🎯 SciVisAgentBench Evaluation Report

codex_cli Generated: 2026-03-17T11:03:22.033995

📊 Overall Performance

Overall Score

73.3%
297/405 Points

Test Cases

13/13
Completed Successfully

Avg Vision Score

62.0%
Visualization Quality
99/160

PSNR (Scaled)

N/A
Peak SNR (0/13 valid)

SSIM (Scaled)

N/A
Structural Similarity

LPIPS (Scaled)

N/A
Perceptual Distance

Completion Rate

100.0%
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

openai
gpt-5.2
N/A
$1.75
$14.00

📝 case_1

10/10 (100.0%)

📋 Task Description

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 "case_1/results/{agent_mode}/answers_basic_vis.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 and earns full points.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
558,051
Output Tokens
7,255
Total Tokens
565,306
Total Cost
$2.8991

📝 case_2

10/10 (100.0%)

📋 Task Description

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 "case_2/results/{agent_mode}/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
382,374
Output Tokens
5,421
Total Tokens
387,795
Total Cost
$1.9932

📝 case_3

10/10 (100.0%)

📋 Task Description

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 "case_3/results/{agent_mode}/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 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
293,761
Output Tokens
4,909
Total Tokens
298,670
Total Cost
$1.5424

📝 case_4

10/10 (100.0%)

📋 Task Description

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 "case_4/results/{agent_mode}/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 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
675,900
Output Tokens
6,935
Total Tokens
682,835
Total Cost
$3.4835

📝 case_5

10/10 (100.0%)

📋 Task Description

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 "case_5/results/{agent_mode}/answers_complex_selection.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
334,561
Output Tokens
6,901
Total Tokens
341,462
Total Cost
$1.7763

📝 case_6

10/10 (100.0%)

📋 Task Description

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 "case_6/results/{agent_mode}/answers_aromatic_selection.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 exactly (case-insensitive match). Therefore it fully satisfies the criterion.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
352,175
Output Tokens
5,400
Total Tokens
357,575
Total Cost
$1.8419

📝 case_7

20/20 (100.0%)

📋 Task Description

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 "case_7/results/{agent_mode}/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

input_cif: /home/liu42/gitRepo/2026_AgentBench/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis/data/1CRN.cif analysis: rmsd_self_angstrom: 0.00000000 n_residues: 46 rmsf_per_residue_angstrom: A:1:THR 0.00000000 A:2:THR 0.00000000 A:3:CYS 0.00000000 A:4:CYS 0.00000000 A:5:PRO 0.00000000 A:6:SER 0.00000000 A:7:ILE 0.00000000 A:8:VAL 0.00000000 A:9:ALA 0.00000000 A:10:ARG 0.00000000 A:11:SER 0.00000000 A:12:ASN 0.00000000 A:13:PHE 0.00000000 A:14:ASN 0.00000000 A:15:VAL 0.00000000 A:16:CYS 0.00000000 A:17:ARG 0.00000000 A:18:LEU 0.00000000 A:19:PRO 0.00000000 A:20:GLY 0.00000000 A:21:THR 0.00000000 A:22:PRO 0.00000000 A:23:GLU 0.00000000 A:24:ALA 0.00000000 A:25:ILE 0.00000000 A:26:CYS 0.00000000 A:27:ALA 0.00000000 A:28:THR 0.00000000 A:29:TYR 0.00000000 A:30:THR 0.00000000 A:31:GLY 0.00000000 A:32:CYS 0.00000000 A:33:ILE 0.00000000 A:34:ILE 0.00000000 A:35:ILE 0.00000000 A:36:PRO 0.00000000 A:37:GLY 0.00000000 A:38:ALA 0.00000000 A:39:THR 0.00000000 A:40:CYS 0.00000000 A:41:PRO 0.00000000 A:42:GLY 0.00000000 A:43:ASP 0.00000000 A:44:TYR 0.00000000 A:45:ALA 0.00000000 A:46:ASN 0.00000000

Judge's Evaluation

Evaluation:

Criterion 1 (RMSD reported): The output explicitly reports an RMSD value under `analysis` as `rmsd_self_angstrom: 0.00000000`, which satisfies reporting the calculated RMSD. Score: 10/10. Criterion 2 (RMSF reported or notes trajectory requirement): The output provides a full per-residue RMSF table under `rmsf_per_residue_angstrom` for residues A:1 through A:46 (all listed with values, here all 0.00000000). This satisfies reporting RMSF values (it does not need to state trajectory requirement since values are provided). Score: 10/10.

📊 Detailed Metrics

Text Q&A Score
20/20
100.0%

📝 case_8

10/10 (100.0%)

📋 Task Description

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 "case_8/results/{agent_mode}/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

9.602983

Judge's Evaluation

Evaluation:

Criterion 1: The provided output is a numeric value (9.602983), which satisfies the requirement to report a numeric Radius of Gyration. No additional formatting or units are required by the criterion, so it fully meets the expectation.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
184,298
Output Tokens
2,702
Total Tokens
187,000
Total Cost
$0.3603

📝 case_9

20/20 (100.0%)

📋 Task Description

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 "case_9/results/{agent_mode}/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

Input CIF: /home/liu42/gitRepo/2026_AgentBench/SciVisAgentBench/SciVisAgentBench-tasks/molecular_vis/data/1CRN.cif Chain: A, Model: 1 Distance CA(res 1) - CA(res 10): 12.602756 Angstrom Residue 5 phi: 103.818494 degrees Residue 5 psi: 161.020614 degrees

Judge's Evaluation

Evaluation:

Criterion 1 (10/10): The output explicitly reports the distance between the alpha carbons of residue 1 and residue 10 as "Distance CA(res 1) - CA(res 10): 12.602756 Angstrom", which directly satisfies the requirement. Criterion 2 (10/10): The output explicitly reports both dihedral angles for residue 5: "Residue 5 phi: 103.818494 degrees" and "Residue 5 psi: 161.020614 degrees", satisfying the requirement to report calculated phi and psi for residue 5.

📊 Detailed Metrics

Text Q&A Score
20/20
100.0%
Input Tokens
458,313
Output Tokens
6,627
Total Tokens
464,940
Total Cost
$0.8948

📝 case_10

10/10 (100.0%)

📋 Task Description

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 "case_10/results/{agent_mode}/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

203

Judge's Evaluation

Evaluation:

Criterion 1 (numeric count of contacts): The output is "203", which is a clear numeric value and can be interpreted as a count. It directly reports a numeric count, satisfying the criterion fully.

📊 Detailed Metrics

Text Q&A Score
10/10
100.0%
Input Tokens
392,123
Output Tokens
4,566
Total Tokens
396,689
Total Cost
$0.7501

📝 curved-membrane

27/45 (60.0%)

📋 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
11/20
Goals
2
Points/Goal
10
Goal 1
7/10
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 side view of a curved bilayer with two leaflets (red PO4 bands) and water (blue) above/below. The result image also appears to be a side view with similarly curved leaflet traces (red points forming two arcs), not a top-down view. However, the rendering is much sparser/point-like and lacks the dense bead representation seen in the ground truth, making the bilayer structure less visually explicit.
Goal 2
4/10
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 is densely present above and below the membrane, and there is a mostly empty central region corresponding to the bilayer core (white gap between the two red PO4 layers). In the result, while there is still a large central empty region, the water is rendered as very sparse blue dots spread broadly, including near the leaflet regions, and the clear separation of dense water phases from the membrane core is not well matched to the ground truth’s appearance.

Overall Assessment

The result captures the overall side-view geometry of the curved membrane (two curved PO4 layers), but the representation of water and the membrane environment is much less faithful to the ground truth: water density/placement and the clear phase separation are not convincingly shown due to the very sparse point rendering.

Score

10/10 (100.0%)

Questions & Correct Answers

1. Q1 correct answer: Yes

Agent's Answers

Q1: yes

Judge's Evaluation

Evaluation:

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

📊 Detailed Metrics

Visualization Quality
11/20
Output Generation
5/5
Efficiency
1/10
Text Q&A Score
10/10
100.0%
Input Tokens
578,212
Output Tokens
13,412
Total Tokens
591,624
Total Cost
$1.1996

📝 ras-raf-membrane

38/65 (58.5%)

📋 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

Agent Result

Result

Score Summary

Total Score
21/30
Goals
3
Points/Goal
10
Goal 1
7/10
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: Ground truth shows a clearly centered protein complex with dense red (RAS) and blue (RAF) beads, making the two components easy to distinguish. The result image is similarly centered and uses red/blue, but the protein appears much smaller and more sparsely rendered (points rather than larger beads), making the RAS/RAF split less visually clear than in the ground truth.
Goal 2
6/10
Criterion: Membrane Placement: Is a lipid bilayer clearly visible above the protein?
Judge's Assessment: In the ground truth, the membrane bilayer is prominently visible as two thick gray bead bands above the protein. In the result, the bilayer is present above the protein in two bands, but it is extremely faint/sparse (tiny dots), reducing clarity and making the membrane much less visually apparent compared to the ground truth.
Goal 3
8/10
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: Both ground truth and result show two membrane leaflets with the lower leaflet closer to the protein and the upper leaflet farther away, matching the expected ordering. The result preserves this spatial relationship, though the faint rendering makes the separation less obvious than in the ground truth.

Overall Assessment

The result captures the overall geometry (protein centered below a two-leaflet membrane with correct leaflet ordering), but the rendering style differs substantially from the ground truth: both membrane and protein are displayed as very small, sparse points rather than prominent beads, which reduces visual clarity and the ability to distinguish components as cleanly as expected.

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: D

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 "D", but the correct answer is "C. 3-5". This does not meet the criterion. Score: 0/10. Total: 10/20.

📊 Detailed Metrics

Visualization Quality
21/30
Output Generation
5/5
Efficiency
2/10
Text Q&A Score
10/20
50.0%
Input Tokens
543,882
Output Tokens
10,083
Total Tokens
553,965
Total Cost
$1.0930

📝 trajectory-inspection

112/175 (64.0%)

📋 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

Agent Result

Result 1

Score Summary

Total Score
31/40
Goals
4
Points/Goal
10
Goal 1
9/10
Criterion: Do both images show a side view of a curved lipid bilayer rather than a top-down view?
Judge's Assessment: Both ground truth and result show a clear side view (x–z projection) of a curved/undulating bilayer with two leaflets. The result matches the intended side-view geometry well, though it is rendered as a 2D plot rather than the 3D VMD-style rendering seen in the ground truth.
Goal 2
9/10
Criterion: Are two lipid species visible with different colors, corresponding to POPC and CDL0 PO4 beads?
Judge's Assessment: Two lipid species are visible in both: POPC PO4 beads in light brown/tan and CDL0 PO4 beads in red. The colors and separation are consistent with the ground truth; the result uses small scatter markers but preserves the species distinction accurately.
Goal 3
7/10
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: The membrane undulation is visible in the result, and CDL0 (red) appears somewhat clustered in certain curved regions similar to the ground truth. However, the enrichment pattern (inner vs outer curvature preference) is less visually obvious in the result than in the ground truth due to the simplified 2D scatter style and lower visual depth/contrast.
Goal 4
6/10
Criterion: Is the simulation box shown in blue with the membrane inside the box
Judge's Assessment: A blue box is present in both, but the ground truth shows a full 3D simulation box (perspective cube) surrounding the membrane, while the result shows only a 2D rectangular frame/outline. Color matches (blue), but the box depiction does not match the 3D appearance well.

Overall Assessment

The result captures the key side-view curved bilayer geometry and correctly colors POPC vs CDL0 PO4 beads. The main mismatches are stylistic/representational: the result is a 2D scatter plot rather than a VMD-like 3D render, making curvature-dependent enrichment less visually compelling, and the simulation box is shown as a 2D rectangle instead of a 3D blue box.

🖼️ 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 curved membrane band rendered as a continuous, wavy heatmap (high density in a red/orange band following the membrane midline, low density in blue outside). The result image is a rectangular 2D histogram heatmap with no clearly visible curved membrane band; it looks like a boxy density field with a mostly horizontal brighter stripe rather than a curved membrane-shaped band. Thus the requirement is only partially met (it is a heatmap, but not a curved membrane band heatmap like the ground truth).
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, higher CDL0 density is clearly concentrated along the inner side of the curved membrane (the red/orange region tracks the inner arc of the wavy membrane). In the result, the highest density appears as a roughly straight horizontal band near mid-y and some patchy regions, without an evident correspondence to the inner side of a curved membrane. The specific inner-curvature enrichment pattern is not reproduced.

Overall Assessment

The result does produce a CDL0 density heatmap, but it does not resemble the ground-truth curved-membrane-band representation, and it fails to show the characteristic enrichment along the inner (negatively curved) side of the membrane seen in the ground truth.

🖼️ Visualization Comparison - Set 3

Ground Truth

Ground Truth 3

Agent Result

Result 3

Score Summary

Total Score
6/20
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 clearly curved membrane band rendered as a smooth heatmap following an S-shaped midline, with density varying across/along the band. The result image is a rectangular, pixelated 2D heatmap over x–y coordinates with no visible curved-band geometry; it does not depict the membrane as a curved strip. While it is a heatmap, it does not match the curved membrane-band representation seen in the ground truth.
Goal 2
2/10
Criterion: Is higher POPC density concentrated along the outer side of the curved membrane in both images?
Judge's Assessment: In the ground truth, higher POPC density is visibly concentrated along the outer side of the curved membrane (brighter/yellower regions aligned with the outer arc of the band). In the result, density variations are speckled and roughly uniform across the rectangular field, with no clear outer-vs-inner curved-side pattern (and no curved membrane boundary to reference). Thus the outer-side enrichment pattern is not reproduced.

Overall Assessment

The result provides a generic 2D POPC density heatmap but fails to reproduce the key geometric feature of the ground truth: a curved membrane band. Consequently, the characteristic higher POPC density along the outer side of the curved membrane is also not evident in the result.

🖼️ Visualization Comparison - Set 4

Ground Truth

Ground Truth 4

Agent Result

Result 4

Score Summary

Total Score
24/30
Goals
3
Points/Goal
10
Goal 1
8/10
Criterion: Do both plots show enrichment values plotted against membrane mean curvature?
Judge's Assessment: Both the ground truth and result plots show relative enrichment plotted against membrane mean curvature (x-axis is mean curvature; y-axis is relative enrichment). However, the result uses different curvature units/range ("arb. units" spanning roughly -1.8 to 1.8) compared to the ground truth (nm^-1 spanning about -0.4 to 0.1), so the visual correspondence is not exact even though the intended relationship is present.
Goal 2
7/10
Criterion: Are two curves corresponding to POPC and CDL0 visible in both plots?
Judge's Assessment: Two curves corresponding to POPC and CDL0 are visible in both plots and are labeled in legends. The result’s curve shapes differ substantially from the ground truth (GT shows strong CDL0 enrichment at negative curvature and depletion at positive curvature with a POPC rise near slightly positive curvature; result shows POPC ~flat near 1 and CDL0 peaking near zero curvature), so it meets the requirement of two curves but does not match the expected trends well.
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/contrast), but the reference line is clearly visible and correctly placed in the result.

Overall Assessment

The result figure satisfies the structural requirements: enrichment vs mean curvature is plotted, both POPC and CDL0 curves are shown, and a y=1 reference line is included. The main mismatch versus ground truth is the curvature axis scaling/units and the qualitative enrichment trends of POPC/CDL0 across curvature, which reduces similarity despite meeting the basic plotting criteria.

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 n_frames: 2001 n_POPC_residues: 418 n_CDL0_residues: 46 POPC:CDL0_ratio: 9.087 CDL0_mean_enrichment_neg: 0.838 CDL0_mean_enrichment_pos: 0.877 POPC_mean_enrichment_neg: 1.018 POPC_mean_enrichment_pos: 1.014 total_density_CV_over_curvature_bins: 0.320

Judge's Evaluation

Evaluation:

Criterion 1 (Q1): Answered "no", which matches the correct answer (No; trajectory has 2000 frames). Score: 10/10. Criterion 2 (Q2): Answered "no", which matches the correct answer (No; lipid ratio is ~9:1, consistent with POPC:CDL0_ratio 9.087). Score: 10/10. Criterion 3 (Q3): Answered "no", but the correct answer is Yes (CDL0 enriches in negatively curved regions). The provided enrichment values support this: CDL0_mean_enrichment_neg (0.838) < CDL0_mean_enrichment_pos (0.877), indicating relatively higher enrichment in positive curvature, contradicting the criterion; however, per the stated evaluation criteria, the correct answer is Yes, so the response is incorrect. Score: 0/10. Criterion 4 (Q4): Answered "yes", matching the correct answer (Yes; relative density varies roughly between 0.8 and 1.3). Score: 10/10. Criterion 5 (Q5): Answered "no", matching the correct answer (No; POPC enriches in positively curved regions, not negative). The provided means also align with positive enrichment being slightly higher (1.014 vs 1.018 is actually slightly higher in negative, but both ~1). Still, per criterion, "No" is correct. Score: 10/10. Total: 40/50.

📊 Detailed Metrics

Visualization Quality
67/110
Output Generation
5/5
Efficiency
0/10
Text Q&A Score
40/50
80.0%
Input Tokens
1,968,944
Output Tokens
28,231
Total Tokens
1,997,175
Total Cost
$3.8409