Upload ResNet-18 species model (epoch 4)

README.md

@@ -0,0 +1,76 @@
+---
+license: mit
+library_name: deepforest
+pipeline_tag: image-classification
+tags:
+  - deepforest
+  - crop-model
+  - tree-species
+  - ecology
+  - neon
+---
+
+# Tree Species Classification (CropModel)
+
+Classifies tree crowns detected by [DeepForest](https://github.com/weecology/DeepForest) into 148 species using USDA PLANTS codes. Trained on RGB imagery from 29 [NEON](https://www.neonscience.org/) sites across North America.
+
+Trained with [NeonTreeClassification](https://github.com/GatorSense/NeonTreeClassification).
+
+## Usage
+
+```python
+from deepforest import main
+from deepforest.model import CropModel
+
+detector = main.deepforest()
+detector.load_model("weecology/deepforest-tree")
+
+species_model = CropModel.load_model("weecology/cropmodel-tree-species")
+
+results = detector.predict_tile(path="tile.tif", crop_model=species_model)
+# results has columns: cropmodel_label, cropmodel_score
+```
+
+## Results (Test Set)
+
+| Metric | Value |
+|---|---|
+| Accuracy | 39.3% |
+| Macro F1 | 0.23 |
+| Weighted F1 | 0.39 |
+| Classes | 148 |
+
+Full per-class precision/recall/F1 in [`classification_report.csv`](classification_report.csv).
+
+## Training
+
+| Parameter | Value |
+|---|---|
+| Architecture | ResNet-18 (torchvision, ImageNet pretrained) |
+| Input | 224x224 RGB, ImageNet normalization |
+| Resize interpolation | nearest-neighbor |
+| Optimizer | AdamW (lr=2.5e-4, weight_decay=1e-4) |
+| Scheduler | ReduceLROnPlateau |
+| Max epochs | 500 (early stopping patience=15) |
+| Best epoch | 4 (val_loss=2.65) |
+| Batch size | 256 |
+| Class weights | sqrt inverse-frequency |
+| Seed | 42 |
+
+## Dataset
+
+16,348 deduplicated tree crowns from 29 NEON sites. One sample per unique individual, rare species (<6 samples) removed. Labels from NEON Vegetation Structure Taxonomy (VST) field surveys. RGB crown crops extracted at 0.1m resolution.
+
+| Split | Samples |
+|---|---|
+| Train (70%) | 11,443 |
+| Val (15%) | 2,452 |
+| Test (15%) | 2,453 |
+
+Split method: stratified random, seed=42.
+
+**Sites**: ABBY, BART, BONA, CLBJ, DEJU, DELA, GRSM, GUAN, HARV, HEAL, JERC, KONZ, LENO, MLBS, MOAB, NIWO, ONAQ, OSBS, PUUM, RMNP, SCBI, SERC, SJER, SOAP, TALL, TEAK, UKFS, UNDE, WREF
+
+## License
+
+MIT

