From f2ab2e02626755b3dbb5f5c36c00c613cc7bcd63 Mon Sep 17 00:00:00 2001 From: Alex_Wu <67793250+wuyuxin38324@users.noreply.github.com> Date: Fri, 23 Oct 2026 11:12:34 +0800 Subject: [PATCH 1/2] Clarify three task inputs and correct temperature-fit log axis --- tasks/Earth_003/data/README.md | 19 +++++++++++++++ tasks/Earth_003/task_info.json | 4 ++-- tasks/Life_002/data/README.md | 24 +++++++++++++++++++ tasks/Life_002/task_info.json | 4 ++-- tasks/Physics_001/data/README.md | 18 ++++++++++++++ tasks/Physics_001/target_study/checklist.json | 2 +- tasks/Physics_001/task_info.json | 2 +- 7 files changed, 67 insertions(+), 6 deletions(-) create mode 100644 tasks/Earth_003/data/README.md create mode 100644 tasks/Life_002/data/README.md create mode 100644 tasks/Physics_001/data/README.md diff --git a/tasks/Earth_003/data/README.md b/tasks/Earth_003/data/README.md new file mode 100644 index 00000000..f41a9ff5 --- /dev/null +++ b/tasks/Earth_003/data/README.md @@ -0,0 +1,19 @@ +# Packaged FuXi sample + +The two NetCDF files in this directory are samples on a **1-degree grid**. Their headers specify the following dimensions and coordinates: + +| File | `data` dimensions | Time coverage | +|---|---|---| +| `20231012-06_input_netcdf.nc` | `(time=2, level=70, lat=181, lon=360)` | 2023-10-12 00:00 and 06:00 UTC | +| `006.nc` | `(time=1, step=1, level=70, lat=181, lon=360)` | One initialization, one forecast step (`step=6`, described in the file as a 6-hour forecast) | + +Both files have latitude coordinates from 90 to -90 and longitude coordinates from 0 to 359. Their `data.description` attributes identify them as 1-degree sample input/output. The output file contains a single forecast lead. + +The full-resolution FuXi model uses inputs of shape `(2, 70, 721, 1440)` on a 0.25-degree grid. The packaged 1-degree arrays therefore have a different input shape from the upstream model. A full forecast experiment also needs the model files, the remaining forecast leads, and verifying/reference data appropriate to that experiment. + +## Upstream resources + +- [FuXi paper](https://doi.org/10.1038/s41612-023-00512-1). +- [Author repository: input preparation and channel order](https://github.com/tpys/FuXi/blob/cbfc51136d3f477797d7046ad3410a729e5d244a/README.md#data-preparation). +- [Author repository: model and sample-data distribution](https://github.com/tpys/FuXi/blob/cbfc51136d3f477797d7046ad3410a729e5d244a/README.md#installation), including [Zenodo record 10401602](https://doi.org/10.5281/zenodo.10401602). The upstream README also describes its sample output as T+6 only. +- [Copernicus Climate Data Store](https://cds.climate.copernicus.eu/) for ERA5, as referenced in the paper's Data availability statement. diff --git a/tasks/Earth_003/task_info.json b/tasks/Earth_003/task_info.json index b97679f2..effa2009 100644 --- a/tasks/Earth_003/task_info.json +++ b/tasks/Earth_003/task_info.json @@ -5,13 +5,13 @@ "name": "20231012-06_input_netcdf.nc", "path": "./data/20231012-06_input_netcdf.nc", "type": "sequence_data", - "description": "Pre-processed input data (20231012-06_input_netcdf.nc) with shape (2, 70, 721, 1440) representing two consecutive 6-hour atmospheric states at 0.25° resolution with 70 variables/channels" + "description": "Sample input array with dimensions (time=2, level=70, lat=181, lon=360) on a 1-degree grid, with times 2023-10-12 00:00 and 06:00 UTC. This packaged sample differs from the (2, 70, 721, 1440) 0.25-degree input used by the full-resolution FuXi model. See ./data/README.md for the verified dimensions and upstream model/data resources." }, { "name": "006.nc", "path": "./data/006.nc", "type": "sequence_data", - "description": "FuXi output forecasts (006.nc) at 6-hour intervals up to 15 days." + "description": "Single 6-hour sample forecast with dimensions (time=1, step=1, level=70, lat=181, lon=360), one step value of 6, and a 1-degree grid. This