This report presents the forensic synthetic code analysis of Biohub/esm, a Jupyter Notebook project with 2,931 GitHub stars. SynthScan v2.0 examined 123,327 lines of code across 180 source files, recording 992 pattern matches distributed across 18 syntactic categories. The overall adjusted score of 13.1 places this repository in the Low AI signal band.
The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).
This chart maps the temporal evolution of the adjusted synthetic code score across successive scan runs. An upward trajectory indicates ongoing incorporation of AI-generated code or expanding LLM-assisted scaffolding; a stable or declining trajectory may reflect active human refactoring, code removal, or the adoption of stricter authorship policies. The dashed secondary line (right axis) independently tracks total raw pattern hit count, which can diverge from the normalised score when codebase size changes significantly between scans.
Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.
This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.
The scanner identified 992 distinct pattern matches across 18 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.
Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | esm/models/esmfold2/config.py | 35 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | esm/models/esmfold2/config.py | 37 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | esm/models/esmfold2/config.py | 341 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | esm/models/esmfold2/config.py | 343 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/experimental.py | 130 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/experimental.py | 132 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/experimental.py | 140 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/experimental.py | 142 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/experimental.py | 525 | # =========================================================================== | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/experimental.py | 527 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/experimental.py | 69 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/experimental.py | 71 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/experimental.py | 157 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | esm/models/esmfold2/experimental.py | 159 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | esm/models/esmfold2/experimental.py | 346 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/experimental.py | 348 | # =========================================================================== | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/constants.py | 6 | # ============================================================================= | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/constants.py | 8 | # ============================================================================= | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/constants.py | 15 | # ============================================================================= | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/constants.py | 17 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 55 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 57 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 164 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 166 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 201 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 203 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 302 | # ============================================================================= | COMMENT |
| MEDIUM | esm/models/esmfold2/constants.py | 304 | # ============================================================================= | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/layers.py | 409 | # =========================================================================== | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/layers.py | 411 | # =========================================================================== | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/layers.py | 1685 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/layers.py | 1687 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/layers.py | 2480 | # =========================================================================== | COMMENT |
