nirs4all-ui 0.1.16 → 0.2.0

package/dist/pipelines/studio-presets.json

@@ -0,0 +1,3996 @@
+{
+    "source": "nirs4all-studio/api/presets",
+    "commit": "2926c6a44b50715ee79a213ebbf523dba5d92f3d",
+    "files_sha256": {
+        "complex_pls.yaml": "d29397856ee3f32c27704b564fcd079ed8f78c03d91ec33b274fa454fff264f2",
+        "complex_trees.yaml": "ab5f88ec1c1f0adeff67e8e32d9a690389ec3b7fffeffc67bc38edbba231dccf",
+        "deep_nonlinear_exploration.yaml": "815f5ff1e960cb73cdec080f29ba1897983a0e37320f771cfd01f1f11f6c34e2",
+        "fast_result.yaml": "9b1a17e4cb3ab5bef0e9e06f0cfd29cfe4d07757417f98a3816656818a5ea074",
+        "nonlinear_exploration.yaml": "fb5bc52da3d05f9dd5de256213f398bca8d1375802cfe05d8928ab55d28a2844",
+        "simple_pls.yaml": "b78ccde2d0145809bfb49067aef71ff9a30abb5ddfe6e3f4e552cee05aefc8f4",
+        "simple_trees_boosting.yaml": "76f1c9948f66ecd07f7c2253fb460dc5e8f6d4acdf324a60662f463846a9958f",
+        "ultra_pls.yaml": "51c9c9ce88f47d813b4ff06b38b647e4e2b48be8796ae963f785022e9feedc65",
+        "ultra_slow.yaml": "e18f81d578c9e89c3e276c6c5f325b40fe1212aac20089a64a5ea0685cffa6f2",
+        "ultra_trees.yaml": "c0346f612ea050ad97f1097e1c1e6b336dcd426e84bb79f9271e1745e061227d"
+    },
+    "presets": [
+        {
+            "id": "simple_pls",
+            "name": "Simple PLS",
+            "description": "Three classic preprocessing choices, KFold, and a single n_components sweep for PLS.",
+            "complexity": 1,
+            "default_variant": "regression",
+            "variants": {
+                "regression": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_or_": [
+                                "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                {
+                                    "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                    "params": {
+                                        "window_length": 15,
+                                        "polyorder": 2,
+                                        "deriv": 1
+                                    }
+                                }
+                            ]
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.KFold",
+                            "params": {
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "model": "sklearn.cross_decomposition._pls.PLSRegression",
+                            "name": "PLS-Sweep",
+                            "_range_": [
+                                2,
+                                30,
+                                4
+                            ],
+                            "param": "n_components"
+                        }
+                    ]
+                },
+                "classification": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_or_": [
+                                "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                {
+                                    "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                    "params": {
+                                        "window_length": 15,
+                                        "polyorder": 2,
+                                        "deriv": 1
+                                    }
+                                }
+                            ]
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.StratifiedKFold",
+                            "params": {
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "model": "nirs4all.operators.models.sklearn.plsda.PLSDA",
+                            "name": "PLSDA-Sweep",
+                            "_range_": [
+                                2,
+                                30,
+                                4
+                            ],
+                            "param": "n_components"
+                        }
+                    ]
+                }
+            },
+            "available_variants": [
+                "regression",
+                "classification"
+            ],
+            "steps_count": 3
+        },
+        {
+            "id": "fast_result",
+            "name": "Fast Result",
+            "description": "Quick SPXY-oriented preset with simple preprocessing, AOM-PLS, and TabPFN for fast first results.",
+            "complexity": 2,
+            "default_variant": "regression",
+            "variants": {
+                "regression": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_or_": [
+                                "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                {
+                                    "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                    "params": {
+                                        "window_length": 15,
+                                        "polyorder": 2,
+                                        "deriv": 1
+                                    }
+                                }
+                            ]
+                        },
+                        {
+                            "class": "nirs4all.operators.splitters.splitters.SPXYFold",
+                            "params": {
+                                "n_splits": 3,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "nirs4all.operators.models.sklearn.aom_pls.AOMPLSRegressor",
+                                "params": {
+                                    "n_components": 12,
+                                    "center": true,
+                                    "scale": false
+                                }
+                            },
+                            "name": "AOM-PLS"
+                        },
+                        {
+                            "model": {
+                                "class": "tabpfn.TabPFNRegressor",
+                                "params": {
+                                    "ignore_pretraining_limits": true
+                                }
+                            },
+                            "name": "TabPFN"
+                        }
+                    ]
+                },
+                "classification": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_or_": [
+                                "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                {
+                                    "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                    "params": {
+                                        "window_length": 15,
+                                        "polyorder": 2,
+                                        "deriv": 1
+                                    }
+                                }
+                            ]
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.StratifiedKFold",
+                            "params": {
+                                "n_splits": 3,
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "nirs4all.operators.models.sklearn.aom_pls_classifier.AOMPLSClassifier",
+                                "params": {