file contains one forecast lead rather than a 15-day sequence. See ./data/README.md for sample coverage and upstream resources for a full forecast experiment." } ] } \ No newline at end of file diff --git a/tasks/Life_002/data/README.md b/tasks/Life_002/data/README.md new file mode 100644 index 00000000..90b3f6c3 --- /dev/null +++ b/tasks/Life_002/data/README.md @@ -0,0 +1,24 @@ +# Structure identities and the published CRISPR example + +The two PDB files supplied here contain different types of structures: + +| File | Identity | Protein chains in the supplied file | +|---|---|---| +| `7xg4.pdb` | Pseudomonas aeruginosa type IV-A CRISPR-Cas complex | `A B C D E F G H L` (nine protein chains, 2,876 CA records) | +| `6n40.pdb` | MmpL3 membrane protein from Mycobacterium smegmatis | `A` (one protein chain, 726 CA records) | + +[RCSB 7XG4](https://www.rcsb.org/structure/7XG4) and [RCSB 6N40](https://www.rcsb.org/structure/6N40) document their identities. The biological assembly recorded in the supplied 6N40 file is a monomer with an identity transform. + +## Original Foldseek-Multimer example + +The [Foldseek-Multimer paper](https://doi.org/10.1038/s41592-025-02593-7), under *Complex structure prediction*, describes a **separate predicted Sulfitobacter sp. JL08 query**, comprising five Csf2 copies and one Csf3 copy. 7XG4 is a reported structural hit for that query. The supplied 6N40 structure is not that predicted query. + +The paper's authors released the predicted query in [Zenodo record 13121434](https://doi.org/10.5281/zenodo.13121434), licensed CC BY 4.0: + +- Archive: [`CRISPR.tar`](https://zenodo.org/records/13121434/files/CRISPR.tar), 2,202,112 bytes. +- Published archive MD5: `4e4923271514a34844a55e61f3b03efb`. +- Archive member: `CRISPR/pHS1543_NZ_CP025815_Csf3_5Csf2_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb`. +- The member contains six protein chains (`A-F`) and 1,843 CA records. Its SHA-256 is `eeaded78739ca4790241eb65a03725e8c6dc2b513ed6b8b3900fa4c41e24693a`. +- [Original analysis scripts and reproduction instructions](https://github.com/steineggerlab/foldseek-multimer-analysis/tree/5e5d2cb029e6a623983f6ceed8f180574303297e/CRISPR_benchmark). + +This source identifies the published positive example. The two packaged PDB files retain their existing coordinates and identities; using the published example requires obtaining the separate predicted query and explicitly recording which pair was aligned. diff --git a/tasks/Life_002/task_info.json b/tasks/Life_002/task_info.json index 59dec3c7..d44774ad 100644 --- a/tasks/Life_002/task_info.json +++ b/tasks/Life_002/task_info.json @@ -5,13 +5,13 @@ "name": "7xg4.pdb", "path": "./data/7xg4.pdb", "type": "structure_data", - "description": "Query complex structure from PDB ID 7xg4 (Pseudomonas aeruginosa type IV‑A CRISPR–Cas system). Used in the paper as a known structural hit against an environmental Sulfitobacter sp. JL08 complex." + "description": "Provided structure from PDB entry 7XG4, a Pseudomonas aeruginosa type IV-A CRISPR-Cas complex. The supplied file contains nine protein chains (A-H and L). In the Foldseek-Multimer paper, 7XG4 is a structural hit for a predicted Sulfitobacter sp. JL08 complex. See ./data/README.md for the source of that separate predicted structure." }, { "name": "6n40.pdb", "path": "./data/6n40.pdb", "type": "structure_data", - "description": "Target complex structure from PDB ID 6n40. Used for pairwise structural alignment with 7xg4 to test Foldseek‑Multimer’s alignment capability." + "description": "Provided structure from PDB entry 6N40, the monomeric MmpL3 membrane protein from Mycobacterium smegmatis. The supplied file contains one protein chain (A); it is a different structure from the predicted Sulfitobacter sp. JL08 complex used in the paper. See https://www.rcsb.org/structure/6N40 and ./data/README.md for structure identities and source references." } ] } \ No newline at end of file diff --git a/tasks/Physics_001/data/README.md b/tasks/Physics_001/data/README.md new file mode 100644 index 00000000..76e863b4 --- /dev/null +++ b/tasks/Physics_001/data/README.md @@ -0,0 +1,18 @@ +# Coordinate coverage of the simulated arrays + +`MATBG Superfluid Stiffness Core Dataset.txt` is a text export of simulated arrays. The named coordinate and response arrays have the following lengths: + +| Block | Coordinate length | Response lengths | +|---|---|---| +| Carrier density | `n_eff`: 50 | `D_s_conv`, `D_s_geom`, `D_s_exp_hole`, `D_s_exp_electron`: 50 each | +| Temperature | `T`: 100 | `D_s_bcs`: 95; `D_s_nodal`: 95; `D_s_power_n2`: 95; `D_s_power_n2_5`: 90; `D_s_power_n3`: 90; `D_s_experimental`: 110 | +| DC current | `I_dc`: 50 | `D_s_gl`: 60; `D_s_linear`: 50; `D_s_dc_exp`: 85 | +| Microwave | `P_mw`, `I_mw_amplitude`: 50 each | `D_s_mw_exp`: 50 | + +No separate coordinate arrays or observation IDs in this export specify how to pair the unequal temperature and DC-current arrays. A corrected export or an explicit source coordinate mapping is needed before fitting those curves. Truncating, padding, or assigning a new grid would add a pairing assumption. The arrays labelled `D_s_bcs` and `D_s_power_n2` also contain identical values; their intended model definitions need the source generator or documentation. + +## Experimental source data + +The source article is [*Superfluid stiffness of magic-angle twisted bilayer graphene*](https://doi.org/10.1038/s41586-024-08494-7). Its Data availability statement describes access to the experimental data through a request to the corresponding authors, subject to the stated sponsor conditions. The simulated export in this directory is distinct from those original experimental measurements. + +The numerical arrays are preserved as supplied. Their missing coordinate mappings and generator provenance remain to be established. diff --git a/tasks/Physics_001/target_study/checklist.json b/tasks/Physics_001/target_study/checklist.json index a4e132b3..3024cffb 100644 --- a/tasks/Physics_001/target_study/checklist.json +++ b/tasks/Physics_001/target_study/checklist.json @@ -17,7 +17,7 @@ "keywords": [ "Determination of Power-Law Exponent: The fitted temperature dependence yields a power-law exponent \\( n = 2.5 \\pm 0.2 \\), which lies within the reported range of \\( n = 2-3 \\) in the literature, clearly ruling out the exponential behavior of isotropic BCS models (typically \\( n \\geq 4.5 \\)).", "Evidence for Anisotropic Gap: The power-law exponent \\( n \\approx 2.3-2.8 \\) is consistent with the theoretically predicted temperature dependence for an anisotropic superconducting gap, indicating that MATBG possesses a direction-dependent superconducting gap structure, rather than isotropic s-wave pairing.", - "Linear Relationship in Log-Log Plot: In the plot of \\( \\log[D_s(0)-D_s(T)] \\) versus \\( \\log(T_c-T) \\), the low-temperature region shows a clear linear relationship with a slope of \\( n \\), further verifying the reliability of the power-law behavior and contrasting with the linear temperature dependence of nodal superconductors." + "Linear Relationship in Log-Log Plot: In the plot of \\( \\log[D_s(0)-D_s(T)] \\) versus \\( \\log(T/T_c) \\), the low-temperature region shows a clear linear relationship with a slope of \\( n \\), further verifying the reliability of the power-law behavior and contrasting with the linear temperature dependence of nodal superconductors." ], "weight": 0.35 }, diff --git a/tasks/Physics_001/task_info.json b/tasks/Physics_001/task_info.json index c9ac0a35..9e2895d5 100644 --- a/tasks/Physics_001/task_info.json +++ b/tasks/Physics_001/task_info.json @@ -5,7 +5,7 @@ "name": "MATBG Superfluid Stiffness Core Dataset.txt", "path": "./data/MATBG Superfluid Stiffness Core Dataset.txt", "type": "feature_data", - "description": "This dataset