Extraction of clinical findings from mammography and breast ultrasound reports: a comparison between specialists and Artificial Intelligence
Authors: Lorenzo Farias, Hanna Reckziegel, Daniela Duarte da Silva Bagatini, Daniel Schulz, Gabriela de Andrade Monteiro, Letícia Zanatta, Ana Laura Brill Thum, Priscila Schmidt Lora, +3 more
Organizations: Department of Engineering, Architecture and Computing, Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS, Brazil · Graduate Program in Industrial Systems and Processes (PPGSPI), Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS, Brazil · Graduate Program in Production and Systems Engineering (PPGEPS), Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, RS, Brazil · Faculty of Medicine (FaMed), Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil · School of Health, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, RS, Brazil · Clínica de Mastologia Dra. Ana Paula Muller Ltda., Porto Alegre, RS, Brazil · Graduate Program in Administration (PPGA) and Graduate Program in Project Management (PPGP), Universidade Nove de Julho (UNINOVE), São Paulo, SP, Brazil
Breast cancer is the leading cause of cancer-related death among women in Brazil, and the time between the request and the release of mammography reports directly influences adherence to screening, making the agility in processing these reports a critical factor for early diagnosis. In this context, this study compares the performance of a Large Language Model (LLM) with manual extraction performed by a team of health researchers in identifying clinical findings from mammography and breast ultrasound reports written in Brazilian Portuguese. Named Entity Recognition (NER) was applied through Prompt Engineering using a few-shot strategy, employing the Gemini 2.5 Flash model, selected from preliminary exploratory tests with four candidate models. The Gemini 2.5 Flash model demonstrated the best performance, achieving a Macro F1 of 0.91 and a Micro F1 of 0.98. The subjective validation, in which 29 exams of different formats were evaluated by health researchers using a Likert scale, yielded an agreement index of 93.1%. The model outperformed human extraction in overall Macro F1 (0.91 vs. 0.72), as in four reports the model correctly identified information that had been omitted or incorrectly recorded during manual extraction, demonstrating its potential as a complementary verification tool alongside specialists. The results confirm the hypothesis that LLMs, when instructed through Prompt Engineering, can achieve performance comparable to or superior to manual extraction by health professionals.
Figures & tables
Figure 1: Mapping process flowchart. Illustrates the stages from bibliographic search for clinical variables, validation with health professionals, identification in reports, FHIR standardization, tabulation in spreadsheet, and final validation.
Model
Benchmark
Latency (s)
Input P.
Output P.
GPT-4o (OpenAI)
1408
0.29
$2.50
$10.00
Claude 3.5 Sonnet (Anthropic)
1283
0.95
$3.00
$15.00
DeepSeek R1
1359
3.40
$1.35
$5.40
Gemini 2.5 Flash (Google)
1394
8.15
$0.15
$3.50
Table 1: Characteristics of models evaluated in exploratory tests. Prices in USD per million tokens. Benchmark : LMArena score [ 22 ] .
Figure 2: Technical methodology flowchart. Shows the stages from report anonymization to prompt preparation, model processing, JSON output, and use in the final prototype.
Clinical Entity
Accuracy
Sensitiv.
Specific.
Precision
F1
Cysts
1.00
1.00
1.00
1.00
1.00
Nodules
1.00
1.00
1.00
1.00
1.00
Calcifications
0.97
0.94
1.00
1.00
0.97
Microcalcifications
0.97
1.00
0.96
0.50
0.66
Macro F1
0.98
0.98
0.99
0.87
0.91
Micro F1 a
–
0.98
–
0.98
0.98
Table 2: Performance per clinical entity of the Gemini 2.5 Flash model after gold standard adjudication.
Figure 3: Global Confusion Matrix (Binary Entities). The model recorded 75 TN and 39 TP, with only 1 FP and 1 FN across 116 evaluated instances.
Figure 4: Confusion Matrix for the BI-RADS Category. All 29 examinations were correctly classified in categories 1 to 6 (Accuracy = 1.00), with no overlap between classes.
Clinical Entity
F1-Score
Sensitivity
Human
AI
Human
AI
Cysts
1.00
1.00
1.00
1.00
Nodules
0.90
1.00
0.90
1.00
Calcifications
0.97
0.97
0.94
0.94
Microcalcifications
0.00 a
0.66
0.00
1.00
Macro F1
0.72
0.91
0.71
0.98
Table 3: Comparison of F1-Score and Sensitivity per clinical entity between human and Gemini 2.5 Flash (adjudicated ground truth as gold standard).
Figure 5: Level of professional agreement with AI. The Global Acceptance Index calculated over 58 evaluations (Likert scale, two professionals) was 93.1%.
Figure 6: Levels of agreement between professionals by examination. Dark green = full agreement (100%); light green = subtle divergence; lilac = disagreement. Only Exam 4 showed substantive divergence regarding the punctiform calcification.
Figure 7: Exam 4: comparison between AI extraction (Gemini 2.5 Flash) and human. The AI applied a dimensional criterion ( < 0.5 cm) to classify the calcification as a microcalcification, while the human adopted morphological and clinical criteria. Disagreement correctable through prompt adjustment.
Figure 8: Exam 15: comparison between AI and human extraction. Report selected for its tendency to induce hallucinations in PDF format; full agreement achieved across all variables with .txt input.
Figure 9: Exam 6: comparison between AI and human extraction. Reference report in tests, with full agreement – absence of cyst, calcification, and microcalcifications, and presence of nodule with description.