| MEDIUM⚡ | esm/models/esmfold2/layers.py | 2482 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 149 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 151 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 175 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 177 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 230 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 232 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 339 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 341 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 362 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 364 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 385 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 387 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 453 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 455 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 536 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 538 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 556 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 558 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 652 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 654 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 780 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 782 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 942 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 944 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 1014 | # =========================================================================== | COMMENT |
| MEDIUM | esm/models/esmfold2/layers.py | 1016 | # =========================================================================== | COMMENT |
| 206 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/misc.py | 40 | def slice_python_object_as_numpy( | CODE |
| LOW | esm/utils/misc.py | 180 | def stack_variable_length_tensors( | CODE |
| LOW | esm/utils/misc.py | 401 | def get_chainbreak_boundaries_from_sequence(sequence: Sequence[str]) -> np.ndarray: | CODE |
| LOW | esm/utils/misc.py | 451 | def iterate_with_intermediate( | CODE |
| LOW | esm/utils/system.py | 10 | def run_subprocess_with_errorcheck( | CODE |
| LOW | esm/utils/encoding.py | 26 | def get_default_secondary_structure(sequence_length: int) -> str: | CODE |
| LOW | esm/utils/encoding.py | 100 | def tokenize_secondary_structure( | CODE |
| LOW | esm/utils/encoding.py | 138 | def tokenize_function_annotations( | CODE |
| LOW | esm/utils/encoding.py | 156 | def get_default_sequence_tokens( | CODE |
| LOW | esm/utils/encoding.py | 172 | def get_default_structure_tokens( | CODE |
| LOW | esm/utils/encoding.py | 185 | def get_default_secondary_structure_tokens( | CODE |
| LOW | esm/utils/encoding.py | 206 | def get_default_function_tokens( | CODE |
| LOW | esm/utils/encoding.py | 219 | def get_default_residue_annotation_tokens( | CODE |
| LOW | esm/utils/generation.py | 37 | def _trim_sequence_tensor_dataclass(o: Any, sequence_len: int): | CODE |
| LOW | esm/utils/generation.py | 240 | def _get_iterative_sampling_mask_for_prompt_and_step( | CODE |
| LOW | esm/utils/generation.py | 349 | def _get_annealed_temperature(step: int, num_steps: int, initial_temperature: float): | CODE |
| LOW | esm/utils/generation.py | 354 | def iterative_sampling_tokens( | CODE |
| LOW | esm/utils/decoding.py | 172 | def decode_secondary_structure( | CODE |
| LOW | esm/utils/decoding.py | 206 | def decode_function_annotations( | CODE |
| LOW | esm/utils/decoding.py | 223 | def decode_residue_annotations( | CODE |
| LOW | esm/utils/sequential_dataclass.py | 97 | def _check_sequence_lengths_match(self): | CODE |
| LOW | esm/utils/residue_constants.py | 429 | def load_stereo_chemical_props() -> Tuple[ | CODE |
| LOW | esm/utils/residue_constants.py | 1038 | def _make_rigid_group_constants(): | CODE |
| LOW | esm/utils/sampling.py | 109 | def get_default_sampling_config( | CODE |
| LOW | esm/utils/sampling.py | 241 | def sample_residue_annotation_logits( | CODE |
| LOW | esm/utils/msa/msa.py | 23 | def remove_insertions_from_sequence(seq: str) -> str: | CODE |
| LOW | esm/utils/constants/models.py | 20 | def forge_only_return_single_layer_hidden_states(model_name: str): | CODE |
| LOW | esm/utils/constants/models.py | 24 | def model_is_locally_supported(x: str): | CODE |
| LOW | esm/utils/function/encode_decode.py | 13 | def encode_function_annotations( | CODE |
| LOW | esm/utils/function/encode_decode.py | 136 | def decode_residue_annotation_tokens( | CODE |
| LOW | esm/utils/structure/mmcif_parsing.py | 384 | def _parse_nonpoly_from_mmcif(self) -> dict[tuple, bs.AtomArray]: | CODE |
| LOW | esm/utils/structure/input_builder.py | 121 | def serialize_structure_prediction_input(all_atom_input: StructurePredictionInput): | CODE |
| LOW | esm/utils/structure/input_builder.py | 195 | def deserialize_structure_prediction_input( | CODE |
| LOW | esm/utils/structure/protein_structure.py | 70 | def compute_alignment_tensors( | CODE |
| LOW | esm/utils/structure/protein_structure.py | 165 | def compute_rmsd_no_alignment( | CODE |
| LOW | esm/utils/structure/protein_structure.py | 263 | def compute_gdt_ts_no_alignment( | CODE |
| LOW | esm/utils/structure/protein_chain.py | 243 | def residue_index_no_insertions(self) -> np.ndarray: | CODE |
| LOW | esm/utils/structure/protein_chain.py | 775 | def chain_iterable_from_mmcif( | CODE |
| LOW | esm/utils/structure/protein_chain.py | 983 | def from_backbone_atom_coordinates( | CODE |
| LOW | esm/utils/structure/protein_chain.py | 1378 | def to_structure_encoder_inputs( | CODE |
| LOW | esm/utils/structure/protein_complex.py | 57 | def _parse_operation_expression(expression): | CODE |
| LOW | esm/utils/structure/protein_complex.py | 89 | def _apply_transformations_fast(chains, transformation_dict, operations): | CODE |
| LOW | esm/utils/structure/protein_complex.py | 380 | def normalize_chain_ids_for_pdb(self): | CODE |
| LOW | esm/utils/structure/protein_complex.py | 393 | def find_assembly_ids_with_chain(self, id: str) -> list[str]: | CODE |
| LOW | esm/utils/structure/protein_complex.py | 695 | def _sanity_check_complexes_are_comparable(self, other: ProteinComplex): | CODE |
| LOW | esm/utils/structure/protein_complex.py | 1245 | def protein_chain_to_protein_complex(chain: ProteinChain) -> ProteinComplex: | CODE |
| LOW | esm/utils/structure/normalize_coordinates.py | 34 | def get_protein_normalization_frame(coords: Tensor) -> Affine3D: | CODE |
| LOW | esm/utils/structure/predicted_aligned_error.py | 37 | def compute_predicted_aligned_error( | CODE |
| LOW | esm/models/hub.py | 115 | def _materialize_uninitialized(self, device: torch.device | str = "cpu") -> None: | CODE |
| LOW | esm/models/hub.py | 136 | def _normalize_checkpoint_layout( | CODE |
| LOW | esm/models/esmfold2/hf_adapter.py | 104 | def _sampler_config_overrides( | CODE |
| LOW⚡ | esm/models/esmfold2/experimental.py | 537 | def _normalize_checkpoint_layout( | CODE |
| LOW | esm/models/esmfold2/experimental.py | 734 | def _output_to_molecular_complex(output: dict, features: dict, chain_infos: list): | CODE |
| LOW | esm/models/esmfold2/experimental.py | 827 | def _compute_lm_hidden_states( | CODE |
| LOW | esm/models/esmfold2/conformers.py | 87 | def _get_ccd_mol_with_significant_h(comp_id: str): | CODE |
| LOW | esm/models/esmfold2/conformers.py | 176 | def get_ligand_idealized_atom_pos(res_name: str, atom_name: str) -> np.ndarray | None: | CODE |
| LOW | esm/models/esmfold2/conformers.py | 195 | def get_ligand_ccd_atoms_with_charges( | CODE |
| LOW | esm/models/esmfold2/model.py | 540 | def _normalize_checkpoint_layout( | CODE |
| LOW | esm/models/esmfold2/model.py | 796 | def _compute_lm_hidden_states( | CODE |
| LOW | esm/models/esmfold2/paired_msa.py | 24 | def protein_letter_to_res_type() -> dict[str, int]: | CODE |
| 340 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/types.py | 1 | CODE | |
| LOW | esm/utils/msa/msa.py | 1 | CODE | |
| LOW | esm/utils/msa/__init__.py | 1 | CODE | |
| LOW | esm/utils/msa/__init__.py | 1 | CODE | |
| LOW | esm/utils/msa/__init__.py | 1 | CODE | |
| LOW | esm/utils/structure/aligner.py | 1 | CODE | |
| LOW | esm/utils/structure/mmcif_parsing.py | 1 | CODE | |
| LOW | esm/utils/structure/affine3d.py | 1 | CODE | |
