sparks-baird / xtal2png Goto Github PK

Masking the pairwise distance matrix with zeros would help show whether that's a useful feature for guiding the algorithm or if it's just confusing the algorithm. Related #134

A similar procedure could be applied for other non-essential info, such as space group number and volume.

i.e. average the channels instead of restricting to a single channel

Not directly relevant to the development of the codebase, but would be interesting to see in an application of xtal2png.

I'd be interested to know if coordinate convolutions would help here seeing as positioning matters.

https://twitter.com/ramav_matsci/status/1538938834188226560

Implementing for now as minimum across all MP compounds, but this is another hyperparameter choice (technically, the hyperparameter might be a scaling factor between 0 and 1 of the minimum). This would be an alternative to leaving each of the parameter ranges as tunable parameters themselves, and might be a reasonable reduction to the search space (i.e. only leave the upper bound limits as individual tunable parameters).

https://mat3ra.com/

Depending on the cost, we could do some hyperparameter optimization here.

• #96

Here I will collate issues/suggestions I found with documentation. See openjournals/joss-reviews#4528 for the full JOSS review.

• Statement of need - the landing page on GitHub has a nice README.md, but the index page of the docs could be expanded with a short blurb. Feel free to reuse something from the paper and don't be afraid of being more technical.
• Functionality documentation - the API docs are built, which is great, but I'm missing a "functionality" page that would link to classes/functions in the API docs. It's up to you if you put it as a subsection of the "Overview" or make a new section. I think such a page should discuss the decisions behind the default output format, link to the key classes/functions in the API docs, and also mention it's possible to customise the output PNGs. Then, reference this overview from the paper to avoid having to write the same thing twice and risking the paper might end up out of date.
• Automated tests - CI is enabled and tests pass. However, it's difficult to figure out what's being tested where. I'd suggest splitting this test file into multiple modules, separating the functionality tests from the validity tests. Also, I think a very useful category of tests is missing - comparing image data directly with a reference png. You can use the instructions here to get a test working. We have written a similar test you can copy, here.

https://checkcif.iucr.org/

E.g. if we wanted to CheckCIF 10 million structures, is the "Send CIF for checking" button through the web app the only option?

This may also give hints to certain types of post-processing steps that we might undertake, though many of these may be less necessary if we use a reasonable symprec (?) tolerance when writing the CIF files to disk.

When running xtal2png with a large crystal, this (expected) error appears:

(xtal2png) kraus@dorje:~/xtal2png::xtal2png --encode -p test-01.cif
/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                                                                                                                                                                    | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/bin/xtal2png", line 10, in <module>
    sys.exit(run())
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/xtal2png/core.py", line 1141, in run
    main(sys.argv[1:])
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/xtal2png/core.py", line 1129, in main
    xc.xtal2png(fpaths, save=True)
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/xtal2png/core.py", line 265, in xtal2png
    self.data, self.id_data, self.id_mapper = self.structures_to_arrays(S)
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/xtal2png/core.py", line 573, in structures_to_arrays
    raise ValueError(
ValueError: crystal supplied with 240 sites, which is more than 52 sites. Remove crystal or increase `max_sites`.

It would be helpful to have a CLI option to increase max_sites with, rather than having to dig into the API.

Back-ping to openjournals/joss-reviews#4528.

https://conda-forge.org/docs/maintainer/adding_pkgs.html

kjappelbaum/element-coder#13

e.g.

Structure Summary
Lattice
    abc : 3.5100414781297133 3.515196078431373 3.5448717948717947
 angles : 59.64705882352941 59.959276018099544 59.93891402714934
 volume : 30.820712660051388
      A : 3.0385369088434473 0.0 1.7571808762296304
      B : 1.0068399538873045 2.861393772226697 1.7763171049499542
      C : 0.0 0.0 3.5448717948717947
PeriodicSite: Ag (0.4705, 0.1010, 1.2526) [0.1431, 0.0353, 0.2647]
PeriodicSite: Cr (1.0788, 0.7294, 1.6928) [0.2706, 0.2549, 0.2157]
PeriodicSite: H (0.1329, 0.0898, 0.1213) [0.0333, 0.0314, 0.0020]
PeriodicSite: H (0.0654, 0.0842, 0.2814) [0.0118, 0.0294, 0.0588]
PeriodicSite: He (0.0278, 0.0112, 0.0416) [0.0078, 0.0039, 0.0059]

Tried with a looser symprec tolerance, which threw an error at 0.2 and higher.

structures[0].get_space_group_info(symprec=0.2)

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\Miniconda3\envs\xtal2png-docs\lib\site-packages\pymatgen\core\structure.py", line 1013, in get_space_group_info
    return a.get_space_group_symbol(), a.get_space_group_number()
  File "C:\Users\sterg\Miniconda3\envs\xtal2png-docs\lib\site-packages\pymatgen\symmetry\analyzer.py", line 97, in get_space_group_symbol
    return self._space_group_data["international"]
TypeError: 'NoneType' object is not subscriptable

Since lucidrains has been (graciously) supporting passing tensors directly, e.g. in imagen-pytorch

from internal discussion with @faris-k

Also, I've noticed that when converting larger datasets to PNG via XtalConverter's xtal2png like the matbench_mp_e_form dataset, you may run into memory issues even on high-RAM runtimes on Colab. Workaround is pretty simple, just convert structures to PNGs individually and then convert each Image object to a tensor or array since you'll be doing that anyway. A minor note on that regard, but it looks like xtal2png only works on sequences of structure objects (i.e. you can't use it on a single structure unless you make it into a list with one structure object).

Is it an issue with holding too many structures at once? Or too many PIL Images?

The memory error is thrown when you'd do something like data = xc.xtal2png(X_train) where X_train is like 90k or 100k structures.

Does a batch approach like the following work? (I haven't verified)

data = []
for x in np.array_split(X_train, 10):
    data.append(xc.xtal2png(x))

https://www.assemblyai.com/blog/diffusion-models-for-machine-learning-introduction/

@hasan-sayeed

https://xtal2png.readthedocs.io/en/latest/api/xtal2png.html#xtal2png.core.XtalConverter.arrays_to_structures

Here's an example:

Either in mp-time-split (when using .get_train_and_val_data() etc., of course only shuffling after splitting into train and val) or in the generative model. Might cause issues if really similar compounds are in the same batch.

• https://datascience.stackexchange.com/questions/24511/why-should-the-data-be-shuffled-for-machine-learning-tasks
• https://stats.stackexchange.com/questions/245502/why-should-we-shuffle-data-while-training-a-neural-network

Probably better to just shuffle the data by default rather than include it as a tunable hyperparameter during hyperparameter optimization. Might leave as a kwarg with default set to True. Of course, if the generative model uses data from a directory without shuffling that data, it could be problematic. Will check on denoising_diffusion_pytorch to see if the data gets shuffled by default.

Follow-up to #36. The idea is to add to https://github.com/sparks-baird/xtal2png/blob/main/notebooks/2.0-materials-project-feature-ranges.ipynb or make a copy and modify it so the structures are reduced to their primitive conventional representations.

 spa = SpacegroupAnalyzer(structure, symprec=0.1, angle_tolerance=5.0) 
# structure = spa.get_primitive_standard_structure()
structure = spa.get_conventional_standard_structure()

@hasan-sayeed you OK with tackling this? Should be pretty straightforward, just splicing the above code into a copy of the linked notebook.

Something along the lines of the following (unfinished):

def test_png2xtal_from_loaded_images():
    # TODO: implement this once API is stable (i.e. 1.0.0+)
    imgs = []
    with Image.open("tests/V4Ni2Se8,volume=243,uid=8b92.png") as img:
        datum = list(img.getdata())
        imgs.append(img)
    with Image.open("tests/Zn8B8Pb4O24,volume=623,uid=b62a.png") as img:
        datum2 = list(img.getdata())
        imgs.append(img)

    data = [datum, datum2]

    xc = XtalConverter()
    decoded_structures = xc.png2xtal(imgs)
    assert_structures_approximate_match(
        example_structures, decoded_structures, tol_multiplier=2.0
    )
    return decoded_structures

See #146 (comment)

E.g. min and max distances, lattice parameter lengths. During hyperparameter optimization. #12

@faris-k, each pixel in the image takes on a value between 0 and 255. I ended up writing my own scaler and unscaler functions as I had trouble getting sklearn functions (e.g. MinMaxScaler) to respect the conversion to a user-specified range (i.e. hard lower and upper limits) and other reason(s) that are a bit fuzzy in my memory. The reason for wanting this behavior is so that two people can independently run xtal2png on different datasets, swap their data, and decode to the same crystal structures. I.e. the PNG representation doesn't depend on the collection of data you give it, it only depends on the data_range-s that are specified in the XtalConverter class:

You can have a look at the relevant functions:

and where they're used:

The default data_range-s are decided based on https://github.com/sparks-baird/xtal2png/blob/main/notebooks/2.0-materials-project-feature-ranges.ipynb as of v0.3.0.

i.e. chemical formulas encoded in place of the top-left matrix of zeros

Almost always fewer than the total number of sites, e.g. mp-19841, mp-500, mp-19770. Would cut down the dimensionality by a significant amount, though it also introduces the possibility of representations that aren't able to be reconstructed (disregarding whether the structure would be realistic or not). See e.g. pyxtal: checking compatibility. There's also the question of how to numerically encode the Wyckoff position types. Might be worth digging more into Wren's representation https://github.com/CompRhys/aviary.