Figure 10: Exam 14: comparison between AI and human extraction, demonstrating full agreement including BI-RADS 6 classification and complete nodule description.
Objectives: Automatic data extraction from free-text radiology reports enables large-scale research, but few studies assessed the performance of large language models (LLMs) on Dutch neuroradiology reports. Methods: We analyzed 947 brain MRI reports from a tertiary memory clinic (2016-2021), authored by consultant neuroradiologists. Trained medical students annotated thirty variables; 100 reports were double-annotated to assess inter-rater reliability. We evaluated the performance of the open-weight LLM LLaMA 3.1 using different languages (Dutch vs. English translation) and few-shot prompting with different example selection strategies. Performance was evaluated using balanced accuracy for categorical variables, accuracy and mean absolute error for counts, and text similarity for free-text. Metrics were computed across 10 random splits of the 947 reports. Results: LLaMA 3.1 demonstrated high zero-shot performance for visual rating scores (mean [95%-CI]): Medial Temporal Atrophy: 90% [77-100%] on the left and 96% [94-99%] on the right, Global Cortical Atrophy: 87% [83-91%], and Fazekas: 94% [93-96%]. Microbleed mentions were detected with 93% accuracy [92-95%] and infarct mentions with 82% [80-84%]. Text similarity for lesion location reached 0.95 [0.95-0.96]. Performance was lower for numerical variables: 80% [78-82%] for the number of microbleeds and 66% [63-68%] for infarcts. English translation yielded comparable results. Few-shot prompting improved performance for numerical variables, achieving 92% [90-93%] for microbleeds and 81% [77-85%] for infarcts using structural similarity-based selection. Conclusion: LLaMA 3.1 shows strong potential for extracting data from Dutch neuroradiology reports. Few-shot prompting enhances performance for numerical variables, whereas challenges remain for location-specific variables.
Kaouther Mouheb, Amos Pomp, Antoine Manenti +9
Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands · Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands · Department of Electrical and Electronics Engineering, ENSEEIHT, Toulouse, France +3
Purpose: To compare four multimodal large language models (MLLMs) with radiologists of varying expertise in breast density assessment, BI-RADS assessment, biopsy candidacy determination, and continuous malignancy probability estimation using digital mammography (DM) and contrast-enhanced mammography (CEM). Methods: This study included 179 women with paired DM/CEM examinations and reference standards. Four MLLMs (ChatGPT-5.2, Gemini-3.1 Pro, Sonnet-4.6, Muse Spark) interpreted images with and without masks; three radiologists interpreted non-masked images. Results: For binary density classification on DM, radiologist accuracies ranged from 55.81% to 78.60%, exceeding most MLLM values (62.33%-71.63%), while masks added limited benefit. Five-category BI-RADS accuracies were higher for radiologists on DM (56.74-67.44%) and CEM (62.33-82.79%) compared with MLLMs (DM 31.16-45.12%; CEM 40.00-55.81%). Binary biopsy-candidacy accuracies were likewise higher for radiologists (DM 85.12-89.77%; CEM 86.98-92.09%) than for MLLMs (DM 61.39-75.35%; CEM 69.30-82.79%), although CEM improved performance across all readers. Lesion masks substantially improved MLLM continuous malignancy-probability accuracies from 64.65%-71.63% to 72.56-78.60% on DM and from 67.91%-77.21% to 72.56%-81.86% on CEM, approaching radiologist ranges (DM 63.72-82.79%; CEM 81.86-88.84%). The corresponding AUCs for the top masked models overlapped those of the human readers. Overall, Muse Spark, followed by Sonnet-4.6, demonstrated the strongest performance among the MLLMs across domains. Conclusion: Radiologists generally outperformed MLLMs in categorical tasks, while selected masked models approached human performance for continuous malignancy probability estimation, suggesting a potential adjunctive role.
Ali Abbasian Ardakani, Afshin Mohammadi, Taha Yusuf Kuzan +11
Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University, Krems an der Donau, Austria · Department of Radiology, Faculty of Medicine, Urmia University of Medical Science, Urmia, Iran · Department of Radiology, Yeditepe University, Istanbul, Türkiye +10
Large Language Models are transforming the support for clinical decision and their application in real scenarios. Yet, most benchmarks are conducted in English, and cross-lingual evaluation is needed to tackle the language gaps in global access. We introduce ClinicalBr, the first bilingual benchmark for clinical decision built from real Brazilian case reports. The corpus contains 2,892 cases drawn from 28 SciELO medical journals, spanning 18 specialties, and is structured as parallel Portuguese-English pairs. Each case supports four evaluation tasks: diagnosis retrieval, differential diagnosis, exam recommendation, and treatment planning. We evaluate four models: MedGemma-27B, Sabiá-4, DeepSeek-R1, and o3-mini, across both languages. The central finding is that the Portuguese-English performance gap is task-dependent, not general. In diagnosis retrieval, English yields a consistent advantage across all models, with +7.5-12.1 accuracy points. This advantage disappears in differential diagnosis, exam recommendation, and treatment planning, where confidence intervals cross zero for most models and Portuguese completeness scores are marginally higher. Brazilian-endemic conditions proved easier than the full corpus, not harder, indicating that tropical presentations are adequately represented in current pre-training. Exam recommendation was the hardest task across all models and both languages, with F1 scores below 0.10, well below the differential diagnosis ceiling of 0.20-0.27.
Giordano de Pinho Souza, Glaucia Melo, Josefino Cabral Melo Lima +1
Federal University of Rio de Janeiro · Toronto Metropolitan University Toronto, CA