🎯 SciVisAgentBench Evaluation Report

claude_code Generated: 2026-03-09T15:27:24.015057

📊 Overall Performance

Overall Score

52.2%
201/385 Points

Test Cases

10/13
Completed Successfully

Avg Vision Score

15.6%
Visualization Quality
38/160

PSNR (Scaled)

N/A
Peak SNR (0/10 valid)

SSIM (Scaled)

N/A
Structural Similarity

LPIPS (Scaled)

N/A
Perceptual Distance

Completion Rate

76.9%
Tasks Completed

ℹ️ About Scaled Metrics

Scaled metrics account for completion rate to enable fair comparison across different evaluation modes. Formula: PSNRscaled = (completed_cases / total_cases) × avg(PSNR), SSIMscaled = (completed_cases / total_cases) × avg(SSIM), LPIPSscaled = 1.0 - (completed_cases / total_cases) × (1.0 - avg(LPIPS)). Cases with infinite PSNR (perfect match) are excluded from the PSNR calculation.

🔧 Configuration

anthropic
claude-sonnet-4-5
N/A
$3.00
$15.00

📝 case_1

❌ FAILED
0/0 (0.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Visualize the molecular using a licorice representation. 4. Take a screenshot of the visualization. Q1. Does it show a licorice representation of the protein? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_basic_vis.txt".

Score

0/0 (0.0%)

Questions & Correct Answers

Agent's Answers

Judge's Evaluation

Evaluation:

📊 Detailed Metrics

Text Q&A Score
0/0
0.0%
Input Tokens
476,313
Output Tokens
5,976
Total Tokens
482,289
Total Cost
$1.5186

📝 case_2

10/10 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Visualize the molecular using a CPK or similar representation where atoms are colored by their chemical element. 4. Take a screenshot of the visualization. Q1. Is the molecule colored according to the chemical element of its atoms (e.g., CPK coloring)? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_element_coloring.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

yes

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided task answer is "yes", which matches the expected correct answer "Yes" (case-insensitive match). Therefore, it fully satisfies the criterion.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
2,026,085
Output Tokens
20,313
Total Tokens
2,046,398
Total Cost
$6.3830

📝 case_3

10/10 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Select all carbon atoms and color them cyan. 4. Take a screenshot of the visualization. Q1. Are all carbon atoms colored cyan? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_selection_coloring.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

yes

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided answer is "yes", which matches the expected correct answer "Yes" (case-insensitive match). Therefore, it fully satisfies the criterion.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
968,562
Output Tokens
11,960
Total Tokens
980,522
Total Cost
$3.0851

📝 case_4

10/10 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Color the molecule according to atomic charge: use one color for positive charges, another for negative charges, and a third for neutral atoms. 4. Take a screenshot of the visualization. Q1. Is the molecule colored by atomic charge (differentiating positive, negative, and neutral)? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_charge_coloring.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

yes

Judge's Evaluation

Evaluation:

Criterion 1 (Q1 correct answer: Yes): The provided task answer is "yes", which matches the expected correct answer "Yes" (case-insensitive match). Therefore, it fully satisfies the evaluation criterion.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
1,041,860
Output Tokens
13,831
Total Tokens
1,055,691
Total Cost
$3.3330

📝 case_5

10/10 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Select all oxygen atoms in residues 1 to 20 and color them red. 4. Take a screenshot of the visualization. Q1. Are all oxygen atoms in residues 1 to 20 colored red? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_complex_selection.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1. Are all oxygen atoms in residues 1 to 20 colored red? (yes/no) yes

Judge's Evaluation

Evaluation:

Criterion 1 expects the answer to Q1 to be "Yes." The provided answer is "yes," which matches the correct answer (case-insensitive) and fully satisfies the criterion.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
1,484,748
Output Tokens
14,438
Total Tokens
1,499,186
Total Cost
$4.6708

📝 case_6

❌ FAILED
0/0 (0.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to visualize a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Select all aromatic residues (PHE, TYR, TRP) and color them purple. 4. Take a screenshot of the visualization. Q1. Are all aromatic residues (PHE, TYR, TRP) colored purple? (yes/no) 5. Answer Q1 in a plain text file "md_analysis/results/answers_aromatic_selection.txt".