| LOW | esm/utils/structure/protein_structure.py | 1 | CODE | |
| LOW | esm/utils/structure/protein_chain.py | 1 | CODE | |
| LOW | esm/utils/structure/protein_complex.py | 1 | CODE | |
| LOW | esm/models/esm3.py | 1 | CODE | |
| LOW | esm/models/esmfold2/config.py | 16 | CODE | |
| LOW | esm/models/esmfold2/experimental.py | 24 | CODE | |
| LOW | esm/models/esmfold2/conformers.py | 7 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 1 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 1 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 1 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 6 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 7 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 8 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 9 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 10 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 11 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 11 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 12 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 12 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 24 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 24 | CODE | |
| LOW | esm/models/esmfold2/__init__.py | 24 | CODE | |
| LOW | esm/models/esmfold2/types.py | 9 | CODE | |
| LOW | esm/models/esmfold2/types.py | 10 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/types.py | 11 | CODE | |
| LOW | esm/models/esmfold2/protein_utils.py | 17 | CODE | |
| LOW | esm/models/esmfold2/layers.py | 11 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 7 | CODE | |
| LOW | esm/models/esmfold2/kernels/fused_dual_gemm.py | 13 | CODE | |
| LOW | esm/models/esmfold2/kernels/trimul_with_residual.py | 37 | CODE | |
| LOW | esm/models/esmfold2/kernels/fused_dropout_residual.py | 26 | CODE | |
| LOW | esm/models/esmfold2/kernels/__init__.py | 11 | CODE | |
| LOW | esm/models/esmfold2/kernels/__init__.py | 12 | CODE | |
| LOW | esm/models/esmfold2/kernels/__init__.py | 13 | CODE | |
| LOW | esm/models/esmfold2/kernels/__init__.py | 14 | CODE | |
| LOW | esm/models/esmfold2/kernels/fused_lnlin_swiglu.py | 27 | CODE | |
| 27 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/generation.py | 37 | CODE | |
| LOW | esm/utils/generation.py | 66 | CODE | |
| LOW | esm/utils/generation.py | 130 | CODE | |
| LOW | esm/utils/sequential_dataclass.py | 97 | CODE | |
| LOW | esm/utils/residue_constants.py | 1114 | CODE | |
| LOW | esm/utils/sampling.py | 133 | CODE | |
| LOW | esm/utils/forge_context_manager.py | 88 | CODE | |
| LOW | esm/utils/constants/esm3.py | 105 | CODE | |
| LOW | esm/utils/structure/mmcif_parsing.py | 101 | CODE | |
| LOW | esm/utils/structure/mmcif_parsing.py | 146 | CODE | |
| LOW | esm/utils/structure/mmcif_parsing.py | 202 | CODE | |
| LOW | esm/utils/structure/mmcif_parsing.py | 384 | CODE | |
| LOW | esm/utils/structure/mmcif_parsing.py | 449 | CODE | |
| LOW | esm/utils/structure/input_builder.py | 121 | CODE | |
| LOW | esm/utils/structure/input_builder.py | 195 | CODE | |
| LOW | esm/utils/structure/molecular_complex.py | 447 | CODE | |
| LOW | esm/utils/structure/molecular_complex.py | 822 | CODE | |
| LOW | esm/utils/structure/molecular_complex.py | 985 | CODE | |
| LOW | esm/utils/structure/molecular_complex.py | 1155 | CODE | |
| LOW | esm/utils/structure/molecular_complex.py | 1388 | CODE | |
| LOW | esm/utils/structure/protein_chain.py | 88 | CODE | |
| LOW | esm/utils/structure/protein_chain.py | 906 | CODE | |
| LOW | esm/utils/structure/protein_chain.py | 1056 | CODE | |
| LOW | esm/utils/structure/protein_complex.py | 815 | CODE | |
| LOW | esm/models/esmfold2/experimental.py | 848 | CODE | |
| LOW | esm/models/esmfold2/conformers.py | 268 | CODE | |
| LOW | esm/models/esmfold2/processor.py | 87 | CODE | |
| LOW | esm/models/esmfold2/model.py | 368 | CODE | |
| LOW | esm/models/esmfold2/model.py | 378 | CODE | |
| LOW | esm/models/esmfold2/paired_msa.py | 95 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 158 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 330 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 676 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 811 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 951 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 1091 | CODE | |
| LOW | esm/models/esmfold2/prepare_input.py | 1131 | CODE | |
| LOW | esm/models/esmfold2/output.py | 18 | CODE | |
| LOW | esm/models/esmfold2/output.py | 129 | CODE | |
| LOW | esm/models/esmc/checkpoint_layout.py | 145 | CODE | |
| LOW | esm/models/esmc/model.py | 675 | CODE | |
| LOW | esm/tokenization/residue_tokenizer.py | 73 | CODE | |
| LOW | esm/sdk/forge.py | 141 | CODE | |
| LOW | esm/sdk/api.py | 56 | CODE | |
| LOW | esm/sdk/api.py | 165 | CODE | |
| LOW | esm/sdk/base_forge_client.py | 245 | CODE | |
| LOW | esm/sdk/base_forge_client.py | 272 | CODE | |
| LOW | esm/sdk/base_forge_client.py | 385 | CODE | |
| LOW | esm/sdk/base_forge_client.py | 426 | CODE | |
| LOW | esm/widgets/utils/prompting.py | 385 | CODE | |
| LOW | esm/widgets/components/results_visualizer.py | 21 | CODE | |
| LOW | esm/widgets/components/results_visualizer.py | 55 | CODE | |
| LOW | esm/widgets/components/sequence_prompt_selector.py | 13 | CODE | |
| LOW | esm/widgets/components/sequence_prompt_selector.py | 96 | CODE | |
| LOW | esm/widgets/components/structure_prompt_selector.py | 19 | CODE | |
| LOW | esm/widgets/components/structure_prompt_selector.py | 94 | CODE | |
| LOW | esm/widgets/components/structure_prompt_selector.py | 309 | CODE | |
| LOW | esm/widgets/views/prediction.py | 14 | CODE | |
| LOW | esm/widgets/views/prediction.py | 80 | CODE | |
| LOW | esm/widgets/views/esm3_generation_launcher.py | 21 | CODE | |
| 7 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/msa/__init__.py | 3 | __all__ = ["MSA", "FastMSA", "remove_insertions_from_sequence"] | CODE |
| LOW | esm/models/esmfold2/hf_adapter.py | 197 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/hf_adapter.py | 408 | __all__ = ["EsmFold2HFAdapter", "translate_features", "upstream_available"] | CODE |
| LOW | esm/models/esmfold2/config.py | 107 | def _set_path(tree: dict, path: str, value) -> None: | CODE |
| LOW | esm/models/esmfold2/config.py | 559 | __all__ = [ | CODE |
| LOW⚡ | esm/models/esmfold2/experimental.py | 134 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW⚡ | esm/models/esmfold2/experimental.py | 137 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 387 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 391 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 472 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 476 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 623 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 632 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/experimental.py | 1178 | __all__ = ["EsmFold2ExperimentalModel"] | CODE |
| LOW | esm/models/esmfold2/hf_checkpoint.py | 258 | __all__ = [ | CODE |
| LOW | esm/models/esmfold2/__init__.py | 30 | __all__ = [ | CODE |
| LOW | esm/models/esmfold2/processor.py | 430 | __all__ = ["ESMFold2InputBuilder", "clean_esmfold2_input"] | CODE |
| LOW | esm/models/esmfold2/types.py | 22 | __all__ = [ | CODE |
| LOW | esm/models/esmfold2/model.py | 90 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 158 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 161 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 643 | def set_esmc_precision(self, precision: str = "bf16") -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 716 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 787 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 1241 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 1245 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 1300 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/model.py | 1304 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW⚡ | esm/models/esmfold2/layers.py | 1682 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW⚡ | esm/models/esmfold2/layers.py | 2464 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW⚡ | esm/models/esmfold2/layers.py | 2473 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW⚡ | esm/models/esmfold2/layers.py | 2609 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 1057 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 1307 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 1520 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2367 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2497 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2500 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2596 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2677 | def set_kernel_backend(self, backend: str | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2681 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2742 | def set_chunk_size(self, chunk_size: int | None) -> None: | CODE |
