Upload BoltzGen

README.md

@@ -0,0 +1,199 @@
+---
+library_name: transformers
+tags: []
+---
+
+# Model Card for Model ID
+
+<!-- Provide a quick summary of what the model is/does. -->
+
+
+
+## Model Details
+
+### Model Description
+
+<!-- Provide a longer summary of what this model is. -->
+
+This is the model card of a 🤗 transformers model that has been pushed on the Hub. This model card has been automatically generated.
+
+- **Developed by:** [More Information Needed]
+- **Funded by [optional]:** [More Information Needed]
+- **Shared by [optional]:** [More Information Needed]
+- **Model type:** [More Information Needed]
+- **Language(s) (NLP):** [More Information Needed]
+- **License:** [More Information Needed]
+- **Finetuned from model [optional]:** [More Information Needed]
+
+### Model Sources [optional]
+
+<!-- Provide the basic links for the model. -->
+
+- **Repository:** [More Information Needed]
+- **Paper [optional]:** [More Information Needed]
+- **Demo [optional]:** [More Information Needed]
+
+## Uses
+
+<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->
+
+### Direct Use
+
+<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. -->
+
+[More Information Needed]
+
+### Downstream Use [optional]
+
+<!-- This section is for the model use when fine-tuned for a task, or when plugged into a larger ecosystem/app -->
+
+[More Information Needed]
+
+### Out-of-Scope Use
+
+<!-- This section addresses misuse, malicious use, and uses that the model will not work well for. -->
+
+[More Information Needed]
+
+## Bias, Risks, and Limitations
+
+<!-- This section is meant to convey both technical and sociotechnical limitations. -->
+
+[More Information Needed]
+
+### Recommendations
+
+<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
+
+Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
+
+## How to Get Started with the Model
+
+Use the code below to get started with the model.
+
+[More Information Needed]
+
+## Training Details
+
+### Training Data
+
+<!-- This should link to a Dataset Card, perhaps with a short stub of information on what the training data is all about as well as documentation related to data pre-processing or additional filtering. -->
+
+[More Information Needed]
+
+### Training Procedure
+
+<!-- This relates heavily to the Technical Specifications. Content here should link to that section when it is relevant to the training procedure. -->
+
+#### Preprocessing [optional]
+
+[More Information Needed]
+
+
+#### Training Hyperparameters
+
+- **Training regime:** [More Information Needed] <!--fp32, fp16 mixed precision, bf16 mixed precision, bf16 non-mixed precision, fp16 non-mixed precision, fp8 mixed precision -->
+
+#### Speeds, Sizes, Times [optional]
+
+<!-- This section provides information about throughput, start/end time, checkpoint size if relevant, etc. -->
+
+[More Information Needed]
+
+## Evaluation
+
+<!-- This section describes the evaluation protocols and provides the results. -->
+
+### Testing Data, Factors & Metrics
+
+#### Testing Data
+
+<!-- This should link to a Dataset Card if possible. -->
+
+[More Information Needed]
+
+#### Factors
+
+<!-- These are the things the evaluation is disaggregating by, e.g., subpopulations or domains. -->
+
+[More Information Needed]
+
+#### Metrics
+
+<!-- These are the evaluation metrics being used, ideally with a description of why. -->
+
+[More Information Needed]
+
+### Results
+
+[More Information Needed]
+
+#### Summary
+
+
+
+## Model Examination [optional]
+
+<!-- Relevant interpretability work for the model goes here -->
+
+[More Information Needed]
+
+## Environmental Impact
+
+<!-- Total emissions (in grams of CO2eq) and additional considerations, such as electricity usage, go here. Edit the suggested text below accordingly -->
+
+Carbon emissions can be estimated using the [Machine Learning Impact calculator](https://mlco2.github.io/impact#compute) presented in [Lacoste et al. (2019)](https://arxiv.org/abs/1910.09700).
+
+- **Hardware Type:** [More Information Needed]
+- **Hours used:** [More Information Needed]
+- **Cloud Provider:** [More Information Needed]
+- **Compute Region:** [More Information Needed]
+- **Carbon Emitted:** [More Information Needed]
+
+## Technical Specifications [optional]
+
+### Model Architecture and Objective
+
+[More Information Needed]
+
+### Compute Infrastructure
+
+[More Information Needed]
+
+#### Hardware
+
+[More Information Needed]
+
+#### Software
+
+[More Information Needed]
+
+## Citation [optional]
+
+<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
+
+**BibTeX:**
+
+[More Information Needed]
+
+**APA:**
+
+[More Information Needed]
+
+## Glossary [optional]
+
+<!-- If relevant, include terms and calculations in this section that can help readers understand the model or model card. -->
+
+[More Information Needed]
+
+## More Information [optional]
+
+[More Information Needed]
+
+## Model Card Authors [optional]
+
+[More Information Needed]
+
+## Model Card Contact
+
+[More Information Needed]

config.json

@@ -0,0 +1,232 @@
+{
+  "affinity_baseline": false,
+  "affinity_confidence_different": false,
+  "affinity_confidence_different_multiple": false,
+  "affinity_ensemble": false,
+  "affinity_model_args": {
+    "affinity_args": {
+      "groups": {
+        "0": 1
+      },
+      "val_groups": [
+        0
+      ]
+    }
+  },
+  "affinity_model_args1": {},
+  "affinity_model_args2": {},
+  "affinity_mw_correction": true,
+  "affinity_pair_transformer": false,
+  "affinity_prediction": false,
+  "affinity_transformer": false,
+  "affinity_transformer_atom": false,
+  "alpha_affinity_absolute": 0.0,
+  "alpha_affinity_binary": 0.0,
+  "alpha_affinity_difference": 0.0,
+  "alpha_affinity_focal": 0.0,
+  "alpha_affinity_score_binder_binder": 0.0,
+  "alpha_affinity_score_binder_decoy": 0.0,
+  "alpha_pae": 1,
+  "architectures": [
+    "BoltzGen"
+  ],
+  "atom_feature_dim": 388,
+  "atom_s": 128,
+  "atom_z": 16,
+  "atoms_per_window_keys": 128,
+  "atoms_per_window_queries": 32,
+  "bond_type_feature": true,
+  "chain_sampling_args": null,
+  "checkpoint_diffusion_conditioning": true,
+  "compile_confidence": false,
+  "compile_msa": false,
+  "compile_pairformer": false,
+  "compile_structure": false,
+  "compile_templates": false,
+  "compute_tistogram": false,
+  "confidence_imitate_trunk": false,
+  "confidence_model_args": {
+    "add_s_input_to_s": true,
+    "add_s_to_z_prod": true,
+    "add_z_input_to_z": true,
+    "confidence_args": {
+      "num_pae_bins": 64,
+      "num_pde_bins": 64,
+      "num_plddt_bins": 50,
+      "relative_confidence": "none",
+      "use_separate_heads": true
+    },
+    "max_dist": 22,
+    "no_trunk_feats": false,
+    "num_dist_bins": 64,
+    "pairformer_args": {
+      "dropout": 0.25,
+      "num_blocks": 8,
+      "num_heads": 16
+    },
+    "use_gaussian": false,
+    "use_miniformer": false,
+    "use_s_diffusion": false
+  },
+  "confidence_prediction": true,
+  "confidence_regression": false,
+  "cyclic_pos_enc": true,
+  "diffusion_loss_args": {
+    "add_bond_loss": false,
+    "add_smooth_lddt_loss": true,
+    "filter_by_plddt": 0.0,
+    "ligand_loss_weight": 10.0,
+    "nucleotide_loss_weight": 5.0
+  },
+  "diffusion_process_args": {
+    "P_mean": -1.2,
+    "P_std": 1.5,
+    "alignment_reverse_diff": true,
+    "coordinate_augmentation": true,
+    "gamma_0": 0.8,
+    "gamma_min": 1.0,
+    "mse_rotational_alignment": true,
+    "noise_scale": 1.0,
+    "rho": 7,
+    "sigma_data": 16.0,
+    "sigma_max": 160.0,
+    "sigma_min": 0.0004,
+    "step_scale": 1.0,
+    "step_scale_random": [
+      1.0,
+      1.1,
+      1.2,
+      1.3,
+      1.4,
+      1.5
+    ],
+    "synchronize_sigmas": false
+  },
+  "dtype": "float32",
+  "dynamic_args": {},
+  "ema": true,
+  "ema_decay": 0.999,
+  "embedder_args": {
+    "add_cyclic_flag": true,
+    "add_method_conditioning": true,
+    "add_modified_flag": true,
+    "add_mol_type_feat": true,
+    "atom_encoder_depth": 3,
+    "atom_encoder_heads": 4
+  },
+  "exclude_ions_from_lddt": true,
+  "fix_sym_check": true,
+  "freeze_template_weights": false,
+  "guidance_args": null,
+  "ignore_ckpt_shape_mismatch": false,
+  "inference_logging": false,
+  "inverse_fold": false,
+  "inverse_fold_args": null,
+  "masker_args": {},
+  "max_dist": 22.0,
+  "maximum_bond_distance": 0,
+  "min_dist": 2.0,
+  "model_type": "boltzgen",
+  "msa_args": {
+    "activation_checkpointing": false,
+    "miniformer_blocks": false,
+    "msa_blocks": 4,
+    "msa_dropout": 0.15,
+    "msa_s": 64,
+    "pairwise_head_width": 32,
+    "pairwise_num_heads": 4,
+    "use_paired_feature": true,
+    "z_dropout": 0.25
+  },
+  "num_bins": 64,
+  "num_distograms": 1,
+  "num_tistogram_axis": 1,
+  "num_val_datasets": 4,
+  "pairformer_args": {
+    "activation_checkpointing": false,
+    "dropout": 0.25,
+    "num_blocks": 64,
+    "num_heads": 16,
+    "post_layer_norm": false
+  },
+  "predict_bfactor": true,
+  "predict_res_type": false,
+  "recycling_detach": true,
+  "refolding_validator": null,
+  "relative_confidence_supervision_weight": 0.0,
+  "representative_lddt": false,
+  "score_model_args": {
+    "activation_checkpointing": false,
+    "atom_decoder_depth": 3,
+    "atom_decoder_heads": 4,
+    "atom_encoder_depth": 3,
+    "atom_encoder_heads": 4,
+    "conditioning_transition_layers": 2,
+    "dim_fourier": 256,
+    "sigma_data": 16,
+    "token_transformer_depth": 24,
+    "token_transformer_heads": 16,
+    "transformer_post_ln": false
+  },
+  "skip_run_structure": false,
+  "structure_prediction_training": false,
+  "symmetry_correction_trunk": false,
+  "tau_affinity_score": -1.0,
+  "template_args": {
+    "activation_checkpointing": false,
+    "template_blocks": 2,
+    "template_dim": 64
+  },
+  "token_distance_args": null,
+  "token_level_confidence": true,
+  "token_s": 384,
+  "token_z": 128,
+  "training_args": {
+    "adam_beta_1": 0.9,
+    "adam_beta_2": 0.95,
+    "adam_eps": 1e-08,
+    "affinity_loss_weight": 0.003,
+    "base_lr": 0.0,
+    "bfactor_loss_weight": 0.001,
+    "confidence_loss_weight": 0.3,
+    "diffusion_loss_weight": 4.0,
+    "diffusion_multiplicity": 32,
+    "diffusion_samples": 1,
+    "distogram_loss_weight": 0.03,
+    "lr_decay_every_n_steps": 50000,
+    "lr_decay_factor": 0.95,
+    "lr_scheduler": "af3",
+    "lr_start_decay_after_n_steps": 50000,
+    "lr_warmup_no_steps": 1000,
+    "max_lr": 0.001,
+    "recycling_steps": 3,
+    "sampling_steps": 50,
+    "sampling_steps_random": [
+      20,
+      50,
+      200
+    ],
+    "symmetry_correction": true,
+    "weight_decay": 0.003,
+    "weight_decay_exclude": true
+  },
+  "transformers_version": "4.57.1",
+  "trunk_resolved_loss": false,
+  "use_atom_backbone_feat": false,
+  "use_kernels": false,
+  "use_miniformer": false,
+  "use_miniformer_plus": false,
+  "use_no_atom_char": false,
+  "use_residue_feats_atoms": false,
+  "use_templates": true,
+  "use_templates_v2": true,
+  "use_token_distances": false,
+  "validation_args": {
+    "diffusion_samples": 5,
+    "recycling_steps": 3,
+    "run_confidence_sequentially": true,
+    "sampling_steps": 200,
+    "symmetry_correction": true
+  },
+  "validators": "[<__main__.DummyValidator object at 0x00000187A3DBD550>, <__main__.DummyValidator object at 0x00000187A5D718D0>, <__main__.DummyValidator object at 0x00000187A5F44350>, <__main__.DummyValidator object at 0x00000187A415B250>]"
+}

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a89b7a724d48b4d2ec9c633880242a1f20dbde00c4812a0e49b44709e4378d4c
+size 2028676823