Score

0/0 (0.0%)

Questions & Correct Answers

Agent's Answers

Judge's Evaluation

Evaluation:

📊 Detailed Metrics

Text Q&A Score
0/0
0.0%
Input Tokens
1,136,579
Output Tokens
14,383
Total Tokens
1,150,962
Total Cost
$3.6255

📝 case_7

20/20 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to perform a structural analysis on a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the Root Mean Square Deviation (RMSD) of the structure against itself. 4. Calculate the Root Mean Square Fluctuation (RMSF) for the structure. 5. Save the computed RMSD and RMSF values as plain text to "md_analysis/results/answers_rmsd_rmsf.txt".

Score

20/20 (100.0%)

Questions & Correct Answers

1. Does the output report the calculated RMSD? 2. Does the output report the calculated RMSF values or state that it requires a trajectory?

Agent's Answers

RMSD: 0.000000 RMSF (average): 9.222054 RMSF per atom: Atom 1: 8.399676 Atom 2: 4.673490 Atom 3: 4.955503 Atom 4: 4.537938 Atom 5: 7.958146 Atom 6: 9.437131 Atom 7: 10.007563 Atom 8: 10.392595 Atom 9: 7.000104 Atom 10: 5.714867 Atom 11: 8.920800 Atom 12: 8.514920 Atom 13: 5.505427 Atom 14: 7.990563 Atom 15: 10.781055 Atom 16: 9.680588 Atom 17: 9.729003 Atom 18: 13.144714 Atom 19: 15.273231 Atom 20: 13.891484 Atom 21: 12.115908 Atom 22: 10.976288 Atom 23: 7.462499 Atom 24: 8.728856 Atom 25: 9.754390 Atom 26: 6.846493 Atom 27: 5.228111 Atom 28: 8.658545 Atom 29: 9.101098 Atom 30: 6.827832 Atom 31: 6.835857 Atom 32: 3.382820 Atom 33: 5.156308 Atom 34: 6.724314 Atom 35: 9.843549 Atom 36: 12.936485 Atom 37: 13.820871 Atom 38: 12.886225 Atom 39: 13.252047 Atom 40: 10.606687 Atom 41: 12.605245 Atom 42: 13.986153 Atom 43: 12.498553 Atom 44: 8.824367 Atom 45: 10.299373 Atom 46: 8.346745

Judge's Evaluation

Evaluation:

Criterion 1 (RMSD reported): 10/10. The output explicitly reports an RMSD value ("RMSD: 0.000000"), satisfying the requirement to report the calculated RMSD. Criterion 2 (RMSF values or trajectory requirement stated): 10/10. The output reports RMSF in multiple forms: an overall average RMSF ("RMSF (average): 9.222054") and a detailed per-atom RMSF list for atoms 1–46. This fully satisfies the requirement to report calculated RMSF values (and does not need to state a trajectory requirement since values are provided).

📊 Detailed Metrics

Text Q&A Score
20/20
100.0%
Input Tokens
331,085
Output Tokens
7,047
Total Tokens
338,132
Total Cost
$1.0990

📝 case_8

10/10 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to calculate the compactness of a protein from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the Radius of Gyration (Rg) of the protein structure. 4. Save the calculated Radius of Gyration as plain text to "md_analysis/results/answers_rg.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Does the output report a numeric value for the calculated Radius of Gyration?

Agent's Answers

9.6030

Judge's Evaluation

Evaluation:

Criterion 1: The output clearly reports a numeric value ("9.6030") for the calculated Radius of Gyration. This directly satisfies the requirement to provide a numeric value.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
213,614
Output Tokens
3,431
Total Tokens
217,045
Total Cost
$0.6923

📝 case_9

20/20 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to calculate specific geometric properties of a molecular structure from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the distance between the alpha carbons of residue 1 and residue 10. 4. Calculate the backbone dihedral angles (phi and psi) for residue 5. 5. Save the computed distance and angles as plain text to "md_analysis/results/answers_distances_angles.txt".