| LOW | …m/models/esmfold2/kernels/fused_attention_pair_bias.py | 696 | __all__ = ["FusedPairBias", "fused_attention_pair_bias", "fused_pair_bias"] | CODE |
| LOW | esm/models/esmfold2/kernels/__init__.py | 18 | __all__ = [ | CODE |
| LOW | esm/models/esmc/__init__.py | 23 | __all__ = [ | CODE |
| LOW | esm/models/esmc/model.py | 311 | def set_input_embeddings(self, value: nn.Embedding) -> None: | CODE |
| LOW | esm/models/esmc/model.py | 565 | def set_output_embeddings(self, new_embeddings: nn.Linear) -> None: | CODE |
| LOW | esm/models/esmc/kernels.py | 25 | logger = logging.getLogger(__name__) | CODE |
| LOW | esm/models/esmc/layers.py | 106 | def _update_cos_sin_cache(self, seqlen: int, device=None, dtype=None) -> None: | CODE |
| LOW | esm/sdk/experimental/__init__.py | 8 | __all__ = [ | CODE |
| LOW | esm/sdk/experimental/constrained_generation.py | 72 | def update_lambda(self, g: float, eta: float, gamma: float) -> None: | CODE |
| LOW | cookbook/tutorials/binder_design.py | 64 | logger = logging.getLogger(__name__) | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/forge_context_manager.py | 137 | except Exception as e: | CODE |
| LOW | esm/utils/structure/mmcif_parsing.py | 98 | except Exception as e: | CODE |
| LOW | esm/utils/structure/mmcif_parsing.py | 142 | except Exception: | CODE |
| LOW | esm/utils/structure/mmcif_parsing.py | 191 | except Exception: | CODE |
| LOW | esm/utils/structure/mmcif_parsing.py | 495 | except Exception: | CODE |
| LOW | esm/utils/structure/molecular_complex.py | 476 | except Exception: | CODE |
| LOW | esm/utils/structure/molecular_complex.py | 540 | except Exception: | CODE |
| LOW | esm/utils/structure/molecular_complex.py | 1151 | except Exception: | CODE |
| LOW | esm/utils/structure/molecular_complex.py | 1223 | except Exception as e: | CODE |
| LOW | esm/models/esmfold2/conformers.py | 59 | except Exception as e: | CODE |
| LOW | esm/models/esmfold2/layers.py | 2423 | except Exception as e: | CODE |
| LOW | esm/sdk/forge.py | 967 | except Exception as e: | STRING |
| LOW | esm/sdk/retry.py | 34 | except Exception: | CODE |
| MEDIUM | esm/sdk/retry.py | 31 | def log_retry_attempt(retry_state): | CODE |
| LOW | esm/sdk/sagemaker.py | 46 | except Exception as e: | CODE |
| LOW | esm/sdk/sagemaker.py | 108 | except Exception as e: | CODE |
| LOW | esm/sdk/base_forge_client.py | 134 | except Exception as e: | CODE |
| LOW | esm/sdk/base_forge_client.py | 165 | except Exception as e: | CODE |
| LOW | esm/sdk/base_forge_client.py | 319 | except Exception as e: | CODE |
| LOW | esm/sdk/base_forge_client.py | 349 | except Exception as e: | CODE |
| LOW | esm/widgets/utils/protein_import.py | 110 | except Exception as e: | CODE |
| MEDIUM | esm/widgets/utils/protein_import.py | 112 | wrapped_print(f"Error: {e}") | CODE |
| LOW | esm/widgets/utils/protein_import.py | 148 | except Exception as e: | CODE |
| MEDIUM | esm/widgets/utils/protein_import.py | 150 | wrapped_print(f"Error: {e}") | CODE |
| MEDIUM | esm/widgets/utils/protein_import.py | 132 | def on_upload(self, _): | CODE |
| LOW | esm/widgets/components/structure_prompt_selector.py | 190 | except Exception as e: | CODE |
| LOW | esm/widgets/components/structure_prompt_selector.py | 331 | except Exception as e: | CODE |
| LOW | esm/widgets/components/function_annotator.py | 123 | except Exception as e: | CODE |
| MEDIUM | esm/widgets/components/function_annotator.py | 125 | print(f"Error: {e}") | CODE |
| LOW | esm/widgets/views/prediction.py | 149 | except Exception as e: | CODE |
| MEDIUM | esm/widgets/views/prediction.py | 80 | def on_click_predict(_): | CODE |
| LOW | esm/widgets/views/esm3_generation_launcher.py | 185 | except Exception: | CODE |
