Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Guo, Jeff, Schwaller, Philippe
Format:	Preprint
Published:	2024
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design
by: Guo, Jeff, et al.
Published: (2024)

Generative Molecular Design with Steerable and Granular Synthesizability Control
by: Guo, Jeff, et al.
Published: (2025)

Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models
by: Guo, Jeff, et al.
Published: (2024)

FSscore: A Machine Learning-based Synthetic Feasibility Score Leveraging Human Expertise
by: Neeser, Rebecca M., et al.
Published: (2023)

Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling
by: Yang, Yuwei, et al.
Published: (2024)

Flow-Based Fragment Identification via Binding Site-Specific Latent Representations
by: Neeser, Rebecca Manuela, et al.
Published: (2025)

Generative molecule evolution using 3D pharmacophore for efficient Structure-Based Drug Design
by: He, Yi, et al.
Published: (2025)

Multi-Objective Latent Space Optimization of Generative Molecular Design Models
by: Abeer, A N M Nafiz, et al.
Published: (2022)

Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Goal Directed Generation
by: Arthur-Loui, Heath, et al.
Published: (2024)

Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
by: Klarner, Leo, et al.
Published: (2024)

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
by: Peng, Xingang, et al.
Published: (2022)

Generative Modeling of Molecular Dynamics Trajectories
by: Jing, Bowen, et al.
Published: (2024)

Rotational Sampling: A Plug-and-Play Encoder for Rotation-Invariant 3D Molecular GNNs
by: Jin, Dian
Published: (2025)

Enhancing Molecular Design through Graph-based Topological Reinforcement Learning
by: Zhang, Xiangyu
Published: (2024)

Unified Guidance for Geometry-Conditioned Molecular Generation
by: Ayadi, Sirine, et al.
Published: (2025)

Graph Diffusion Transformers for Multi-Conditional Molecular Generation
by: Liu, Gang, et al.
Published: (2024)

NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries
by: Nowara, Ewa M., et al.
Published: (2024)

Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space
by: Ketata, Mohamed Amine, et al.
Published: (2024)

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming
by: Xu, Minkai, et al.
Published: (2021)

MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models
by: Kapuśniak, Kacper, et al.
Published: (2025)

Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion
by: Xu, Dong, et al.
Published: (2025)

PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation
by: Luo, Yizhen, et al.
Published: (2025)

Generative Flows on Synthetic Pathway for Drug Design
by: Seo, Seonghwan, et al.
Published: (2024)

IBEX: Information-Bottleneck-EXplored Coarse-to-Fine Molecular Generation under Limited Data
by: Xu, Dong, et al.
Published: (2025)

ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
by: Kyro, Gregory W., et al.
Published: (2023)

Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization
by: Bergues, Noémie, et al.
Published: (2025)

Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design
by: Tagasovska, Nataša, et al.
Published: (2024)

Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders
by: Abeer, A N M Nafiz, et al.
Published: (2024)

Drug Repurposing Targeting COVID-19 3CL Protease using Molecular Docking and Machine Learning Regression Approach
by: Aqeel, Imra, et al.
Published: (2023)

Conditional Latent Space Molecular Scaffold Optimization for Accelerated Molecular Design
by: Boyar, Onur, et al.
Published: (2024)

Cross-Chirality Generalization by Axial Vectors for Hetero-Chiral Protein-Peptide Interaction Design
by: Yang, Ziyi, et al.
Published: (2026)

Molecular Diffusion Models with Virtual Receptors
by: Halfon, Matan, et al.
Published: (2024)

What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?
by: Karczewski, Rafał, et al.
Published: (2024)

Platform for Representation and Integration of multimodal Molecular Embeddings
by: Zheng, Erika Yilin, et al.
Published: (2025)

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

A Standardized Benchmark for Machine-Learned Molecular Dynamics using Weighted Ensemble Sampling
by: Aghili, Alexander, et al.
Published: (2025)

Accelerated Learning on Large Scale Screens using Generative Library Models
by: Weinstein, Eli N., et al.
Published: (2025)

Protein Discovery with Discrete Walk-Jump Sampling
by: Frey, Nathan C., et al.
Published: (2023)

DisorderUnetLM: Validating ProteinUnet for efficient protein intrinsic disorder prediction
by: Kotowski, Krzysztof, 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	"99d9ff75d149f58ec3d2de810bf21397"
ui	"standard"
language	"en"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790847234.2894 "_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=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	"216.73.216.147"
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	"57759"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2405_17066/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2405_17066/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790847234.2747
REQUEST_TIME	1790847234

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"99d9ff75d149f58ec3d2de810bf21397"
ui	"standard"
language	"en"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790847234.2894 "_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=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	"216.73.216.147"
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	"57759"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2405_17066/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2405_17066/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790847234.2747
REQUEST_TIME	1790847234

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Similar Items

Similar Items

Environment & details:

Environment & details: