Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2506.21567

BioPars: A Pretrained Biomedical Large Language Model for Persian Biomedical Text Mining

Baqer M. Merzah·Tania Taami·Salman Asoudeh·Saeed Mirzaee·Amir reza Hossein pour·Amir Ali Bengari
View original source ↗Read source document ↗Export metadata ↓

Abstract

Large Language Models (LLMs) have recently gained attention in the life sciences due to their capacity to model, extract, and apply complex biological information. Beyond their classical use as chatbots, these systems are increasingly used for complex analysis and problem-solving in specialized fields, including bioinformatics. First, we introduce BIOPARS-BENCH, a dataset from over 10,000 scientific articles, textbooks, and medical websites. BioParsQA was also introduced to evaluate the proposed model, which consists of 5,231 Persian medical questions and answers. This study then introduces BioPars, a simple but accurate measure designed to assess LLMs for three main abilities: acquiring subject-specific knowledge, interpreting and synthesizing such knowledge, and demonstrating proper evidence. Comparing ChatGPT, Llama, and Galactica, our study highlights their ability to remember and retrieve learned knowledge but also reveals shortcomings in addressing higher-level, real-world questions and fine-grained inferences. These findings indicate the need for further fine-tuning to address the capabilities of LLM in bioinformatics tasks. To our knowledge, BioPars is the first application of LLM in Persian medical QA, especially for generating long answers. Evaluation of four selected medical QA datasets shows that BioPars has achieved remarkable results compared to comparative approaches. The model on BioParsQA achieved a ROUGE-L score of 29.99, which is an improvement over GPT-4 1.0. The model achieved a BERTScore of 90.87 with the MMR method. The MoverScore and BLEURT values were also higher in this model than the other three models. In addition, the reported scores for the model are MoverScore=60.43 and BLEURT=50.78. BioPars is an ongoing project and all resources related to its development will be made available via the following GitHub repository: https://github.com/amirap80/BioPars.

Explore related subjects

cs.CLcs.AIcs.LG

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Baqer M. Merzah, Tania Taami, Salman Asoudeh, Saeed Mirzaee, Amir reza Hossein pour, Amir Ali Bengari. 2025-07-01. BioPars: A Pretrained Biomedical Large Language Model for Persian Biomedical Text Mining. https://arxiv.org/abs/2506.21567

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

DA-Cramming: Enhancing Cost-Effective Language Model Pretraining with Dependency Agreement Integration

Pretraining language models is still a challenge for many researchers due to its substantial computational costs. As such, there is growing interest in developing more affordable pretraining methods. One notable advancement in this area is the Cramming technique (Geiping and Goldstein, 2022), which enables the pretraining of BERT-style language models using just one GPU in a single day. Building on this innovative approach, we introduce the Dependency Agreement Cramming (DA-Cramming), an efficient framework that integrates information about dependency agreements into the pretraining process. Unlike existing methods that leverage similar semantic information during finetuning, our approach represents a pioneering effort focusing on enhancing the foundational language understanding with semantic information during pretraining. We meticulously design a dual-stage pretraining work flow with four dedicated submodels to capture representative dependency agreements at the chunk level, effectively transforming these agreements into embeddings to benefit the pretraining. Extensive empirical results demonstrate that our method significantly outperforms previous methods across various tasks.

cs.CL↗
arXiv2026

BigO(Bench): Can LLMs Generate Code with Controlled Time and Space Complexity?

We introduce BigO(Bench), a novel coding benchmark designed to evaluate the capabilities of generative language models in understanding and generating code with specified time and space complexities. This benchmark addresses the gap in current evaluations that often overlook the ability of models to comprehend and produce code constrained by computational complexity. BigO(Bench) includes tooling to infer the algorithmic complexity of any Python function from profiling measurements, including human- or LLM-generated solutions. BigO(Bench) also includes of set of 3,105 coding problems and 1,190,250 solutions from Code Contests annotated with inferred (synthetic) time and space complexity labels from the complexity framework, as well as corresponding runtime and memory footprint values for a large set of input sizes. We present results from evaluating multiple state-of-the-art language models on this benchmark, highlighting their strengths and weaknesses in handling complexity requirements. In particular, token-space reasoning models are unrivaled in code generation but not in complexity understanding, hinting that they may not generalize well to tasks for which no reward was given at training time.

cs.CL↗
arXiv2026

UR$^2$: Unify RAG and Reasoning through Reinforcement Learning

Large Language Models (LLMs) have shown strong capabilities through two complementary paradigms: Retrieval-Augmented Generation (RAG) for knowledge grounding and Reinforcement Learning from Verifiable Rewards (RLVR) for complex reasoning. However, existing attempts to unify these paradigms remain narrow in scope, typically limited to open-domain QA with fixed retrieval settings, which constrains generalization to broader domains. To address this limitation, we propose UR$^2$ (Unified RAG and Reasoning)), a general reinforcement learning framework that dynamically coordinates retrieval and reasoning. UR$^2$ introduces two key designs: a difficulty-aware curriculum that selectively invokes retrieval only for challenging instances, and a hybrid knowledge access strategy that combines domain-specific offline corpora with on-the-fly LLM-generated summaries. Together, these components mitigate the imbalance between retrieval and reasoning and improve robustness to noisy information. Experiments on open-domain QA, MMLU-Pro, medical, and mathematical reasoning tasks show that UR$^2$, built on Qwen-2.5-3/7B and LLaMA-3.1-8B, consistently outperforms existing RAG and RL baselines, and achieves performance comparable to GPT-4o-mini and GPT-4.1-mini on several benchmarks. Code, models, and data are available at https://github.com/Tsinghua-dhy/UR2.

cs.CL↗