ClinicalEncoder26AM: A Multlilingual Diagnosable ColBERT Model; Evidences from the MultiClinNER Shared Task

Fuente: arXiv

Salvato in:

Dettagli Bibliografici
Autore principale:	Remy, François
Natura:	Preprint
Pubblicazione:	2026
Soggetti:	Computation and Language
Accesso online:	Acceder al recurso
Tags:	Aggiungi Tag Nessun Tag, puoi essere il primo ad aggiungerne!!

Documenti analoghi

Diagnosable ColBERT: Debugging Late-Interaction Retrieval Models Using a Learned Latent Space as Reference
di: Remy, François
Pubblicazione: (2026)

ColBERT-Zero: To Pre-train Or Not To Pre-train ColBERT models
di: Chaffin, Antoine, et al.
Pubblicazione: (2026)

Simple Projection Variants Improve ColBERT Performance
di: Clavié, Benjamin, et al.
Pubblicazione: (2025)

ColBERT Retrieval and Ensemble Response Scoring for Language Model Question Answering
di: Gichamba, Alex, et al.
Pubblicazione: (2024)

Extending Translate-Train for ColBERT-X to African Language CLIR
di: Yang, Eugene, et al.
Pubblicazione: (2024)

ModernBERT + ColBERT: Enhancing biomedical RAG through an advanced re-ranking retriever
di: Rivera, Eduardo Martínez, et al.
Pubblicazione: (2025)

FGR-ColBERT: Identifying Fine-Grained Relevance Tokens During Retrieval
di: Jarolím, Antonín, et al.
Pubblicazione: (2026)

ColBERT-XM: A Modular Multi-Vector Representation Model for Zero-Shot Multilingual Information Retrieval
di: Louis, Antoine, et al.
Pubblicazione: (2024)

ColBERT: Using BERT Sentence Embedding in Parallel Neural Networks for Computational Humor
di: Annamoradnejad, Issa, et al.
Pubblicazione: (2020)

Reproduction Beyond Benchmarks: ConstBERT and ColBERT-v2 Across Backends and Query Distributions
di: Ghosh, Utshab Kumar, et al.
Pubblicazione: (2026)

Jina-ColBERT-v2: A General-Purpose Multilingual Late Interaction Retriever
di: Jha, Rohan, et al.
Pubblicazione: (2024)

Multi-Task Pre-Finetuning of Lightweight Transformer Encoders for Text Classification and NER
di: Zhu, Junyi, et al.
Pubblicazione: (2025)

A model and package for German ColBERT
di: Dang, Thuong, et al.
Pubblicazione: (2025)

Video-ColBERT: Contextualized Late Interaction for Text-to-Video Retrieval
di: Reddy, Arun, et al.
Pubblicazione: (2025)

LegalTurk Optimized BERT for Multi-Label Text Classification and NER
di: Zeidi, Farnaz, et al.
Pubblicazione: (2024)

Multilingual Clinical NER for Diseases and Medications Recognition in Cardiology Texts using BERT Embeddings
di: Danu, Manuela Daniela, et al.
Pubblicazione: (2025)

Diagnosing Representation Dynamics in NER Model Extension
di: Zhang, Xirui, et al.
Pubblicazione: (2025)

ClinSeekAgent: Automating Multimodal Evidence Seeking for Agentic Clinical Reasoning
di: Wu, Juncheng, et al.
Pubblicazione: (2026)

Do LLMs Surpass Encoders for Biomedical NER?
di: Obeidat, Motasem S, et al.
Pubblicazione: (2025)

Beyond Questions: Leveraging ColBERT for Keyphrase Search
di: Gabín, Jorge, et al.
Pubblicazione: (2024)

ColBERT-serve: Efficient Multi-Stage Memory-Mapped Scoring
di: Huang, Kaili, et al.
Pubblicazione: (2025)

Overview of the ClinIQLink 2025 Shared Task on Medical Question-Answering
di: Colelough, Brandon, et al.
Pubblicazione: (2025)

L3Cube-MahaSocialNER: A Social Media based Marathi NER Dataset and BERT models
di: Chaudhari, Harsh, et al.
Pubblicazione: (2023)

WojoodNER 2024: The Second Arabic Named Entity Recognition Shared Task
di: Jarrar, Mustafa, et al.
Pubblicazione: (2024)

ClinDEF: A Dynamic Evaluation Framework for Large Language Models in Clinical Reasoning
di: Tang, Yuqi, et al.
Pubblicazione: (2025)

WikiNER-fr-gold: A Gold-Standard NER Corpus
di: Cao, Danrun, et al.
Pubblicazione: (2024)

m3BERT: A Modern, Multi-lingual, Matryoshka Bidirectional Encoder
di: Wang, Yaoxiang, et al.
Pubblicazione: (2026)

Noise reduction in BERT NER models for clinical entity extraction
di: Jiwani, Kuldeep, et al.
Pubblicazione: (2026)

BioClinical ModernBERT: A State-of-the-Art Long-Context Encoder for Biomedical and Clinical NLP
di: Sounack, Thomas, et al.
Pubblicazione: (2025)

ColBERT-Att: Late-Interaction Meets Attention for Enhanced Retrieval
di: Patel, Raj Nath, et al.
Pubblicazione: (2026)

HLTCOE at LiveRAG: GPT-Researcher using ColBERT retrieval
di: Duh, Kevin, et al.
Pubblicazione: (2025)

Comparative Analysis of Encoder-Based NER and Large Language Models for Skill Extraction from Russian Job Vacancies
di: Matkin, Nikita, et al.
Pubblicazione: (2024)

ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish
di: Gallego, Fernando, et al.
Pubblicazione: (2024)

Fine-tuning the SwissBERT Encoder Model for Embedding Sentences and Documents
di: Grosjean, Juri, et al.
Pubblicazione: (2024)

ClinStructor: AI-Powered Structuring of Unstructured Clinical Texts
di: K, Karthikeyan, et al.
Pubblicazione: (2025)

TurkColBERT: A Benchmark of Dense and Late-Interaction Models for Turkish Information Retrieval
di: Ezerceli, Özay, et al.
Pubblicazione: (2025)

MaLei at MultiClinSUM: Summarisation of Clinical Documents using Perspective-Aware Iterative Self-Prompting with LLMs
di: Ren, Libo, et al.
Pubblicazione: (2025)

MosaicBERT: A Bidirectional Encoder Optimized for Fast Pretraining
di: Portes, Jacob, et al.
Pubblicazione: (2023)

ClinConsensus: A Physician-Calibrated Benchmark for Evaluating Clinical Rubric Coverage in Chinese Medical LLMs
di: Zheng, Xiang, et al.
Pubblicazione: (2026)

Content-based 3D Image Retrieval and a ColBERT-inspired Re-ranking for Tumor Flagging and Staging
di: Jush, Farnaz Khun, et al.
Pubblicazione: (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
language	"it"
ui	"standard"
VUFIND_SESSION	"dc1ce73b6db65677e9114df007a35cde"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790665573.6679 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "dc1ce73b6db65677e9114df007a35cde" ]`]
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	"language=it; ui=standard; VUFIND_SESSION=dc1ce73b6db65677e9114df007a35cde"
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	"63515"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2605_28521/Similar """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2605_28521/Similar"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790665573.6635
REQUEST_TIME	1790665573

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler