fix: clean up __init__.py exports and fix invalid escape sequence

pyhealth/metrics/calibration.py

@@ -119,7 +119,7 @@ def ece_confidence_multiclass(prob:np.ndarray, label:np.ndarray, bins=20, adapti
     Explanation of the example: The bins are [0, 0.5] and (0.5, 1].
     In the first bin, we have one sample with top-class prediction of 0.49, and its
     accuracy is 0. In the second bin, we have average confidence of 0.7 and average
-    accuracy of 1. Thus, the ECE is :math:`\\frac{1}{3} \cdot 0.49 + \\frac{2}{3}\cdot 0.3=0.3633`.
+    accuracy of 1. Thus, the ECE is :math:`\\frac{1}{3} \\cdot 0.49 + \\frac{2}{3} \\cdot 0.3=0.3633`.
 
     Args:
         prob (np.ndarray): (N, C)

pyhealth/models/__init__.py

@@ -6,26 +6,29 @@
 from .concare import ConCare, ConCareLayer
 from .contrawr import ContraWR, ResBlock2D
 from .deepr import Deepr, DeeprLayer
+from .ehrmamba import EHRMamba, MambaBlock
 from .embedding import EmbeddingModel
 from .gamenet import GAMENet, GAMENetLayer
-from .jamba_ehr import JambaEHR, JambaLayer
-from .logistic_regression import LogisticRegression
 from .gan import GAN
 from .gnn import GAT, GCN
 from .graph_torchvision_model import Graph_TorchvisionModel
 from .graphcare import GraphCare
 from .grasp import GRASP, GRASPLayer
+from .jamba_ehr import JambaEHR, JambaLayer
+from .logistic_regression import LogisticRegression
 from .medlink import MedLink
 from .micron import MICRON, MICRONLayer
 from .mlp import MLP
 from .molerec import MoleRec, MoleRecLayer
 from .retain import MultimodalRETAIN, RETAIN, RETAINLayer
 from .rnn import MultimodalRNN, RNN, RNNLayer
 from .safedrug import SafeDrug, SafeDrugLayer
+from .sdoh import SdohClassifier
 from .sparcnet import DenseBlock, DenseLayer, SparcNet, TransitionLayer
 from .stagenet import StageNet, StageNetLayer
 from .stagenet_mha import StageAttentionNet, StageNetAttentionLayer
 from .tcn import TCN, TCNLayer
+from .text_embedding import TextEmbedding
 from .tfm_tokenizer import (
     TFMTokenizer,
     TFM_VQVAE2_deep,
@@ -37,10 +40,47 @@
 from .torchvision_model import TorchvisionModel
 from .transformer import Transformer, TransformerLayer
 from .transformers_model import TransformersModel
-from .ehrmamba import EHRMamba, MambaBlock
+from .unified_embedding import UnifiedMultimodalEmbeddingModel, SinusoidalTimeEmbedding
 from .vae import VAE
 from .vision_embedding import VisionEmbeddingModel
-from .text_embedding import TextEmbedding
-from .sdoh import SdohClassifier
-from .medlink import MedLink
-from .unified_embedding import UnifiedMultimodalEmbeddingModel, SinusoidalTimeEmbedding
+
+__all__ = [
+    "AdaCare", "AdaCareLayer", "MultimodalAdaCare",
+    "Agent", "AgentLayer",
+    "BaseModel",
+    "BIOT",
+    "CNN", "CNNLayer",
+    "ConCare", "ConCareLayer",
+    "ContraWR",
+    "Deepr", "DeeprLayer",
+    "EHRMamba", "MambaBlock",
+    "EmbeddingModel",
+    "GAMENet", "GAMENetLayer",
+    "GAN",
+    "GAT", "GCN",
+    "Graph_TorchvisionModel",
+    "GraphCare",
+    "GRASP", "GRASPLayer",
+    "JambaEHR", "JambaLayer",
+    "LogisticRegression",
+    "MedLink",
+    "MICRON", "MICRONLayer",
+    "MLP",
+    "MoleRec", "MoleRecLayer",
+    "MultimodalRETAIN", "RETAIN", "RETAINLayer",
+    "MultimodalRNN", "RNN", "RNNLayer",
+    "SafeDrug", "SafeDrugLayer",
+    "SdohClassifier",
+    "SparcNet",
+    "StageNet", "StageNetLayer",
+    "StageAttentionNet", "StageNetAttentionLayer",
+    "TCN", "TCNLayer",
+    "TextEmbedding",
+    "TFMTokenizer",
+    "TorchvisionModel",
+    "Transformer", "TransformerLayer",
+    "TransformersModel",
+    "UnifiedMultimodalEmbeddingModel",
+    "VAE",
+    "VisionEmbeddingModel",
+]

pyhealth/processors/__init__.py

@@ -61,22 +61,28 @@ def get_processor(name: str):
     "FeatureProcessor",
     "ModalityType",
     "TemporalFeatureProcessor",
+    "AudioProcessor",
+    "BinaryLabelProcessor",
+    "DeepNestedFloatsProcessor",
+    "DeepNestedSequenceProcessor",
+    "GraphProcessor",
+    "IgnoreProcessor",
     "ImageProcessor",
-    "LabelProcessor",
+    "MultiClassLabelProcessor",
     "MultiHotProcessor",
+    "MultiLabelProcessor",
     "NestedFloatsProcessor",
     "NestedSequenceProcessor",
     "RawProcessor",
+    "RegressionLabelProcessor",
     "SequenceProcessor",
     "SignalProcessor",
     "StageNetProcessor",
     "StageNetTensorProcessor",
     "TensorProcessor",
     "TemporalTimeseriesProcessor",
     "TextProcessor",
-    "TimeseriesProcessor",
     "TimeImageProcessor",
-    "GraphProcessor",
-    "AudioProcessor",
+    "TimeseriesProcessor",
     "TupleTimeTextProcessor",
 ]