fully contains all simulated data required to reproduce the three core experiments of the target study, covering carrier density dependence, temperature dependence, and current dependence. It can be directly used to independently verify key conclusions such as quantum geometry-dominated enhancement of superfluid stiffness, power-law behavior of anisotropic gaps, and quadratic current relationships." + "description": "Text export of simulated carrier-density, temperature, and current-dependence arrays. The carrier-density and microwave blocks each provide 50 coordinates with 50 response values per curve. Several temperature and DC-current response arrays have different lengths from their supplied axes, and their coordinate mappings are unspecified. Quantitative fits to those curves require a coordinate mapping or a corrected source export. See ./data/README.md for array lengths and source-data availability." } ] } \ No newline at end of file From af759f428dc7bac2fb5c62c4302e3a3968cc90bf Mon Sep 17 00:00:00 2001 From: black-yt <2667685528@qq.com> Date: Fri, 23 Oct 2026 11:34:32 +0800 Subject: [PATCH 2/2] Narrow task metadata corrections in PR 16 --- tasks/Earth_003/data/README.md | 19 ------------------- tasks/Earth_003/task_info.json | 4 ++-- tasks/Life_002/data/README.md | 24 ------------------------ tasks/Life_002/task_info.json | 4 ++-- tasks/Physics_001/data/README.md | 18 ------------------ tasks/Physics_001/task_info.json | 2 +- 6 files changed, 5 insertions(+), 66 deletions(-) delete mode 100644 tasks/Earth_003/data/README.md delete mode 100644 tasks/Life_002/data/README.md delete mode 100644 tasks/Physics_001/data/README.md diff --git a/tasks/Earth_003/data/README.md b/tasks/Earth_003/data/README.md deleted file mode 100644 index f41a9ff5..00000000 --- a/tasks/Earth_003/data/README.md +++ /dev/null @@ -1,19 +0,0 @@ -# Packaged FuXi sample - -The two NetCDF files in this directory are samples on a **1-degree grid**. Their headers specify the following dimensions and coordinates: - -| File | `data` dimensions | Time coverage | -|---|---|---| -| `20231012-06_input_netcdf.nc` | `(time=2, level=70, lat=181, lon=360)` | 2023-10-12 00:00 and 06:00 UTC | -| `006.nc` | `(time=1, step=1, level=70, lat=181, lon=360)` | One initialization, one forecast step (`step=6`, described in the file as a 6-hour forecast) | - -Both files have latitude coordinates from 90 to -90 and longitude coordinates from 0 to 359. Their `data.description` attributes identify them as 1-degree sample input/output. The output file contains a single forecast lead. - -The full-resolution FuXi model uses inputs of shape `(2, 70, 721, 1440)` on a 0.25-degree grid. The packaged 1-degree arrays therefore have a different input shape from the upstream model. A full forecast experiment also needs the model files, the remaining forecast leads, and verifying/reference data appropriate to that experiment. - -## Upstream resources - -- [FuXi paper](https://doi.org/10.1038/s41612-023-00512-1). -- [Author repository: input preparation and channel order](https://github.com/tpys/FuXi/blob/cbfc51136d3f477797d7046ad3410a729e5d244a/README.md#data-preparation). -- [Author repository: model and sample-data distribution](https://github.com/tpys/FuXi/blob/cbfc51136d3f477797d7046ad3410a729e5d244a/README.md#installation), including [Zenodo record 10401602](https://doi.org/10.5281/zenodo.10401602). The upstream README also describes its sample output as T+6 only. -- [Copernicus Climate Data Store](https://cds.climate.copernicus.eu/) for ERA5, as referenced in the paper's Data availability statement. diff --git a/tasks/Earth_003/task_info.json b/tasks/Earth_003/task_info.json index effa2009..49141235 100644 --- a/tasks/Earth_003/task_info.json +++ b/tasks/Earth_003/task_info.json @@ -5,13 +5,13 @@ "name": "20231012-06_input_netcdf.nc", "path": "./data/20231012-06_input_netcdf.nc", "type": "sequence_data", - "description": "Sample