Score

20/20 (100.0%)

Questions & Correct Answers

1. Does the output report the calculated distance between the alpha carbons of residue 1 and 10? 2. Does the output report the calculated phi and psi dihedral angles for residue 5?

Agent's Answers

Molecular Structure Analysis Results ================================================== Structure: 1CRN Source file: /Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis/data/1CRN.cif 1. Distance between alpha carbons: Residue 1 (CA) to Residue 10 (CA): 12.603 Å 2. Backbone dihedral angles for residue 5: Phi angle: -76.182° Psi angle: -18.979°

Judge's Evaluation

Evaluation:

Criterion 1 (10/10): The output explicitly reports the distance between the alpha carbons (CA) of residue 1 and residue 10 as 12.603 Å, directly satisfying the requirement. Criterion 2 (10/10): The output explicitly reports both backbone dihedral angles for residue 5, giving a phi angle of -76.182° and a psi angle of -18.979°, which fully satisfies the requirement.

📊 Detailed Metrics

Text Q&A Score
20/20
100.0%
Input Tokens
211,904
Output Tokens
3,510
Total Tokens
215,414
Total Cost
$0.6884

📝 case_10

10/10 (100.0%)

📋 Task Description

Your agent_mode is "claude_code_claude-sonnet-4-5_exp1", use it when saving results. Your working directory is "/Users/liu42/gitRepo/LC/2026_AgentBenchmark/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis", and you should have access to it. In the following prompts, we will use relative path with respect to your working path. But remember, when you load or save any file, always stick to absolute path. 1. I want you to calculate the number of contacts in a folded protein from a CIF file. 2. Load the data/1CRN.cif. 3. Calculate the number of contacts within an 8 Angstrom cutoff. 4. Save the total count of contacts as plain text to "md_analysis/results/answers_native_contacts.txt".

Score

10/10 (100.0%)

Questions & Correct Answers

1. Does the output report a numeric count of contacts?

Agent's Answers

11172

Judge's Evaluation

Evaluation:

Criterion 1 (numeric count of contacts): The output is "11172", which is a numeric value and can be interpreted as a count. It directly reports a number without ambiguity, satisfying the requirement to report a numeric count of contacts.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
189,200
Output Tokens
2,484
Total Tokens
191,684
Total Cost
$0.6049

📝 curved-membrane

⚠️ LOW SCORE
21/45 (46.7%)

📋 Task Description

1. Please load the Martini coarse-grained simulation file from "curved-membrane/data/curved-membrane.gro" into VMD. 2. Use VMD to show a zoomed in view of the membrane side coloring the water blue and the lipid phosphate (PO4 beads) red, and take a screenshot. 3. Analyze the visualization and answer the following questions: Q1: Is there any water that penetrates into the membrane phase? (yes/no) 4. Save your work: Save the VMD state as "curved-membrane/results/{agent_mode}/curved-membrane.vmd". Save the screenshot of the visualization as "curved-membrane/results/{agent_mode}/curved-membrane.png". Save the answers to the analysis questions in plain text as "curved-membrane/results/{agent_mode}/answers.txt".

🖼️ Visualization Comparison

Ground Truth

Ground Truth

Agent Result

Result

Score Summary

Total Score
3/20
Goals
2
Points/Goal
10
Goal 1
2/10
Criterion: Does the visualization show a side view of a bilayer rather than a top-down or oblique view?
Judge's Assessment: Ground truth shows a clear VMD-style side view of a curved bilayer: two dense water regions (blue) separated by a central membrane region with red PO4 beads outlining the interfaces. The result image is a 2D scatter plot (Y vs Z) rather than a rendered molecular side view, and it does not visually present the bilayer surfaces/curvature in the same way. This largely fails the intended side-view membrane visualization criterion.
Goal 2
1/10
Criterion: Is water present above and below the bilayer, with a mostly empty region in the middle corresponding to the bilayer core?
Judge's Assessment: In the ground truth, water (blue) is mostly outside the membrane, with a largely empty/low-water middle corresponding to the bilayer core, and PO4 (red) concentrated at the two interfaces. In the result, blue water points appear throughout the entire Z range including the central region, and red PO4 points are broadly scattered rather than forming two clear leaflets/interfaces. It does not reproduce the 'water above and below with an empty bilayer core' appearance seen in the ground truth.

