Chen, Xiang
Veröffentlicht: (2024)

KGOT: Unified Knowledge Graph and Optimal Transport Pseudo-Labeling for Molecule-Protein Interaction Prediction
von: Qin, Jiayu, et al.
Veröffentlicht: (2025)

MUDiff: Unified Diffusion for Complete Molecule Generation
von: Hua, Chenqing, et al.
Veröffentlicht: (2023)

Functional BART with Shape Priors: A Bayesian Tree Approach to Constrained Functional Regression
von: Cao, Jiahao, et al.
Veröffentlicht: (2025)

A Unified Graph Language Model for Multi-Domain Multi-Task Graph Alignment Instruction Tuning
von: Chen, Haibo, et al.
Veröffentlicht: (2026)

UniIF: Unified Molecule Inverse Folding
von: Gao, Zhangyang, et al.
Veröffentlicht: (2024)

SpectraLLM: Uncovering the Ability of LLMs for Molecular Structure Elucidation from Multi-Spectral Data
von: Su, Yunyue, et al.
Veröffentlicht: (2025)

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	"99d9ff75d149f58ec3d2de810bf21397"
ui	"standard"
language	"de"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790847202.1005 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "99d9ff75d149f58ec3d2de810bf21397" ]`]
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=99d9ff75d149f58ec3d2de810bf21397; ui=standard; language=de"
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	"216.73.216.147"
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	"28253"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2510_20615/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2510_20615/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790847202.0962
REQUEST_TIME	1790847202

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler