Instruction tuning has become essential for adapting large language models (LLMs) to follow domain-specific prompts. Yet, in specialized fields such as medicine, the scarcity of high-quality French instruction data limits effective supervision. To address this gap, we introduce MedInjection-FR, a large-scale French biomedical instruction dataset comprising 571K instruction-response pairs drawn from three complementary sources: native, synthetic, and translated data. We design a controlled experimental framework to systematically assess how data provenance affects instruction tuning, using Qwen-4B-Instruct fine-tuned across seven configurations combining these sources. Results show that native data yield the strongest performance, while mixed setups, particularly native and translated, provide complementary benefits. Synthetic data alone remains less effective but contributes positively when balanced with native supervision. Evaluation on open-ended QA combines automatic metrics, LLM-as-a-judge assessment, and human expert review; although LLM-based judgments correlate best with human ratings, they show sensitivity to verbosity. These findings highlight that data authenticity and diversity jointly shape downstream adaptation and that heterogeneous supervision can mitigate the scarcity of native French medical instructions.
Figures & tables
Figure 1: Sample instances from the three MedInjection-FR components. Each includes the task type (MCQ, MCQU, or OEQ) and, when applicable, its supporting context. The figure illustrates the diversity of medical reasoning tasks and prompt styles across data sources.
Figure 2: Distribution of medical specialties in MedInjection-FR (native + synthetic components). Proportions are normalized across fourteen major medical categories derived from specialty metadata.
Component
Train
Validation
Test
Total
Native
57563
5055
14629
77247
Generated
76506
–
–
76506
Translated
366370
38011
13293
417674
Total
500439
43066
27931
571436
Table 1: Number of instruction–response pairs in each component (native, synthetic, and translated) and their respective splits into training, validation, and test sets.
QA Type
OEQ
MCQ
MCQU
Count
57509
59592
454335
Table 2: Counts of OEQ, MCQ and MCQU question types within MedInjection-FR.
Model
BLEU
COMET
GPT-4o-mini
51.01
0.8751
Gemini 2.0 Flash
53.72
0.8783
WMT 2024 best system
53.54
0.8760
Table 3: BLEU and COMET scores obtained by Gemini 2.0 Flash-001 and GPT-4o-mini on biomedical translation benchmarks, compared to the best WMT 2024 system.
Figure 3: Quality evaluation of synthetic data by four LLM judges. The left panel reports OEQ scores on a 1-5 scale, and the right panel reports MCQ scores on a 1-3 scale.
Figure 4: t-SNE visualization of instruction embeddings across the three data sources (native, translated, synthetic).
pearson_r
p_value
LLMs
MedGemma-27B
0.61
1.70\times10−11
GEMINI-FLASH-2.0
0.57
7.33\times10−10
GPT-4.1-mini
0.49
1.80\times10−7
HuatuoGPT-o1-72B
0.47
7.78\times10−7
GPT-5
0.38
9.56\times10−5
Metrics
ROUGE-2
0.36
2.22\times10−4
Table 4: Pearson correlation coefficients ( r ) and associated significance levels ( p ) between human expert judgments and automated evaluation metrics on 100 sampled OEQ responses.
MCQ
MCQU
Aggregation
Model
Greedy
Constrained
Greedy
Constrained
Greedy
Constrained
EM
Hamming
EM
Hamming
EM
EM
QWEN-4B (base)
15.92
43.78
18.44
53.42
53.14
56.17 *
34.53
37.31
QWEN-4B-NAT
27.5
59.73
27.5
59.82
53.49
53.67
40.5
40.59
QWEN-4B-TRAD
18.56
53.08
18.0
52.8
54.65
54.88
36.6
36.44
QWEN-4B-SYN
13.3
49.79
12.73
49.94
46.46
46.73
29.88
29.73
Table 5: Performance of all fine-tuning configurations on MCQ and MCQU under greedy and constrained decoding. Results are reported as Exact Match (EM) and Hamming scores. The aggregated columns report the average of EM scores across MCQ and MCQU formats. Since both settings correspond to MCQA and differ only in the number of correct options (single-answer vs. multiple-answer), we treat them as complementary variants of the same task. The aggregation therefore provides a compact summary of overall MCQA performance. Bold values indicate the best-performing models, while asterisks (*) denote the second-best results within each column.
Figure 5: Relationship between mean output length and LLM-judge accuracy across fine-tuned models. Each point represents one configuration, with the dashed line indicating the best-fit linear trend.
Model
OEQ
BLEU
ROUGE-2
METEOR
BERTScore_F1
LLM-as-a-Judge
QWEN-4B (base)
12.08
20.82
30.78
27.22
0.36
QWEN-4B-NAT
31.85 *
22.67
25.58
33.44
0.24
QWEN-4B-TRAD
29.48
21.42
26.49
27.39
0.22
QWEN-4B-SYN
26.73
20.81
24.79
27.54
0.31 *
QWEN-4B-NAT-TRAD
32.09
23.05 *
25.90
35.60 *
0.23
Table 6: Results on OEQ evaluated with automatic text similarity metrics and the LLM-as-a-judge (MedGemma-27B) framework. Bold numbers mark the best results, and asterisks (*) indicate the second-best within each column.
Figure 6: Comparison between average output length and reference length for each model. The vertical dashed line marks the mean reference length ( ≈90tokens ), and the horizontal line represents a perfect length ratio of 1.
Figure 7: System prompt used to generate OEQA synthetic instruction–response pairs from the MORFITT abstract corpus.
Figure 8: System prompt used to generate OEQA synthetic instruction–response pairs from DEFT clinical cases.
Figure 9: System prompt used to generate OEQA synthetic instruction–response pairs from DiaMed clinical cases.
Figure 10: System prompt used to generate MCQA items from the MORFITT abstract corpus.
Figure 11: System prompt used to generate MCQA items from DEFT and DiaMed clinical cases.
Figure 12: System prompt used to automatically evaluate OEQA synthetic question–answer pairs.
Figure 13: System prompt used to automatically evaluate MCQA synthetic question–answer items.
Figure 14: System prompt provided to LLM judges to score answer equivalence against the ground truth.
QCM
QCMU
Aggregation
Model
Greedy
Constrained
Greedy
Constrained
Greedy
Constrained
EM
Hamming
EM
Hamming
EM
EM
QWEN-4B (base)
10.76 4.43
37.09 5.84
12.72 5.10
45.10 7.25
30.98 19.18
33.68 * 19.64
20.87 13.92
23.20 14.35
QWEN-4B-NAT
18.27 7.95
49.20 9.27
18.27 7.95
49.23 9.32
32.80 18.03
32.86 18.14
25.53 13.93
25.56 14.00
QWEN-4B-TRAD
12.48 5.63
45.41 6.83
11.91 5.56
44.96 6.86
33.45 18.54
33.54 18.70
22.97 13.70
22.73 13.79
QWEN-4B-SYN
9.90 2.88
44.47 4.55
9.29 2.91
44.62 4.63
31.18 13.28
31.27 13.43
20.54 9.61
20.28 9.72
Table 7: Performance of all configurations on QCM and QCMU under three answer-order permutations to assess positional bias. Results are macro-averaged across datasets and reported as Exact Match (EM) and Hamming scores. Standard deviations (superscript) correspond to the sample standard deviation across the three answer-order runs, reflecting sensitivity to option reordering. Aggregated columns report the average EM across QCM and QCMU. Bold values indicate the best-performing models, and asterisks (*) indicate the second-best within each column.
Large vision language models (LVLMs) have demonstrated impressive performance across a wide range of tasks. These capabilities largely stem from visual instruction tuning, which fine-tunes models on datasets consisting of curated image-instruction-output triplets. However, in the medical domain, constructing large-scale, high-quality instruction datasets is particularly challenging due to the need for specialized expert knowledge. To address this issue, we propose an instruction-free tuning approach that reduces reliance on handcrafted instructions, leveraging only image-description pairs for fine-tuning. Specifically, we introduce a momentum proxy instruction as a replacement for curated text instructions, which preserves the instruction-following capability of the pre-trained LVLM while promoting updates to parameters that remain valid during inference. Consequently, the fine-tuned LVLM can flexibly respond to domain-specific instructions, even though explicit instructions are absent during fine-tuning. Additionally, we incorporate a response shuffling strategy to mitigate the model's over-reliance on previous words, facilitating more effective fine-tuning. Our approach achieves state-of-the-art accuracy on multiple-choice visual question answering tasks across SKINCON, WBCAtt, CBIS, and MIMIC-CXR datasets, significantly enhancing the fine-tuning efficiency of LVLMs in medical domains.
Myeongkyun Kang, Soopil Kim, Xiaoxiao Li +1
Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada · Department of Robotics and Mechatronics Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea · Division of Intelligent Robot, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea +2
The development of large language models (LLMs) has led to an increased focus on their adaptation to specialized domains and languages, yet the effectiveness of domain adaptation strategies remains unclear. We present a study of medical domain adaptation using French medical question-answering (QA) as a case study. We compare continual pretraining (CPT), supervised fine-tuning (SFT), and their combination across three model families, multiple sizes, and three initialization types, explicitly disentangling adaptation effects from base model choice. We evaluate both multiple-choice (MCQA) and open-ended QA (OEQA) under greedy and constrained decoding using automatic metrics and LLM-as-a-Judge evaluation. For MCQA, CPT+SFT most often achieves the best scores, but gains over SFT are small and frequently not statistically significant, making SFT a strong and cost-effective default. For OEQA, CPT consistently improves overlap-based metrics, while SFT often degrades generation quality; instruction tuning and CPT+SFT are preferred by LLM-based evaluation. Cross-lingual experiments further show effective transfer from French adaptation to English benchmarks. Overall, we provide practical guidelines for selecting adaptation strategies under computational constraints.
Ikram Belmadani, Oumaima El Khettari, Carlos Ramisch +3
Aix-Marseille Univ., CNRS, LIS UMR 7020, 13000 Marseille, France · Nantes Univ., École Centrale Nantes, CNRS, LS2N UMR 6004, 44000 Nantes, France · Grenoble Alpes Univ., CNRS, INRIA, Grenoble INP, LIG UMR 5217, 38000 Grenoble, France
The effectiveness of instruction-tuned Large Language Models (LLMs) is often limited in low-resource linguistic settings due to a lack of high-quality training data. We introduce LuxIT, a novel, monolingual instruction tuning dataset for Luxembourgish developed to mitigate this challenge. We synthesize the dataset from a corpus of native Luxembourgish texts, utilizing DeepSeek-R1-0528, chosen for its shown proficiency in Luxembourgish. Following generation, we apply a quality assurance process, employing an LLM-as-a-judge approach, retaining 227,507 high-quality instruction-answer pairs. To investigate the practical utility of the dataset, we fine-tune 14 smaller-scale LLMs (≤15B parameters) on LuxIT and evaluate them on standardized Luxembourgish proficiency exams and five downstream NLP tasks. Training on LuxIT yields a mean accuracy change of +5.37 percentage points on language exams across all 14 models, with 12 of 14 showing improvement. On NLP downstream tasks, 9 of 14 models improve in macro-averaged F1, though gains on the two benchmarks do not systematically correlate. These results underscore the feasibility of leveraging monolingual synthetic data to improve LLM capabilities in low-resource languages, while highlighting the multi-faceted nature of language proficiency.
Julian Valline, Cedric Lothritz, Siwen Guo +1
Luxembourg Institute of Science and Technology 5 Av. des Hauts-Fourneaux L-4362 Esch-sur-Alzette