+                                    "n_components": 12
+                                }
+                            },
+                            "name": "AOM-PLS"
+                        },
+                        {
+                            "model": {
+                                "class": "tabpfn.TabPFNClassifier",
+                                "params": {
+                                    "ignore_pretraining_limits": true
+                                }
+                            },
+                            "name": "TabPFN"
+                        }
+                    ]
+                }
+            },
+            "available_variants": [
+                "regression",
+                "classification"
+            ],
+            "steps_count": 4
+        },
+        {
+            "id": "simple_trees_boosting",
+            "name": "Simple Trees / Boosting",
+            "description": "Same lightweight preprocessing pattern as Simple PLS, with LightGBM and RandomForest sweeps.",
+            "complexity": 3,
+            "default_variant": "regression",
+            "variants": {
+                "regression": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_or_": [
+                                "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                {
+                                    "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                    "params": {
+                                        "window_length": 15,
+                                        "polyorder": 2,
+                                        "deriv": 1
+                                    }
+                                }
+                            ]
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.KFold",
+                            "params": {
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "lightgbm.LGBMRegressor",
+                                "params": {
+                                    "random_state": 42,
+                                    "verbose": -1
+                                }
+                            },
+                            "name": "LightGBM-Sweep",
+                            "finetune_params": {
+                                "n_trials": 6,
+                                "sampler": "grid",
+                                "approach": "single",
+                                "eval_mode": "best",
+                                "verbose": 0,
+                                "model_params": {
+                                    "n_estimators": [
+                                        100,
+                                        200,
+                                        400
+                                    ],
+                                    "max_depth": [
+                                        6,
+                                        10
+                                    ],
+                                    "learning_rate": [
+                                        0.05
+                                    ]
+                                }
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "sklearn.ensemble._forest.RandomForestRegressor",
+                                "params": {
+                                    "random_state": 42
+                                }
+                            },
+                            "name": "RandomForest-Sweep",
+                            "finetune_params": {
+                                "n_trials": 6,
+                                "sampler": "grid",
+                                "approach": "single",
+                                "eval_mode": "best",
+                                "verbose": 0,
+                                "model_params": {
+                                    "n_estimators": [
+                                        200,
+                                        400,
+                                        800
+                                    ],
+                                    "max_depth": [
+                                        8,
+                                        16
+                                    ]
+                                }
+                            }
+                        }
+                    ]
+                },
+                "classification": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_or_": [
+                                "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                {
+                                    "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                    "params": {
+                                        "window_length": 15,
+                                        "polyorder": 2,
+                                        "deriv": 1
+                                    }
+                                }
+                            ]
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.StratifiedKFold",
+                            "params": {
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "lightgbm.LGBMClassifier",
+                                "params": {
+                                    "random_state": 42,
+                                    "verbose": -1
+                                }
+                            },
+                            "name": "LightGBM-Sweep",
+                            "finetune_params": {
+                                "n_trials": 6,
+                                "sampler": "grid",
+                                "approach": "single",
+                                "eval_mode": "best",
+                                "verbose": 0,
+                                "model_params": {
+                                    "n_estimators": [
+                                        100,
+                                        200,
+                                        400
+                                    ],
+                                    "max_depth": [
+                                        6,
+                                        10
+                                    ],
+                                    "learning_rate": [
+                                        0.05
+                                    ]
+                                }
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "sklearn.ensemble._forest.RandomForestClassifier",
+                                "params": {
+                                    "random_state": 42
+                                }
+                            },
+                            "name": "RandomForest-Sweep",
+                            "finetune_params": {
+                                "n_trials": 6,
+                                "sampler": "grid",
+                                "approach": "single",
+                                "eval_mode": "best",
+                                "verbose": 0,
+                                "model_params": {
+                                    "n_estimators": [
+                                        200,
+                                        400,
+                                        800
+                                    ],
+                                    "max_depth": [
+                                        8,
+                                        16
+                                    ]
+                                }
+                            }
+                        }
+                    ]
+                }
+            },
+            "available_variants": [
+                "regression",
+                "classification"
+            ],
+            "steps_count": 4
+        },
+        {
+            "id": "complex_pls",
+            "name": "Complex PLS",
+            "description": "Benchmark-style cartesian preprocessing with fixed PLS, tuned PLS, tuned Ridge, and AOM-PLS.",
+            "complexity": 4,
+            "default_variant": "regression",
+            "variants": {
+                "regression": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_cartesian_": [
+                                {
+                                    "_or_": [
+                                        null,
+                                        "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                        "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.ExtendedMultiplicativeScatterCorrection",
+                                            "params": {
+                                                "degree": 1
+                                            }
+                                        },
+                                        "nirs4all.operators.transforms.nirs.ExtendedMultiplicativeScatterCorrection"
+                                    ]
+                                },
+                                {
+                                    "_or_": [
+                                        null,
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 15,
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 21,
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 31,
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 15,
+                                                "deriv": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 21,
+                                                "deriv": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 31,
+                                                "deriv": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.signal.Gaussian",
+                                            "params": {
+                                                "order": 0
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.signal.Gaussian",
+                                            "params": {
+                                                "order": 0,
+                                                "sigma": 2
+                                            }
+                                        }
+                                    ]
+                                },
+                                {
+                                    "_or_": [
+                                        null,
+                                        "nirs4all.operators.transforms.nirs.ASLSBaseline",
+                                        "nirs4all.operators.transforms.signal.Detrend"
+                                    ]
+                                },
+                                {
+                                    "_or_": [
+                                        null,
+                                        "nirs4all.operators.transforms.orthogonalization.OSC",
+                                        {
+                                            "class": "nirs4all.operators.transforms.orthogonalization.OSC",
+                                            "params": {
+                                                "n_components": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.orthogonalization.OSC",
+                                            "params": {
+                                                "n_components": 3
+                                            }
+                                        }
+                                    ]
+                                }
+                            ],
+                            "count": 150
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.KFold",
+                            "params": {
+                                "n_splits": 3,
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "class": "sklearn.preprocessing._data.StandardScaler",
+                            "params": {
+                                "with_std": false
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "sklearn.cross_decomposition._pls.PLSRegression",
+                                "params": {
+                                    "n_components": 12,
+                                    "scale": false
+                                }
+                            },
+                            "name": "PLS-12"
+                        },
+                        {
+                            "model": {
+                                "class": "sklearn.cross_decomposition._pls.PLSRegression",
+                                "params": {
+                                    "scale": false
+                                }
+                            },
+                            "name": "PLS-Finetuned",
+                            "finetune_params": {
+                                "n_trials": 25,
+                                "sampler": "binary",
+                                "model_params": {
+                                    "n_components": [
+                                        "int",
+                                        1,
+                                        25
+                                    ]
+                                }
+                            }
+                        },
+                        {
+                            "model": "sklearn.linear_model._ridge.Ridge",
+                            "name": "Ridge-Finetuned",
+                            "finetune_params": {
+                                "n_trials": 40,
+                                "sampler": "tpe",
+                                "model_params": {
+                                    "alpha": [
+                                        "log_float",
+                                        1e-05,
+                                        10000.0
+                                    ],
+                                    "fit_intercept": [
+                                        "categorical",
+                                        [
+                                            true,
+                                            false
+                                        ]
+                                    ],