Overall Assessment

The result does not match the ground-truth VMD side-view rendering of a curved membrane. It is a 2D scatter plot with water distributed across the membrane region, so both the side-view bilayer presentation and the correct water-outside/empty-core structure are not achieved.

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1: Is there any water that penetrates into the membrane phase? A1: yes

Judge's Evaluation

Evaluation:

Criterion 1 expects the answer to Q1 to be 'Yes'. The provided answer (A1: 'yes') matches the correct answer exactly in meaning; capitalization does not affect correctness here. Therefore it fully meets the evaluation criterion.

📊 Detailed Metrics

Visualization Quality
3/20
Output Generation
5/5
Efficiency
3/10
Text Q&A Score
10/10
100.0%
Input Tokens
999,759
Output Tokens
11,892
Total Tokens
1,011,651
Total Cost
$3.1777

📝 ras-raf-membrane

❌ FAILED
0/65 (0.0%)

📋 Task Description

1. Please load the Martini coarse-grained simulation file from "ras-raf-membrane/data/ras-raf-membrane.gro" into VMD. The simulations has a membrane and a RAS-RAF protein complex. 2. Use VMD to show a zoomed in side view of the membrane and center on the protein with the protein below the membrane. For the bilayer only show the PO4 lipids beads and ROH cholesterol bead and color them gray. Also show the protein back bone beads coloring RAS (resid 2 to 187) red and RAF (resid 188 to 329) blue. Take a screenshot of the visualization. 3. Analyze the visualization and answer the following questions: Q1: Are there any cholesterol head groups in the bilayer center? (yes/no) Q2: How many lipids are there within 1.5 nm of the RAF protein? A. 0 B. 0-3 C. 3-5 D. >5 4. Save your work: Save the VMD state as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.vmd". Save the screenshot of the visualization as "ras-raf-membrane/results/{agent_mode}/ras-raf-membrane.png". Save the answers to the analysis questions in plain text as "ras-raf-membrane/results/{agent_mode}/answers.txt".

🖼️ Visualization Comparison

Ground Truth

Ground Truth
Image not available

Score Summary

Total Score
0/30
Goals
3
Points/Goal
10
Goal 1
0/10
Criterion: Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components?
Judge's Assessment: Not evaluated
Goal 2
0/10
Criterion: Membrane Placement: Is a lipid bilayer clearly visible above the protein?
Judge's Assessment: Not evaluated
Goal 3
0/10
Criterion: Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away?
Judge's Assessment: Not evaluated

Overall Assessment

No overall explanation available

Score

10/20 (50.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes 2. Q2 correct answer: C. 3-5

Agent's Answers

Q1: yes Q2: B

Judge's Evaluation

Evaluation:

Criterion 1 (Q1): The provided answer is "yes", which matches the correct answer "Yes" (case-insensitive match). Score: 10/10. Criterion 2 (Q2): The provided answer is "B", but the correct answer is "C. 3-5". This does not match the required option or range. Score: 0/10. Total: 10/20.

📊 Detailed Metrics

Visualization Quality
0/30
Output Generation
5/5
Efficiency
3/10
Text Q&A Score
10/20
50.0%
Input Tokens
730,915
Output Tokens
11,913
Total Tokens
742,828
Total Cost
$2.3714

📝 trajectory-inspection

⚠️ LOW SCORE
80/175 (45.7%)