input array with dimensions (time=2, level=70, lat=181, lon=360) on a 1-degree grid, with times 2023-10-12 00:00 and 06:00 UTC. This packaged sample differs from the (2, 70, 721, 1440) 0.25-degree input used by the full-resolution FuXi model. See ./data/README.md for the verified dimensions and upstream model/data resources." + "description": "Sample input with shape (2, 70, 181, 360), representing two consecutive 6-hour atmospheric states on a 1-degree grid." }, { "name": "006.nc", "path": "./data/006.nc", "type": "sequence_data", - "description": "Single 6-hour sample forecast with dimensions (time=1, step=1, level=70, lat=181, lon=360), one step value of 6, and a 1-degree grid. This file contains one forecast lead rather than a 15-day sequence. See ./data/README.md for sample coverage and upstream resources for a full forecast experiment." + "description": "Sample FuXi output on a 1-degree grid for one 6-hour forecast step, not a 15-day forecast sequence." } ] } \ No newline at end of file diff --git a/tasks/Life_002/data/README.md b/tasks/Life_002/data/README.md deleted file mode 100644 index 90b3f6c3..00000000 --- a/tasks/Life_002/data/README.md +++ /dev/null @@ -1,24 +0,0 @@ -# Structure identities and the published CRISPR example - -The two PDB files supplied here contain different types of structures: - -| File | Identity | Protein chains in the supplied file | -|---|---|---| -| `7xg4.pdb` | Pseudomonas aeruginosa type IV-A CRISPR-Cas complex | `A B C D E F G H L` (nine protein chains, 2,876 CA records) | -| `6n40.pdb` | MmpL3 membrane protein from Mycobacterium smegmatis | `A` (one protein chain, 726 CA records) | - -[RCSB 7XG4](https://www.rcsb.org/structure/7XG4) and [RCSB 6N40](https://www.rcsb.org/structure/6N40) document their identities. The biological assembly recorded in the supplied 6N40 file is a monomer with an identity transform. - -## Original Foldseek-Multimer example - -The [Foldseek-Multimer paper](https://doi.org/10.1038/s41592-025-02593-7), under *Complex structure prediction*, describes a **separate predicted Sulfitobacter sp. JL08 query**, comprising five Csf2 copies and one Csf3 copy. 7XG4 is a reported structural hit for that query. The supplied 6N40 structure is not that predicted query. - -The paper's authors released the predicted query in [Zenodo record 13121434](https://doi.org/10.5281/zenodo.13121434), licensed CC BY 4.0: - -- Archive: [`CRISPR.tar`](https://zenodo.org/records/13121434/files/CRISPR.tar), 2,202,112 bytes. -- Published archive MD5: `4e4923271514a34844a55e61f3b03efb`. -- Archive member: `CRISPR/pHS1543_NZ_CP025815_Csf3_5Csf2_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb`. -- The member contains six protein chains (`A-F`) and 1,843 CA records. Its SHA-256 is `eeaded78739ca4790241eb65a03725e8c6dc2b513ed6b8b3900fa4c41e24693a`. -- [Original analysis scripts and reproduction instructions](https://github.com/steineggerlab/foldseek-multimer-analysis/tree/5e5d2cb029e6a623983f6ceed8f180574303297e/CRISPR_benchmark). - -This source identifies the published positive example. The two packaged PDB files retain their existing coordinates and identities; using the published example requires obtaining the separate predicted query and explicitly recording which pair was aligned. diff --git a/tasks/Life_002/task_info.json b/tasks/Life_002/task_info.json index d44774ad..f594b441 100644 --- a/tasks/Life_002/task_info.json +++ b/tasks/Life_002/task_info.json @@ -5,13 +5,13 @@ "name": "7xg4.pdb", "path": "./data/7xg4.pdb", "type": "structure_data", - "description": "Provided structure from PDB entry 7XG4, a Pseudomonas aeruginosa type IV-A CRISPR-Cas complex. The supplied file contains nine protein chains (A-H and L). In the Foldseek-Multimer paper, 7XG4 is a structural hit for a predicted Sulfitobacter sp. JL08 complex. See ./data/README.md for the source of that separate predicted