+                                    "solver": [
+                                        "categorical",
+                                        [
+                                            "auto",
+                                            "svd",
+                                            "cholesky",
+                                            "lsqr"
+                                        ]
+                                    ]
+                                }
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "nirs4all.operators.models.sklearn.aom_pls.AOMPLSRegressor",
+                                "params": {
+                                    "n_components": 12,
+                                    "center": true,
+                                    "scale": false
+                                }
+                            },
+                            "name": "AOM-PLS"
+                        }
+                    ]
+                },
+                "classification": {
+                    "format": "yaml",
+                    "pipeline": [
+                        {
+                            "_cartesian_": [
+                                {
+                                    "_or_": [
+                                        null,
+                                        "nirs4all.operators.transforms.scalers.StandardNormalVariate",
+                                        "nirs4all.operators.transforms.nirs.MultiplicativeScatterCorrection",
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.ExtendedMultiplicativeScatterCorrection",
+                                            "params": {
+                                                "degree": 1
+                                            }
+                                        },
+                                        "nirs4all.operators.transforms.nirs.ExtendedMultiplicativeScatterCorrection"
+                                    ]
+                                },
+                                {
+                                    "_or_": [
+                                        null,
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 15,
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 21,
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 31,
+                                                "polyorder": 2,
+                                                "deriv": 1
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 15,
+                                                "deriv": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 21,
+                                                "deriv": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.nirs.SavitzkyGolay",
+                                            "params": {
+                                                "window_length": 31,
+                                                "deriv": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.signal.Gaussian",
+                                            "params": {
+                                                "order": 0
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.signal.Gaussian",
+                                            "params": {
+                                                "order": 0,
+                                                "sigma": 2
+                                            }
+                                        }
+                                    ]
+                                },
+                                {
+                                    "_or_": [
+                                        null,
+                                        "nirs4all.operators.transforms.nirs.ASLSBaseline",
+                                        "nirs4all.operators.transforms.signal.Detrend"
+                                    ]
+                                },
+                                {
+                                    "_or_": [
+                                        null,
+                                        "nirs4all.operators.transforms.orthogonalization.OSC",
+                                        {
+                                            "class": "nirs4all.operators.transforms.orthogonalization.OSC",
+                                            "params": {
+                                                "n_components": 2
+                                            }
+                                        },
+                                        {
+                                            "class": "nirs4all.operators.transforms.orthogonalization.OSC",
+                                            "params": {
+                                                "n_components": 3
+                                            }
+                                        }
+                                    ]
+                                }
+                            ],
+                            "count": 150
+                        },
+                        {
+                            "class": "sklearn.model_selection._split.StratifiedKFold",
+                            "params": {
+                                "n_splits": 3,
+                                "shuffle": true,
+                                "random_state": 42
+                            }
+                        },
+                        {
+                            "class": "sklearn.preprocessing._data.StandardScaler",
+                            "params": {
+                                "with_std": false
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "nirs4all.operators.models.sklearn.plsda.PLSDA",
+                                "params": {
+                                    "n_components": 12
+                                }
+                            },
+                            "name": "PLSDA-12"
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+                                "n_trials": 30,
+                                "sampler": "tpe",
+                                "model_params": {
+                                    "n_components": [
+                                        "int",
+                                        1,
+                                        25
+                                    ]
+                                }
+                            }
+                        },
+                        {
+                            "model": {
+                                "class": "tabpfn.TabPFNClassifier",
+                                "params": {
+                                    "ignore_pretraining_limits": true
+                                }
+                            },
+                            "name": "TabPFN"
+                        }
+                    ]
+                }
+            },
+            "available_variants": [
+                "regression",
+                "classification"
+            ],
+            "steps_count": 8
+        }
+    ]
+}