Fix json op issue by puja-trivedi · Pull Request #85 · sensein/structsense

puja-trivedi · 2026-03-02T18:37:35Z

Resolving issue #84

This should be merged after #65 is merged

gemini-code-assist · 2026-03-02T18:42:53Z

Summary of Changes

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This pull request establishes a robust framework for benchmarking Named Entity Recognition (NER) capabilities of different large language models within the biomedical domain. It integrates a new dataset, a data processing utility, and a suite of evaluation results and analysis tools. The changes aim to provide a clear and quantifiable assessment of model performance, highlighting the impact of human-in-the-loop processes on NER accuracy and ontology alignment.

Highlights

New Benchmarking Dataset: Introduced a new benchmarking dataset for evaluating StructSense, including named entity recognition (NER) annotations from NCBI Disease and JNLPBA biomedical corpora.
BIO-tagged Data Conversion Utility: Added a Python utility script (bio_txt.py) to convert BIO-tagged TSV/CSV data into continuous text and JSONL entity mappings, handling various parsing complexities.
Comprehensive NER Evaluation Results: Incorporated extensive Named Entity Recognition (NER) evaluation results for various Large Language Models (LLMs) such as Claude 3.7 Sonnet, GPT-4o-mini, and DeepSeek V3 0324 on biomedical literature.
Performance Metrics and Human-in-the-Loop Analysis: Provided detailed performance metrics, including token usage, entity detection rates, ontology mapping completeness, and judge scores, comparing model performance both with and without human-in-the-loop (HIL) intervention.
New Analysis Scripts and Configurations: Included new Python analysis scripts and YAML configuration files to support comprehensive NER evaluation, visualization of results, and detailed statistical analysis of model performance.

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Changelog

evaluation/benchmark/readme.md
- Documented the new benchmarking dataset for StructSense and its structure.
evaluation/benchmark/script/bio_txt.py
- Implemented a Python script for converting BIO-tagged data to continuous text and JSONL formats.
evaluation/combined_all_token_cost_data/old/combined_all_csv.csv
- Added a comprehensive CSV file detailing token usage, cost, and speed for various LLMs across multiple NER tasks.
evaluation/ner/old/evaluation/Integrating-brainstem/with_hil/Integrating-brainstem-token-usage-with-hl.csv
- Added token usage data for NER evaluation on the 'Integrating brainstem' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/with_hil/ner_config_claudesonet_s41593-024-01787-0_with_hil.json
- Added judged NER terms for Claude 3.7 Sonnet on the 'Integrating brainstem' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/with_hil/ner_config_deepseek_s41593-024-01787-0_with_hil.json
- Added judged NER terms for DeepSeek V3 0324 on the 'Integrating brainstem' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/with_hil/ner_config_gpt_s41593-024-01787-0_with_hil.json
- Added judged NER terms for GPT-4o-mini on the 'Integrating brainstem' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/without_hil/Integrating-brainstem-token-usage-without-hl.csv
- Added token usage data for NER evaluation on the 'Integrating brainstem' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/without_hil/ner_config_claudesonet_s41593-024-01787-0_without_hil.json
- Added judged NER terms for Claude 3.7 Sonnet on the 'Integrating brainstem' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/without_hil/ner_config_deepseek_s41593-024-01787-0_without_hil.json
- Added judged NER terms for DeepSeek V3 0324 on the 'Integrating brainstem' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Integrating-brainstem/without_hil/ner_config_gpt_s41593-024-01787-0_without_hil.json
- Added judged NER terms for GPT-4o-mini on the 'Integrating brainstem' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/comprehensive_analysis_report.txt
- Added a text report summarizing comprehensive NER analysis results for the 'Latent-circuit' task.
evaluation/ner/old/evaluation/Latent-circuit/results/comprehensive_summary_table.csv
- Added a CSV table summarizing NER evaluation metrics for the 'Latent-circuit' task.
evaluation/ner/old/evaluation/Latent-circuit/results/entities_missing_ontology.csv
- Added a CSV file listing entities that lacked ontology information.
evaluation/ner/old/evaluation/Latent-circuit/results/entity_pool_summary_with_hil.csv
- Added a CSV file summarizing the entity pool for the 'Latent-circuit' task with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/entity_pool_summary_without_hil.csv
- Added a CSV file summarizing the entity pool for the 'Latent-circuit' task without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/judge_score_detailed_statistics.csv
- Added a CSV file with detailed judge score statistics for NER evaluations.
evaluation/ner/old/evaluation/Latent-circuit/results/judge_score_statistics_with_hil.csv
- Added a CSV file with judge score statistics for the 'Latent-circuit' task with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/judge_score_statistics_without_hil.csv
- Added a CSV file with judge score statistics for the 'Latent-circuit' task without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/label_distribution_statistics.csv
- Added a CSV file detailing the distribution of entity labels.
evaluation/ner/old/evaluation/Latent-circuit/results/location_statistics.csv
- Added a CSV file with statistics on entity detection by paper location.
evaluation/ner/old/evaluation/Latent-circuit/results/missed_entities_details_with_hil.csv
- Added a CSV file listing entities missed by models for the 'Latent-circuit' task with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/missed_entities_details_without_hil.csv
- Added a CSV file listing entities missed by models for the 'Latent-circuit' task without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/model_rankings.csv
- Added a CSV file containing model rankings based on NER evaluation.
evaluation/ner/old/evaluation/Latent-circuit/results/ontology_coverage_summary.csv
- Added a CSV file summarizing ontology coverage in NER evaluations.
evaluation/ner/old/evaluation/Latent-circuit/results/shared_entities_all_models_with_hil.csv
- Added a CSV file listing entities shared by all models for the 'Latent-circuit' task with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/results/shared_entities_all_models_without_hil.csv
- Added a CSV file listing entities shared by all models for the 'Latent-circuit' task without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/with_hil/ner_config_claudesonet_s41593-025-01869-7_with_hil.json
- Added judged NER terms for Claude 3.7 Sonnet on the 'Latent-circuit' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/with_hil/ner_config_deepseek_s41593-025-01869-7_with_hil.json
- Added judged NER terms for DeepSeek V3 0324 on the 'Latent-circuit' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/with_hil/ner_config_gpt_s41593-025-01869-7_with_hil.json
- Added judged NER terms for GPT-4o-mini on the 'Latent-circuit' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/with_hil/ner_token_usage_with_hil_latent.csv
- Added token usage data for NER evaluation on the 'Latent-circuit' paper with human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/without_hil/ner_config_claudesonet_s41593-024-01787-0_without_hil.json
- Added judged NER terms for Claude 3.7 Sonnet on the 'Latent-circuit' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/without_hil/ner_config_deepseek_s41593-025-01869-7_without_hil.json
- Added judged NER terms for DeepSeek V3 0324 on the 'Latent-circuit' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/without_hil/ner_config_gpt_s41593-025-01869-7_without_hil.json
- Added judged NER terms for GPT-4o-mini on the 'Latent-circuit' paper without human-in-the-loop.
evaluation/ner/old/evaluation/Latent-circuit/without_hil/ner_token_usage_without_hil_latent.csv
- Added token usage data for NER evaluation on the 'Latent-circuit' paper without human-in-the-loop.
evaluation/ner/old/ner_config_claudesonet.yaml
- Added YAML configuration for the Claude 3.7 Sonnet NER agent.
evaluation/ner/old/ner_config_deepseek.yaml
- Added YAML configuration for the DeepSeek V3 0324 NER agent.
evaluation/ner/old/ner_config_gpt.yaml
- Added YAML configuration for the GPT-4o-mini NER agent.
evaluation/notebook/README.md
- Documented the token cost and speed analysis script.
evaluation/notebook/ner_comprehensive_summary.py
- Added a Python script for generating comprehensive NER evaluation summaries and visualizations.
evaluation/notebook/ner_data_loader.py
- Added a Python script for loading and preprocessing NER evaluation data.
evaluation/notebook/ner_entity_pool_analysis.py
- Added a Python script for analyzing entity detection performance and false negatives.
evaluation/notebook/ner_judge_score_analysis.py
- Added a Python script for analyzing judge scores and quality assessments in NER.
evaluation/notebook/ner_label_distribution.py
- Added a Python script for analyzing the distribution of entity labels.
evaluation/notebook/ner_location_analysis.py
- Added a Python script for analyzing entity detection patterns across paper locations.
evaluation/notebook/old/integrating-brainstem_w-hil/integrating-brainstem_w-hil_cost_violin.svg
- Added an SVG plot visualizing cost distribution for the 'Integrating brainstem' task with human-in-the-loop.
evaluation/notebook/old/integrating-brainstem_w-hil/integrating-brainstem_w-hil_speed_violin.svg
- Added an SVG plot visualizing speed distribution for the 'Integrating brainstem' task with human-in-the-loop.
evaluation/notebook/old/integrating-brainstem_w-hil/integrating-brainstem_w-hil_speed_vs_cost.svg
- Added an SVG plot visualizing speed versus cost for the 'Integrating brainstem' task with human-in-the-loop.

Activity

The pull request was created by puja-trivedi.
New benchmarking data and scripts for NER evaluation were added.
Comprehensive evaluation results for various LLMs were included.
Analysis and visualization scripts for NER performance metrics were introduced.

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Code Review

This pull request introduces a new benchmarking dataset for StructSense, including a Python script (bio_txt.py) to convert BIO-tagged data into continuous text and JSONL formats. It also adds numerous evaluation results for Named Entity Recognition (NER) tasks, specifically for 'Integrating brainstem' and 'Latent-circuit' papers, comparing various LLMs (Claude 3.7 Sonnet, DeepSeek V3 0324, GPT-4o-mini) both with and without Human-in-the-Loop (HIL). These results are presented in new CSV and JSON files, detailing token usage, costs, speed, entity detection, ontology mapping, and judge scores. Additionally, new Python scripts (ner_comprehensive_summary.py, ner_data_loader.py, ner_entity_pool_analysis.py, ner_judge_score_analysis.py, ner_label_distribution.py, ner_location_analysis.py, ner_ontology_analysis.py) are added to analyze and visualize these NER evaluation metrics, along with a README.md for token cost analysis. Review comments highlight several issues: redundant nested judge_ner_terms keys in JSON output files, an inconsistency in schema definitions where paper_title is specified as a string but examples show it as an array, hardcoded file paths in analysis scripts, and extraneous \ No newline at end of file artifacts in CSV files.

_{Note: Security Review is unavailable for this PR.}

...old/evaluation/Latent-circuit/without_hil/ner_config_gpt_s41593-025-01869-7_without_hil.json

evaluation/ner/old/ner_config_deepseek.yaml

...on/Integrating-brainstem/without_hil/ner_config_deepseek_s41593-024-01787-0_without_hil.json

...luation/Integrating-brainstem/without_hil/ner_config_gpt_s41593-024-01787-0_without_hil.json

.../old/evaluation/Latent-circuit/with_hil/ner_config_deepseek_s41593-025-01869-7_with_hil.json

evaluation/notebook/ner_entity_pool_analysis.py

gemini-code-assist · 2026-03-02T18:58:35Z

evaluation/notebook/ner_judge_score_analysis.py

+    structsense_root = Path(__file__).parent.parent.parent
+    output_dir = structsense_root / "evaluation/ner/evaluation/Latent-circuit/results"


The output directory path is hardcoded. This reduces the script's flexibility. It would be better to pass the output directory as a command-line argument, for example using Python's argparse module. This would allow the script to be run for different evaluation sets without code modification.

gemini-code-assist · 2026-03-02T18:58:35Z

evaluation/notebook/ner_label_distribution.py

+    structsense_root = Path(__file__).parent.parent.parent
+    output_dir = structsense_root / "evaluation/ner/evaluation/Latent-circuit/results"


The output directory path is hardcoded. This reduces the script's flexibility. It would be better to pass the output directory as a command-line argument, for example using Python's argparse module. This would allow the script to be run for different evaluation sets without code modification.

gemini-code-assist · 2026-03-02T18:58:35Z

evaluation/notebook/ner_location_analysis.py

+    structsense_root = Path(__file__).parent.parent.parent
+    output_dir = structsense_root / "evaluation/ner/evaluation/Latent-circuit/results"


The output directory path is hardcoded. This reduces the script's flexibility. It would be better to pass the output directory as a command-line argument, for example using Python's argparse module. This would allow the script to be run for different evaluation sets without code modification.

gemini-code-assist · 2026-03-02T18:58:35Z

evaluation/notebook/old/combined_analysis/data/combined_all_csv.csv

+"Jun 27, 12:53 PM",Favicon for OpenAI,GPT-4o-mini,liteLLM,1236,495,0.000482,47.0 tps,stop,"Multi-animal pose estimation, identification and tracking with DeepLabCut",Resource extraction,NO
+"Jun 27, 12:53 PM",Favicon for OpenAI,GPT-4o-mini,liteLLM,300,262,0.000202,69.8 tps,stop,"Multi-animal pose estimation, identification and tracking with DeepLabCut",Resource extraction,NO
+"Jun 27, 12:53 PM",Favicon for OpenAI,GPT-4o-mini,liteLLM,59016,634,0.00923,67.6 tps,stop,"Multi-animal pose estimation, identification and tracking with DeepLabCut",Resource extraction,NO
+"Jun 27, 12:53 PM",Favicon for OpenAI,GPT-4o-mini,liteLLM,59239,262,0.00904,80.6 tps,stop,"Multi-animal pose estimation, identification and tracking with DeepLabCut",Resource extraction,NO


The file ends with the text \ No newline at end of file. This appears to be an artifact from a version control or diff tool and should be removed. This extra text can cause parsing errors in tools that expect a clean CSV format.

"Jun 27, 12:53 PM",Favicon for OpenAI,GPT-4o-mini,liteLLM,59239,262,0.00904,80.6,tps,stop,"Multi-animal pose estimation, identification and tracking with DeepLabCut",Resource extraction,NO

tekrajchhetri · 2026-03-09T17:16:43Z

@puja-trivedi could you confirm that you've tested and everything is working as expected?

djarecka · 2026-03-16T15:35:56Z

@tekrajchhetri - what is the stage of thi PR.

tekrajchhetri · 2026-03-16T15:39:01Z

@tekrajchhetri - what is the stage of thi PR.
@djarecka It's WIP.

djarecka · 2026-03-16T16:16:48Z

And do we know what is the issue? At the beginning I understood that this is issue with passing the information form agent to another agent/output due to some keys mismatch etc. Is this the case here? Or possibly the agent is just not finding anything interesting?

…ful for scientific articles

…aged output

djarecka · 2026-03-18T15:58:38Z

@tekrajchhetri - even after merging #65 this PR has 277 files changed. Does anything else should be merge first?

Could you please create a PR that has only relevant changes?

tekrajchhetri · 2026-03-18T16:31:34Z

@tekrajchhetri - even after merging #65 this PR has 277 files changed. Does anything else should be merge first?

Could you please create a PR that has only relevant changes?

@djarecka the 277 file changes is coming from the evaluation directory, which can be ignored as it only contains the old evaluation files + some config file --> something I had communicated in meeting. I will see what I can do to remove those files changes it's showing.

Regarding the changes, some of the things are absolutely necessary, like local concept mapping tool and hence it's included here.

tekrajchhetri · 2026-03-18T16:58:19Z

And do we know what is the issue? At the beginning I understood that this is issue with passing the information form agent to another agent/output due to some keys mismatch etc. Is this the case here? Or possibly the agent is just not finding anything interesting?

Yes, we do and they are:

First, we realized from the @puja-trivedi output that we had different task detected, which should not have happened as different task has different post processing strategy. We've fixed it -- detect once and preserve it and use throughout the pipeline (see _get_detected_task_type in app.py where we cache).
Key mismatch. LLM's producing different keys--despite explicit instruction, we did have variations of what we ask but now we have updated to look entities agnostic of keys it holds at any stage (See call to _detect_container_key app.py) and also check promote_stage_output_to_canonical in postprocessing where we promote different keys for consistency.

tekrajchhetri · 2026-03-18T17:50:39Z

Update: After PR 67 & 69 merge we no longer have 277 changes as before.

tekrajchhetri · 2026-03-18T18:04:42Z

@puja-trivedi @djarecka can you test other pdf from your side so that we can merge this?

The parameter was renamed to input_source in the signature but the method body still referenced source, causing a TypeError when called from the CLI.

puja-trivedi · 2026-03-18T21:46:06Z

@tekrajchhetri - There is an inconsistency with the parameter naming source vs input_source. I created PR for this change #97

Fix StructSenseFlow.__init__ parameter name: input_source -> source

tekrajchhetri · 2026-03-19T13:36:52Z

Since @puja-trivedi is able to produce output, we can merge this PR to improvement and improvement to main. The question of less number of entities, depends on the model choice and other parameter--issues independent of output being able to save.

Let me know if @djarecka @puja-trivedi have any concerns?

djarecka · 2026-03-20T16:03:28Z

@tekrajchhetri - the test stopped working due to the issue with poetry, can you please updat

tekrajchhetri · 2026-03-20T18:09:25Z

@tekrajchhetri - the test stopped working due to the issue with poetry, can you please updat

@djarecka can you share the logs because it's unclear what's causing the issue. Also, this means that we will always have an issue if test is failing just because we updated the dependencies.

tekrajchhetri · 2026-03-26T20:43:45Z

before merging this PR we should merge the following PR in order.

Merge this Evaluation result paper #104 to performance_cost_optimization branch.
Merge this Performance cost optimization #100 PR, i.e., from performance_cost_optimization to fix_json_op_issue, i.e., current and fix_json_op_issue to improvement --> main.

tekrajchhetri added 8 commits February 24, 2026 10:50

added prev agents json keys

05b61dc

add dict root level keys check

70ab4d4

json-repair added

da35117

trustcall added

e198e5d

json repair tool using trustcall + json_repair library

3332e19

json repair tool added as default for all agents

0ede87b

normalization of resources to prevent error

97ee75a

prevent no output case

4c51e98

gemini-code-assist bot reviewed Mar 2, 2026

View reviewed changes

puja-trivedi assigned puja-trivedi and tekrajchhetri and unassigned puja-trivedi Mar 2, 2026

Create puja_test_2024withouthil.json

139d4f3

tekrajchhetri changed the base branch from improvement to evaluation_data March 11, 2026 16:46

tekrajchhetri changed the base branch from evaluation_data to improvement March 11, 2026 16:47

tekrajchhetri marked this pull request as draft March 12, 2026 20:42

updated task detection call

9489a39

tekrajchhetri added 8 commits March 16, 2026 18:08

local concept mapping tool

0b4fd25

asyncio_mode added

0f05e44

updated to include local concept mapping information

6f5aa73

fix local model issue -- returning empty NER

34833fe

fallback mechanism added for pdfs where grobid fails as grobid is use…

ee492a3

…ful for scientific articles

updated json structure to align with agents

4e57d78

local concept mapping tool information added

f5594b0

entities not saved issues fixed + improved concept mapping + added st…

f9f5583

…aged output

tekrajchhetri added 3 commits March 18, 2026 11:09

updated ConceptMappingInput types

1e0ba65

added concept mapping local information

a2e0fdd

added link to concept mapping tool

3ae3307

tekrajchhetri marked this pull request as ready for review March 18, 2026 16:44

Merge branch 'improvement' into fix_json_op_issue

c002494

Fix StructSenseFlow.__init__ parameter name: input_source -> source

23ee024

The parameter was renamed to input_source in the signature but the method body still referenced source, causing a TypeError when called from the CLI.

Merge pull request #97 from sensein/test_fix_json_op_issue_20260312

7183fcc

Fix StructSenseFlow.__init__ parameter name: input_source -> source

		structsense_root = Path(__file__).parent.parent.parent
		output_dir = structsense_root / "evaluation/ner/evaluation/Latent-circuit/results"

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puja-trivedi commented Mar 2, 2026 •

edited by djarecka

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