📋 Task Description

1. Please load the Martini coarse-grained membrane simulation from "trajectory-inspection/data/trajectory-inspection.gro" into VMD. 2. Load the trajectory file "trajectory-inspection/data/trajectory-inspection_3to5us.xtc". 3. Render a titled side view of the membrane using the last frame of the trajectory. - Show the PO4 beads of POPC lipids in light brown. - Show the PO4 beads of CDL0 lipids in red. - Display the simulation box in blue. Save the rendered image as: "trajectory-inspection/results/{agent_mode}/membrane-curved-tilted-side-5us.jpg" 4. Perform curvature-based lipid distribution analysis for all the frames in the trajectory and generate the following figures: - A 2D density heatmap of CDL0 lipids across the curved membrane surface. - A 2D density heatmap of POPC lipids across the curved membrane surface. - A plot of lipid relative enrichment versus membrane mean curvature for both POPC and CDL0. Save the generated figures as: "trajectory-inspection/results/{agent_mode}/avg_2d_dens_CDL0.png" "trajectory-inspection/results/{agent_mode}/avg_2d_dens_POPC.png" "trajectory-inspection/results/{agent_mode}/relative_enrichment.png" 5. Analyze the trajectory and answer the following questions: Q1: Are there more than 3000 frames in the trajectory? (yes/no) Q2: Is the ratio of POPC lipids to the neutral cardiolipin (CDL0) 8:1? (yes/no) Q3: Do the CDL0 lipids enrich in the negatively curved membrane regions? (yes/no) Q4: Does the total lipid density change significantly with membrane mean curvature? (yes/no) Q5: Do the POPC lipids enrich in the negatively curved membrane regions? (yes/no) 6. Save the answers to the analysis questions in plain text as "trajectory-inspection/results/{agent_mode}/answers.txt".

🖼️ Visualization Comparison - Set 1

Ground Truth

Ground Truth 1
Image not available

Score Summary

Total Score
0/40
Goals
4
Points/Goal
10
Goal 1
0/10
Criterion: Do both images show a side view of a curved lipid bilayer rather than a top-down view?
Judge's Assessment: Not evaluated
Goal 2
0/10
Criterion: Are two lipid species visible with different colors, corresponding to POPC and CDL0 PO4 beads?
Judge's Assessment: Not evaluated
Goal 3
0/10
Criterion: Does the membrane visibly undulate, with one lipid type enriched on the inner curvature and the other on the outer curvature?
Judge's Assessment: Not evaluated
Goal 4
0/10
Criterion: Is the simulation box shown in blue with the membrane inside the box
Judge's Assessment: Not evaluated

Overall Assessment

No overall explanation available

🖼️ Visualization Comparison - Set 2

Ground Truth

Ground Truth 2

Agent Result

Result 2

Score Summary

Total Score
6/20
Goals
2
Points/Goal
10
Goal 1
4/10
Criterion: Do both images show a curved membrane band visualized as a heatmap density map?
Judge's Assessment: Ground truth shows a clearly curved, sinusoidal membrane band rendered as a 2D heatmap (high density along a curved midline with lower density outside). The result image is a rectangular 2D heatmap with mostly vertical banding and no obvious curved membrane outline/band geometry, so it does not visually depict the curved membrane surface in the same way.
Goal 2
2/10
Criterion: Is higher CDL0 density concentrated along the inner side of the curved membrane in both images?
Judge's Assessment: In the ground truth, the highest CDL0 density is concentrated along the inner (concave/negatively curved) side of the curved membrane band. In the result, the brightest regions appear as two vertical high-density stripes and do not align with an inner side of a curved membrane (since curvature is not visibly represented), so the specific inner-side enrichment pattern is not reproduced.

Overall Assessment

The result provides a CDL0 density heatmap, but it does not match the ground truth’s key visual feature: a curved membrane band with density concentrated along the inner/concave side. The result looks like a flat XY density map with vertical striping, making curvature-based localization/enrichment not visually comparable to the ground truth.

🖼️ Visualization Comparison - Set 3

Ground Truth

Ground Truth 3

Agent Result

Result 3

Score Summary

Total Score
7/20
Goals
2
Points/Goal
10
Goal 1
4/10
Criterion: Do both images show a curved membrane band represented as a heatmap density map?
Judge's Assessment: Ground truth shows a curved, band-like membrane trace rendered as a smooth 2D heatmap following a sinusoidal midline, with contours aligned to the curved surface. The result image is a rectangular, pixelated 2D heatmap over the whole XY plane and does not depict the membrane as a curved band/surface. Thus the key visual structure (curved membrane band heatmap) is not matched.
Goal 2
3/10
Criterion: Is higher POPC density concentrated along the outer side of the curved membrane in both images?
Judge's Assessment: In the ground truth, POPC density is clearly higher along the outer side of the curved membrane band (outer leaflet/outer arc of the sinusoid) relative to the inner side. In the result, density appears as broad vertical striping and patchy noise across the rectangular domain, not specifically concentrated on the outer side of a curved membrane. Therefore the outer-side enrichment pattern is not reproduced.