E.g. 1700^(1/3) instead of 1700

Another option for hyperparameter optimization

The task is to use a hyperparameter-tuned XGBoost model for a Matbench submission on regressing formation energy using only the lattice parameter lengths, angles, and unit cell volume as inputs. This will help us know how "good" the xtal2png representation is from a model accuracy perspective.

@cseeg

Would be via get_all_neighbors(...) or probably preferably get_sites_in_sphere(...)

Pairwise distances could be calculated using get_distance(...) or by digging into how distance_matrix is calculated, which probably uses get_distance(...).

Better method would probably be to extract the Cartesian coordinates of each site from get_sites_in_sphere(...) and just use all_distance per what happens with distance_matrix.

e.g. $He \rightarrow H\space\mathrm{or}\space Li$

Issue with generated structures having noble gases might be helped by:

• #81

i.e. using multi-dimensional scaling (MDS), or could be a trained network. If a trained network, an interesting approach might be to map the representation (including redundant information) to the directly used non-redundant inputs Structure(lattice, elements, coords).

If using MDS, the hyperparameter would probably be the weighted average of the direct fractional coordinates and the reconstructed fractional coordinates, so a scalar hyperparameter between 0 and 1.

See also:

Anand, N.; Eguchi, R.; Huang, P.-S. Fully Differentiable Full-Atom Protein Backbone Generation. 2019. https://openreview.net/forum?id=SJxnVL8YOV

which uses pairwise distance matrix reconstruction.

Good discussion and examples about reconstructing directly vs. using a neural network in:

(1) Ovchinnikov, S.; Huang, P.-S. Structure-Based Protein Design with Deep Learning. Current Opinion in Chemical Biology 2021, 65, 136–144. https://doi.org/10.1016/j.cbpa.2021.08.004.

This would be an interesting (and I think informative) study of the effect that the redundancy has on the generative performance. Could have major implications on the choice of the representation, for example reducing max_sites, removing other redundancies such as repeat volume or space group number scalars.

@hasan-sayeed sorry got some things mixed up when I was doing pyscaffold. It made a new project at sgbaird instead of sparks-baird. This is the repo to work in, renamed the other one as xtal2png-deprecated (still a private repo).

'Ca2He2H1,volume=23,uid=3533.cif'
'Cr1Ag1H2He1,volume=31,uid=3d40.cif'
'Cs1Li1Ca1H2,volume=62,uid=8e9d.cif'
'Cs1Rb1La1Sn1Sb1Pd1H3I1Ne1He1,volume=177,uid=5495.cif'
'Cu1H3I1He1,volume=37,uid=3870.cif'
'K1Ca1Ac1Mg1Ti1Mn1Al1Cr1In2Ga1Co1Tc1Cu1Ag1Hg1Ge1Te2As1Pd1H3Rh1Se1C1Xe1I1Kr1He1,volume=1358,uid=eccb.cif'
'Li1Ti1H2Xe1Cl1,volume=37,uid=070b.cif'
'Mo1H1C1Kr1He1,volume=24,uid=879d.cif'
'Na1Li1H1Kr1,volume=18,uid=5905.cif'
'Na1Sr1Sc1H1C1Br1He3,volume=102,uid=7fcc.cif'
'Rb1Na1Li1Sc1Ti1Ni1Ru2H2Cl1,volume=123,uid=5fa0.cif'
'Rb1Sc1He1,volume=18,uid=90e7.cif'
'Rb1Ti1V1Ga1Ni1Ge1H2,volume=83,uid=cf25.cif'
'Sc1Cr1F1Ne1H1He1,volume=47,uid=5b5d.cif'
'Sr1Gd1Dy1Y1Ni1Pd1He1H2,volume=108,uid=cf05.cif'
'Zr1Tc1Cu1H4Se1Br1F1,volume=69,uid=4e8d.cif'

See also #79

@kjappelbaum thoughts?