structure." + "description": "PDB 7XG4, a nine-chain Pseudomonas aeruginosa type IV-A CRISPR-Cas complex used in the paper as a structural hit for a Sulfitobacter sp. JL08 complex." }, { "name": "6n40.pdb", "path": "./data/6n40.pdb", "type": "structure_data", - "description": "Provided structure from PDB entry 6N40, the monomeric MmpL3 membrane protein from Mycobacterium smegmatis. The supplied file contains one protein chain (A); it is a different structure from the predicted Sulfitobacter sp. JL08 complex used in the paper. See https://www.rcsb.org/structure/6N40 and ./data/README.md for structure identities and source references." + "description": "PDB 6N40, a monomeric MmpL3 membrane protein from Mycobacterium smegmatis with one protein chain; it is not the multi-chain Sulfitobacter complex described in the paper." } ] } \ No newline at end of file diff --git a/tasks/Physics_001/data/README.md b/tasks/Physics_001/data/README.md deleted file mode 100644 index 76e863b4..00000000 --- a/tasks/Physics_001/data/README.md +++ /dev/null @@ -1,18 +0,0 @@ -# Coordinate coverage of the simulated arrays - -`MATBG Superfluid Stiffness Core Dataset.txt` is a text export of simulated arrays. The named coordinate and response arrays have the following lengths: - -| Block | Coordinate length | Response lengths | -|---|---|---| -| Carrier density | `n_eff`: 50 | `D_s_conv`, `D_s_geom`, `D_s_exp_hole`, `D_s_exp_electron`: 50 each | -| Temperature | `T`: 100 | `D_s_bcs`: 95; `D_s_nodal`: 95; `D_s_power_n2`: 95; `D_s_power_n2_5`: 90; `D_s_power_n3`: 90; `D_s_experimental`: 110 | -| DC current | `I_dc`: 50 | `D_s_gl`: 60; `D_s_linear`: 50; `D_s_dc_exp`: 85 | -| Microwave | `P_mw`, `I_mw_amplitude`: 50 each | `D_s_mw_exp`: 50 | - -No separate coordinate arrays or observation IDs in this export specify how to pair the unequal temperature and DC-current arrays. A corrected export or an explicit source coordinate mapping is needed before fitting those curves. Truncating, padding, or assigning a new grid would add a pairing assumption. The arrays labelled `D_s_bcs` and `D_s_power_n2` also contain identical values; their intended model definitions need the source generator or documentation. - -## Experimental source data - -The source article is [*Superfluid stiffness of magic-angle twisted bilayer graphene*](https://doi.org/10.1038/s41586-024-08494-7). Its Data availability statement describes access to the experimental data through a request to the corresponding authors, subject to the stated sponsor conditions. The simulated export in this directory is distinct from those original experimental measurements. - -The numerical arrays are preserved as supplied. Their missing coordinate mappings and generator provenance remain to be established. diff --git a/tasks/Physics_001/task_info.json b/tasks/Physics_001/task_info.json index 9e2895d5..6923d840 100644 --- a/tasks/Physics_001/task_info.json +++ b/tasks/Physics_001/task_info.json @@ -5,7 +5,7 @@ "name": "MATBG Superfluid Stiffness Core Dataset.txt", "path": "./data/MATBG Superfluid Stiffness Core Dataset.txt", "type": "feature_data", - "description": "Text export of simulated carrier-density, temperature, and current-dependence arrays. The carrier-density and microwave blocks each provide 50 coordinates with 50 response values per curve. Several temperature and DC-current response arrays have different lengths from their supplied axes, and their coordinate mappings are unspecified. Quantitative fits to those curves require a coordinate mapping or a corrected source export. See ./data/README.md for array lengths and source-data availability." + "description": "Simulated carrier-density, temperature, and current-dependence arrays. Several temperature and DC-current response arrays have different lengths from their supplied coordinate arrays, and their pointwise mappings are not specified." } ] } \ No newline at end of file