| LOW | esm/widgets/views/inverse_folding.py | 86 | except Exception as e: | CODE |
| MEDIUM | esm/widgets/views/inverse_folding.py | 54 | def on_click_inverse_fold(_): | CODE |
| LOW | .github/scripts/airtable_issue_sync.py | 402 | except Exception as err: # noqa: BLE001 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/layers/transformer_stack.py | 26 | CODE | |
| LOW | esm/layers/blocks.py | 73 | CODE | |
| LOW | esm/utils/structure/protein_complex.py | 949 | CODE | |
| LOW | esm/models/esm3.py | 267 | CODE | |
| LOW | esm/models/vqvae.py | 49 | CODE | |
| LOW | esm/models/esmfold2/hf_adapter.py | 210 | CODE | |
| LOW | esm/models/esmfold2/experimental.py | 848 | CODE | |
| LOW | esm/models/esmfold2/processor.py | 328 | CODE | |
| LOW | esm/models/esmfold2/model.py | 929 | CODE | |
| LOW | esm/models/esmfold2/layers.py | 718 | CODE | |
| LOW | esm/models/esmfold2/layers.py | 797 | CODE | |
| LOW | esm/models/esmfold2/layers.py | 950 | CODE | |
| LOW | esm/models/esmfold2/layers.py | 1443 | CODE | |
| LOW | esm/models/esmfold2/layers.py | 1781 | CODE | |
| LOW | …m/models/esmfold2/kernels/fused_attention_pair_bias.py | 693 | CODE | |
| LOW | esm/models/esmc/sae.py | 201 | CODE | |
| LOW | esm/models/esmc/model.py | 221 | CODE | |
| LOW | esm/models/esmc/model.py | 376 | CODE | |
| LOW | esm/models/esmc/model.py | 572 | CODE | |
| LOW | esm/models/esmc/model.py | 675 | CODE | |
| LOW | esm/models/esmc/model.py | 775 | CODE | |
| LOW | esm/sdk/forge.py | 1262 | CODE | |
| LOW | esm/sdk/forge.py | 1435 | CODE | |
| LOW | esm/sdk/sagemaker.py | 59 | CODE | |
| LOW | esm/sdk/sagemaker.py | 119 | CODE | |
| LOW | esm/sdk/base_forge_client.py | 177 | CODE | |
| LOW | esm/widgets/utils/drawing/draw_category_array.py | 13 | CODE | |
| LOW | cookbook/tutorials/binder_design.py | 1436 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | esm/utils/residue_constants.py | 490 | # Create a fast lookup dict for bond lengths. | COMMENT |
| MEDIUM | esm/utils/residue_constants.py | 866 | # Define a restype name for all unknown residues. | COMMENT |
| MEDIUM | esm/utils/structure/mmcif_parsing.py | 330 | # Create a basic mapping based on the chain_data | COMMENT |
| MEDIUM | esm/utils/structure/molecular_complex.py | 580 | # Create a mapping from chain_id to numeric indices | COMMENT |
| MEDIUM | esm/models/esm3.py | 391 | # The following methods are for the ESM3InferenceClient interface | COMMENT |
| MEDIUM | esm/widgets/components/function_annotator.py | 33 | # Create a text box input and a list of children to select from | COMMENT |
| MEDIUM | cookbook/snippets/sae_example.py | 19 | # Create a protein | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | tests/compatibility/esmfold2_hf_adapter_test.py | 0 | flash-attn imports on a cpu box but needs a cuda runtime to run. | STRING |
| HIGH | tests/models/esmfold2_msa_test.py | 0 | flash-attn imports on a cpu box but needs a cuda runtime to run. | STRING |
| HIGH | tests/models/esmfold2_api_test.py | 0 | flash-attn imports on a cpu box but needs a cuda runtime to run. | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/layers/rotary.py | 1 | # Copyright 2022 EleutherAI and the HuggingFace Inc. team. All rights reserved. | COMMENT |
| LOW | esm/utils/residue_constants.py | 1 | # Copyright 2025 EvolutionaryScale | COMMENT |
| LOW | esm/utils/residue_constants.py | 861 | # 1-to-1 mapping of 3 letter names to one letter names. The latter contains | COMMENT |
| LOW | esm/models/esmfold2/config.py | 1 | # Copyright 2026 Biohub. All rights reserved. | COMMENT |
| LOW | esm/models/esmfold2/experimental.py | 1 | # coding=utf-8 | COMMENT |
| LOW | esm/models/esmfold2/protein_utils.py | 1 | # coding=utf-8 | COMMENT |
| LOW | tests/conftest.py | 41 | # --------------------------------------------------------------------------- | COMMENT |
| LOW | tests/conftest.py | 241 | reference[name] = { | COMMENT |
| LOW | tests/models/esmfold2_execution_test.py | 61 | COMMENT | |
| LOW | tests/models/esmfold2_execution_test.py | 501 | # would otherwise only show up as a diffuse shift in every radius. | COMMENT |
| LOW | tests/models/esmfold2_sampler_test.py | 181 | COMMENT | |
| LOW | tests/models/esmfold2_sampler_test.py | 481 | for a in apart | COMMENT |