When I execute xtal2png without any command line arguments, I get a ValueError:

(xtal2png) kraus@dorje:~::xtal2png 
Traceback (most recent call last):
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/bin/xtal2png", line 10, in <module>
    sys.exit(run())
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/xtal2png/core.py", line 1141, in run
    main(sys.argv[1:])
  File "/home/kraus/Applications/miniconda3/envs/xtal2png/lib/python3.10/site-packages/xtal2png/core.py", line 1112, in main
    raise ValueError("Specify at least one of --encode or --decode")
ValueError: Specify at least one of --encode or --decode

It would be much cleaner to print the usage message, or a different prompt telling the user what to do, rather than crashing on the user.

Related methods from CDVAE (emphasis added):

There are infinitely many different ways of choosing the lattice for the same material. We compute the Niggli reduced lattice (Grosse-Kunstleve et al., 2004) with pymatgen (Ong et al., 2013), which is a unique lattice for any given material.

See get_reduced_structure()

Originally posted by @sgbaird in #94 (comment)

get_reduced_structure instead of get_primitive_standard_structure.

Related methods from CDVAE (emphasis added):

Since the lattice matrix L is not rotation invariant, we instead predict the 6 lattice parameters, i.e. the lengths of the 3 lattice vectors and the angles between them. We normalize the lengths of lattice vectors with [N^(1/3)], where N is the number of atoms, to ensure that the lengths for materials of different sizes are at the same scale.

See get_reduced_structure()

Originally posted by @sgbaird in #94 (comment)

@hasan-sayeed

The task is to use a CNN model for a Matbench submission on regressing formation energy using the xtal2png representation (as an image and/or as an array would be fine). This will help with knowing how "good" the xtal2png representation is from a model accuracy perspective, though I don't expect this to set new benchmarks necessarily.

This might look like using skorch with some type of pytorch CNN module (e.g. ResNetUNet, Net) and an MSE loss function. This skorch tutorial looks like it might help with loading images, though this SO answer is probably better for making the actual dataset to pass to skorch.

If regression is too much of a pain (CNNs aren't used as often for property regression in the image-processing domain), an easy fallback is to do the mp_is_metal binary classification task instead of the e_form regression task.

Related:

• Ordinal regression: https://github.com/Raschka-research-group/coral-pytorch
• Ordinal regression tutorial: https://github.com/Raschka-research-group/coral-pytorch/blob/main/docs/tutorials/pytorch_lightning/ordinal-corn_mnist.ipynb
• Predict ages based on images: https://github.com/christianbv/AgeNet#49

Maybe Faris interested in working on this given that he'll be doing some image processing

Hyperparameter would be level of perturbation per type of perturbation, e.g. perturbation for atomic numbers, perturbation for distance matrix, fractional coordinates, etc. Might be reasonable to simply perturb the final grayscale image; however, this will not preserve the Euclidean nature of the distance matrix.

Hello @sgbaird,
In this issue, I will collate points that relate to the software paper itself. Link to review is: openjournals/joss-reviews#4528

• the reference to the software repo seems unnecessary here (and throughout the paper). The link to the repo is right there in the front-matter!
  

  xtal2png/reports/paper.md

  Line 45 in cc644f3

  diffusion models. Using `xtal2png` [@xtal2png] to encode/decode crystal structures via grayscale PNG images (see

• the summary is not clear about what is being encoded into what. My understanding is that xtal2png can take a coordinate file and create a fingerprint / QR-code-like representation of that coordinate file. If that's the case, it should be more explicit in the summary.
  

  xtal2png/reports/paper.md

  Line 46 in cc644f3

  e.g. \autoref{fig:64-bit}) is akin to making/reading a QR code for crystal structures.

• streamlined results? Is the point here that it feeds well into image-based pipelines?
  

  xtal2png/reports/paper.md

  Line 47 in cc644f3

  This allows you, as a materials informatics practitioner, to get streamlined results for

• The references in this section on domain transfer make it hard to read. Please rewrite - perhaps put the citations behind the dates.
  

  xtal2png/reports/paper.md

  Lines 64 to 67 in cc644f3

  	Another example of state-of-the-art algorithm domain transfer is refactoring image-processing models for crystal structure applications, with
  	introduction [@kipfSemisupervisedClassificationGraph2016], domain transfer (preprint)
  	[@xieCrystalGraphConvolutional2017], and peer-reviewed domain transferred
  	[@xieCrystalGraphConvolutional2018] publication dates of Sep 2016, Oct 2017, and Apr

• Here, rather than to-from, I'd say between coordinate file and png representation (or something similar):
  

  xtal2png/reports/paper.md

  Lines 73 to 74 in cc644f3

  	is a Python package that allows you to encode/decode a crystal structure to/from a
  	grayscale PNG image for direct use with image-based machine learning models. Let's take

• I am not sure I understand the relevance of Pallette. Please elaborate.

