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Zulfat Miftahutdinov

5 accepted papers

2026

When Single Answer Is Not Enough: Rethinking Single-Step Retrosynthesis Benchmarks for LLMs

ICML 2026poster

Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance remains limited. Existing benchmarks and metrics typically rely on published synthetic procedures and Top-K accuracy based…

Cited by 0SourceScholar
2025

nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder

AAAI 2025technical

Recent advancements have integrated Language Models (LMs) into a drug discovery pipeline. However, existing models mostly work with SMILES and SELFIES chemical string representations, which lack spatial features vital for drug discovery. Additionally, attempts to translate chemical 3D structures int…

Cited by 0SourcePDFScholar
2022

A Comprehensive Evaluation of Biomedical Entity-centric Search

EMNLP 2022industry

Biomedical information retrieval has often been studied as a task of detecting whether a system correctly detects entity spans and links these entities to concepts from a given terminology. Most academic research has focused on evaluation of named entity recognition (NER) and entity linking (EL) mod…

Cited by 3SourcePDFScholar
2022

RuCCoN: Clinical Concept Normalization in Russian

ACL 2022findings

We present RuCCoN, a new dataset for clinical concept normalization in Russian manually annotated by medical professionals. It contains over 16,028 entity mentions manually linked to over 2,409 unique concepts from the Russian language part of the UMLS ontology. We provide train/test splits for diff…

2020

Fair Evaluation in Concept Normalization: a Large-scale Comparative Analysis for BERT-based Models

COLING 2020main

Linking of biomedical entity mentions to various terminologies of chemicals, diseases, genes, adverse drug reactions is a challenging task, often requiring non-syntactic interpretation. A large number of biomedical corpora and state-of-the-art models have been introduced in the past five years. Howe…