Pipeline
The SynthesisPerformancePipeline is the main orchestrator for end-to-end extraction.
It chains material extraction, synthesis extraction, judge evaluation, and optional
figure/performance linking.
SynthesisPerformancePipeline
SynthesisPerformancePipeline(material_extractor, synthesis_extractor, judge=None, linking_judge=None, plot_extractor=None, series_linker=None, plot_filter_config=None, figure_segmenter='dino', florence_repo_id='amayuelas/plot-visualization-florence-2-lora-32')
End-to-end pipeline: Paper → Materials → Synthesis → Performance Linking.
This pipeline processes scientific papers to extract: 1. Materials synthesized in the paper 2. Detailed synthesis procedures for each material 3. Performance data from plots, linked to specific materials
The pipeline is modular - each component can be customized or replaced.
Initialize the pipeline.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
material_extractor
|
Extractor for identifying materials in paper |
required | |
synthesis_extractor
|
Extractor for synthesis procedures |
required | |
judge
|
Optional judge for evaluating synthesis quality |
None
|
|
linking_judge
|
Optional judge for evaluating linking quality |
None
|
|
plot_extractor
|
Optional plot extractor (e.g. ClaudeLinePlotDataExtractor). |
None
|
|
series_linker
|
SeriesMaterialLinker | None
|
Optional linker for matching series to materials |
None
|
plot_filter_config
|
PlotFilterConfig | None
|
Optional config for filtering plots |
None
|
figure_segmenter
|
str
|
Backend for figure segmentation,
|
'dino'
|
florence_repo_id
|
str
|
HuggingFace LoRA repo used when
|
'amayuelas/plot-visualization-florence-2-lora-32'
|
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
Methods:
extract_materials(paper_text)
Step 1: Extract list of materials from paper text.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
paper_text
|
str
|
Full paper text |
required |
Returns:
| Type | Description |
|---|---|
list[str]
|
List of material names |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
extract_synthesis(paper_text, material)
Step 2: Extract synthesis procedure for a single material.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
paper_text
|
str
|
Full paper text |
required |
material
|
str
|
Material name to extract synthesis for |
required |
Returns:
| Type | Description |
|---|---|
tuple[GeneralSynthesisOntology, Any]
|
Tuple of (synthesis ontology, evaluation result or None) |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
extract_figures(markdown_text)
Step 3: Extract and classify figures from markdown.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
markdown_text
|
str
|
Markdown text with embedded base64 images |
required |
Returns:
| Type | Description |
|---|---|
list[FigureInfo]
|
List of quantitative figure info objects |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
extract_plot_data(figures, paper_text, si_text='')
Step 4: Extract data from quantitative plots.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
figures
|
list[FigureInfo]
|
List of FigureInfo for quantitative figures |
required |
paper_text
|
str
|
Full paper text for context |
required |
si_text
|
str
|
Supplementary information text |
''
|
Returns:
| Type | Description |
|---|---|
tuple[list[ExtractedLinePlotData], list[FigureInfo]]
|
Tuple of (list of plot data, list of corresponding figures) |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
link_performance(materials, plots, figures)
Step 5: Link plot series to materials.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
materials
|
list[str]
|
List of material names |
required |
plots
|
list[ExtractedLinePlotData]
|
List of extracted plot data |
required |
figures
|
list[FigureInfo]
|
List of corresponding figure info |
required |
Returns:
| Type | Description |
|---|---|
tuple[list[PlotMaterialMapping], LinkingStats]
|
Tuple of (list of mappings, linking statistics) |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
process_paper(paper, skip_figures=False)
Process a single paper through the full pipeline.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
paper
|
Paper
|
Paper object with text content |
required |
skip_figures
|
bool
|
If True, skip figures and performance linking |
False
|
Returns:
| Type | Description |
|---|---|
PipelineResult | None
|
PipelineResult or None if processing failed |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
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process_paper_async(paper, semaphore, skip_figures=False)
async
Process one paper with concurrent LLM calls (asyncio + semaphore).
Same as process_paper but runs independent LLM calls in parallel: - Materials: one call, then synthesis+judge per material in parallel - Plot extraction: one call per figure in parallel - Linking: one call per plot in parallel
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
paper
|
Paper
|
Paper object with text content |
required |
semaphore
|
Semaphore
|
Cap on concurrent LLM calls |
required |
skip_figures
|
bool
|
If True, skip figures and performance linking |
False
|
Returns:
| Type | Description |
|---|---|
PipelineResult | None
|
PipelineResult or None if processing failed |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
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save_results(result, output_dir)
staticmethod
Save pipeline results to disk.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
result
|
PipelineResult
|
PipelineResult to save |
required |
output_dir
|
str
|
Base output directory |
required |
Source code in src/llm_synthesis/services/pipelines/synthesis_performance_pipeline.py
Result models
PipelineResult
Bases: BaseModel
Complete result from the synthesis + performance pipeline.
SynthesisWithPerformanceEntry
Bases: BaseModel
A material's synthesis procedure with linked performance data.