| LOW | tests/models/esmfold2_test.py | 1221 | candidate = run() | COMMENT |
| LOW | tests/models/esmfold2_builds_test.py | 501 | # reduction-order nondeterminism separates them), then the worst case across all | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | esm/utils/residue_constants.py | 794 | Maps the given sequence into a one-hot encoded matrix. Args: sequence: An amino acid sequence. mapping: | STRING |
| HIGH | esm/models/esm3.py | 283 | Performs forward pass through the ESM3 model. Check utils to see how to tokenize inputs from raw data. | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/structure/mmcif_parsing.py | 286 | # Check if there are duplicate residue numbers in this chain | COMMENT |
| LOW | esm/utils/structure/molecular_complex.py | 298 | # Check if token is a standard 3-letter amino acid code | COMMENT |
| LOW | esm/utils/structure/molecular_complex.py | 459 | # Check if input is a file path or mmCIF string content | COMMENT |
| LOW | esm/utils/structure/molecular_complex.py | 1258 | # Check if both tokens have atoms | COMMENT |
| LOW | esm/utils/structure/molecular_complex.py | 1326 | # Check if both tokens have atoms | COMMENT |
| LOW | esm/models/esmfold2/prepare_input.py | 227 | # Check if standard residue (has predefined atom list) | COMMENT |
| LOW | esm/widgets/components/sequence_prompt_selector.py | 123 | a = 0.5 # Set alpha to 0.5 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | cookbook/snippets/esm3.py | 204 | "To try this script with a Forge/Biohub Platform API, please run ESM_API_KEY=your_api_key python esm3.py" | CODE |
| HIGH | cookbook/snippets/esmc.py | 147 | "ESM_API_KEY=your_api_key python esmc.py" | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | esm/models/esmfold2/layers.py | 1570 | # Step 2: normalize noisy coords | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1574 | # Step 3: atom encoder | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1590 | # Step 4: add conditioned s | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1593 | # Step 5: token transformer | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1603 | # Step 6: token norm | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1606 | # Step 7: atom decoder | COMMENT |
| LOW | esm/models/esmfold2/layers.py | 1558 | # Step 1: conditioning (pair z is cached across diffusion steps) | COMMENT |
| LOW | esm/models/esmfold2/layers.py | 1618 | # Step 8: compute denoised output | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW⚡ | esm/models/esmfold2/layers.py | 1570 | # Step 2: normalize noisy coords | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1574 | # Step 3: atom encoder | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1590 | # Step 4: add conditioned s | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1593 | # Step 5: token transformer | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1603 | # Step 6: token norm | COMMENT |
| LOW⚡ | esm/models/esmfold2/layers.py | 1606 | # Step 7: atom decoder | COMMENT |
| LOW | esm/models/esmfold2/layers.py | 1558 | # Step 1: conditioning (pair z is cached across diffusion steps) | COMMENT |
| LOW | esm/models/esmfold2/layers.py | 1618 | # Step 8: compute denoised output | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | esm/utils/misc.py | 281 | # For MPS, just return a no-op context manager (nullcontext) since MPS does not support autocast. | COMMENT |
| MEDIUM | esm/utils/structure/molecular_complex.py | 347 | # Normalize to uppercase and strip whitespace for robust matching | COMMENT |
| LOW | esm/models/esmfold2/kernels/fused_lnlin_swiglu.py | 377 | # If LN_B was None (no bias), ATen returns dLN_B=None and we just pass it through. | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | cookbook/tutorials/binder_design.py | 1353 | .run_commands("apt update && apt install -y git build-essential") | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | README.md | 35 | The **[ESM Atlas](https://biohub.ai/esm/protein/atlas)** is a map of 6.8 billion proteins covering the full breadth of l | CODE |
| MEDIUM | cookbook/tutorials/README.md | 38 | | Generating proteins with ESM3 | `esm3_generate.ipynb`<br>[![Open In Colab](https://colab.research.google.com/assets/c | CODE |