• It would be helpful to discuss the technical limitations somewhere. Perhaps it's in the docs, but in my view it could be commented on in the paper:
  

  xtal2png/reports/paper.md

  Lines 94 to 97 in cc644f3

  	the representation are given in \autoref{fig:example-and-legend}. Due to the encoding of
  	numerical values as grayscale PNG images (allowable values are integers between 0 and
  	255), a small round-off error is present during a single round of encoding and decoding.
  	An example comparing an original vs. decoded structure is given in

• First, is there a reason 64x64 pixel image has to be used? I understand it's possible to encode at most 52 atoms within the unit cell. Just by reading the paper, it's not obvious why the cell parameters (lattice constants, angles, volume, point group) occupy rows - seems like a waste of space. If that information was moved into the upper-left zero sector, there would be more space for the pairwise distance matrix.

• Second, the issue of 255 possible values is a limitation of the grayscale requirement. If this was lifted, the precision could go up dramatically.

• Third, I'm sure there's a good reason for it, but what's the distance matrix for? It can be calculated from the fractional coordinates. If all we want is to do is to represent the CIF file, there's no reason to include it.

• I would rewrite this section, as a "potential" time saving is only potential.
  

  xtal2png/reports/paper.md

  Lines 105 to 106 in cc644f3

  	dataset types, potentially saving days or weeks during the process of obtaining
  	preliminary results on a newly released model.

• There is no mention of any other software that provides similar functionality. If there truly is not any encoder/decoder for crystal structure to image data, perhaps a short section discussing existing software for molecules and/or textual representation could be included.

matches(...)

https://matsci.org/t/how-do-i-do-a-time-split-of-materials-project-entries-e-g-pre-2018-vs-post-2018/42584/5

#12

Perhaps 70/20/10 split, train/val/test.

xref: sparks-baird/matbench-genmetrics#77

If the sites aren't already sorted, best to sort. Perhaps using s.copy(sanitize=True). Can add as a hyperparameter. Shouldn't affect the xtal2png encoding and decoding process to swap the order of sites.

Data augmentation is something I've considered, but with 52 sites, the combinatorial space is enormous and probably intractable. In the worst case with 52 sites and if I'm thinking about this correct, that's nPr ==$52P52$ == 8.07E67. Could maybe do partial data augmentation where sites with a shared periodic element undergo permutation data augmentation locally, but even that might be intractable.

Reported by @faris-k

In v0.6.2 encoding and decoding as primitive is False by default. In v0.6.3 this will be set to True as a temporary fix, followed by a refactor in v0.7.0 that converts these kwargs to encode_cell_type and decode_cell_type.

• Min and max for abc lattice parameter lengths (abc_range)
• Min and max for pairwise distances (distance_range)
• Min and max for unit cell volume (volume)

i.e. take all Materials Project entries with less than or equal to 52 sites, and determine the minimum and maximum lattice parameter lengths across all a, b, and c values. Same for distances and volume.

many matminer featurizers have a fit method that allows to set some hyperparameter of the featurizer given a dataset (see, for example, the SOAP featurizer)

How could it be of use here? If you have a collection of cifs, and then call .fit it would automatically set the relevant atom types, perhaps also the maximum number of sites.

E.g.

from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from tqdm import tqdm
structures = df.structures.tolist()
for structure in tqdm(structures):
    spa = SpacegroupAnalyzer(structure, symprec=0.1)
    new_structure = spa.find_primitive()

@faris-k

EDIT: see also issues with the "notion of best" label

Relaxation is probably the most straightforward - use some crystal distance. Prediction can be about checking against known allotropes, where we take the lowest crystal distance among the allotropes. Generation is the least straightforward. Perhaps a Pareto hypervolume metric via a fictitious adaptive design campaign (e.g. bulk modulus vs. energy above hull)? Perform hyperparameter optimization and then do DFT as the final validation.

e.g. https://xtal2png.readthedocs.io/en/latest/api/xtal2png.html#xtal2png.core.XtalConverter

as it is an option for decoding and can make issues when installing it might make sense to have it as

[options.extras_require]
   m3gnet = m3gnet