Overall Assessment

The result does not replicate the defining curved-band heatmap representation of the membrane seen in the ground truth, and consequently does not show the characteristic higher POPC density along the outer arc of the curved membrane. The output looks like an XY histogram/heatmap of positions rather than a curvature-aligned membrane surface density map.

🖼️ Visualization Comparison - Set 4

Ground Truth

Ground Truth 4

Agent Result

Result 4

Score Summary

Total Score
22/30
Goals
3
Points/Goal
10
Goal 1
7/10
Criterion: Do both plots show enrichment values plotted against membrane mean curvature?
Judge's Assessment: Ground truth shows relative enrichment plotted against mean curvature (nm^-1) with smooth curves and uncertainty bands. The result image also plots relative enrichment vs mean curvature, but uses different curvature units/range (1/Å with a much narrower range) and shows discrete point-to-point lines rather than the smooth trend seen in the ground truth. Core requirement (enrichment vs curvature) is met, but the mapping/scale differs noticeably.
Goal 2
6/10
Criterion: Are two curves corresponding to POPC and CDL0 visible in both plots?
Judge's Assessment: Both ground truth and result show two curves corresponding to POPC and CDL0 with a legend. However, the result’s trends are qualitatively different from the ground truth: in the ground truth CDL0 is >1 over negative curvature and drops below 1 at positive curvature while POPC is mostly <1 then rises; in the result POPC stays ~1.04–1.12 across the full range and CDL0 stays mostly <1 with a sharp dip near 0. Two curves are present, but they do not match the expected behavior.
Goal 3
9/10
Criterion: Is a horizontal reference line around enrichment = 1 present in both plots?
Judge's Assessment: A horizontal reference line at enrichment = 1 is present in both plots (dashed line). Styling differs slightly (dash pattern/weight), but the reference line is clearly visible and correctly placed in the result.

Overall Assessment

The result plot satisfies the basic structural requirements: enrichment is plotted vs mean curvature, both POPC and CDL0 curves are shown, and an enrichment=1 reference line is included. However, compared to the ground truth, the curvature axis units/range and the qualitative enrichment trends differ substantially, reducing match quality for goals 1 and 2.

Score

40/50 (80.0%)

Questions & Correct Answers

1. Q1 correct answer: No (the trajectory contains 2000 frames). 2. Q2 correct answer: No (the lipid ratio is 9:1). 3. Q3 correct answer: Yes (CDL0 lipids enrich in negatively curved regions). 4. Q4 correct answer: Yes (relative density varies roughly between 0.8 and 1.3). 5. Q5 correct answer: No (POPC lipids enrich in positively curved regions, not negative).

Agent's Answers

Q1: no Q2: no Q3: no Q4: yes Q5: no

Judge's Evaluation

Evaluation:

Criterion 1 (Q1): Answered "no", which matches the correct answer (No; trajectory contains 2000 frames). Score: 10/10. Criterion 2 (Q2): Answered "no", which matches the correct answer (No; lipid ratio is 9:1). Score: 10/10. Criterion 3 (Q3): Answered "no", but the correct answer is Yes (CDL0 lipids enrich in negatively curved regions). This is incorrect. Score: 0/10. Criterion 4 (Q4): Answered "yes", which matches the correct answer (Yes; relative density varies roughly between 0.8 and 1.3). Score: 10/10. Criterion 5 (Q5): Answered "no", which matches the correct answer (No; POPC enrich in positively curved regions, not negative). Score: 10/10. Total: 40/50. Only Q3 fails to meet the evaluation criterion; all other answers match the expected responses.

📊 Detailed Metrics

Visualization Quality
35/110
Output Generation
5/5
Efficiency
0/10
Text Q&A Score
40/50
80.0%
Input Tokens
1,756,500
Output Tokens
18,557
Total Tokens
1,775,057
Total Cost
$5.5479