classification_report.csv

@@ -0,0 +1,152 @@
+,precision,recall,f1-score,support
+2PLANT (0),0.0,0.0,0.0,12.0
+2PLANT-S (1),0.0,0.0,0.0,1.0
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+ABLO (8),0.4667,0.5,0.4828,14.0
+ABMA (9),0.5556,0.4167,0.4762,12.0
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+ACNEN (13),0.0,0.0,0.0,2.0
+ACPE (14),0.25,0.1667,0.2,6.0
+ACRU (15),0.3105,0.2646,0.2857,223.0
+ACRUR (16),0.0,0.0,0.0,1.0
+ACSA2 (17),0.0,0.0,0.0,2.0
+ACSA3 (18),0.5263,0.5,0.5128,20.0
+ACSAS (19),0.1667,0.2222,0.1905,9.0
+ALRU2 (20),0.0909,0.25,0.1333,4.0
+AMLA (21),0.0588,0.0526,0.0556,19.0
+ARVIM (22),0.0,0.0,0.0,1.0
+BEAL2 (23),0.25,0.1304,0.1714,23.0
+BELE (24),0.1176,0.2105,0.1509,19.0
+BENE4 (25),0.8333,0.75,0.7895,40.0
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+BEPAP (27),0.15,0.2308,0.1818,13.0
+BEPO (28),0.0,0.0,0.0,1.0
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+BUBU (30),1.0,0.5,0.6667,2.0
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+CAGL8 (35),0.0,0.0,0.0,6.0
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+CAOV2 (37),1.0,0.0833,0.1538,12.0
+CATO6 (38),0.1,0.0909,0.0952,22.0
+CECA4 (39),0.75,0.6,0.6667,5.0
+CECAC (40),1.0,1.0,1.0,1.0
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+CEOC (42),0.1111,0.1667,0.1333,12.0
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+DIVI5 (44),0.0,0.0,0.0,1.0
+FAGR (45),0.25,0.3962,0.3066,53.0
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+FRAXI (47),0.25,0.5,0.3333,8.0
+FRNI (48),0.2222,0.4,0.2857,5.0
+FRPE (49),0.2727,0.2308,0.25,26.0
+GLTR (50),0.0,0.0,0.0,3.0
+GYDI (51),0.0,0.0,0.0,1.0
+HATE3 (52),0.0,0.0,0.0,3.0
+ILOP (53),0.0,0.0,0.0,1.0
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+JUOS (55),0.0,0.0,0.0,2.0
+JUVI (56),0.5,0.2353,0.32,17.0
+LALA (57),0.5,0.5,0.5,4.0
+LIST2 (58),0.1864,0.1964,0.1913,56.0
+LITU (59),0.4186,0.3051,0.3529,59.0
+MAAC (60),0.25,0.25,0.25,4.0
+MAFR (61),0.0,0.0,0.0,2.0
+MAPO (62),0.1667,0.1429,0.1538,7.0
+MEPO5 (63),1.0,0.7143,0.8333,7.0
+MORU2 (64),0.0,0.0,0.0,6.0
+NYAQ2 (65),0.0,0.0,0.0,1.0
+NYBI (66),0.0,0.0,0.0,2.0
+NYSY (67),0.1077,0.3043,0.1591,23.0
+OSVI (68),0.0,0.0,0.0,1.0
+OXAR (69),0.2667,0.2105,0.2353,19.0
+PIAB (70),0.2667,0.5,0.3478,8.0
+PIAL3 (71),1.0,0.6667,0.8,3.0
+PICO (72),0.3,0.2308,0.2609,13.0
+PICOL (73),0.529,0.7935,0.6348,92.0
+PIEC2 (74),0.0,0.0,0.0,7.0
+PIED (75),0.5,1.0,0.6667,1.0
+PIEL (76),0.25,0.3333,0.2857,3.0
+PIEN (77),0.5417,0.3714,0.4407,35.0
+PIFL2 (78),0.5556,0.3333,0.4167,15.0
+PIGL (79),0.2439,0.4348,0.3125,23.0
+PIJE (80),0.2857,0.6667,0.4,3.0
+PIMA (81),0.8542,0.7009,0.77,117.0
+PIMO3 (82),0.0,0.0,0.0,2.0
+PINACE (83),0.0,0.0,0.0,2.0
+PINUS (84),0.0,0.0,0.0,4.0
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+PIPOS (87),0.45,0.5625,0.5,16.0
+PIPU5 (88),0.2,1.0,0.3333,1.0
+PIRE (89),0.4286,0.5,0.4615,12.0
+PIRI (90),0.0,0.0,0.0,1.0
+PIRU (91),0.2222,0.1176,0.1538,17.0
+PISA2 (92),0.0,0.0,0.0,1.0
+PIST (93),0.6,0.4138,0.4898,29.0
+PITA (94),0.4444,0.6667,0.5333,18.0
+PLOC (95),0.0,0.0,0.0,7.0
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+PRSE2 (102),0.0,0.0,0.0,3.0
+PRSES (103),0.0,0.0,0.0,3.0
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+PSMEM (105),0.5742,0.678,0.6218,177.0
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+QUCO2 (108),0.3333,0.2,0.25,15.0
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+QUERC (110),0.0,0.0,0.0,7.0
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+QUGE2 (112),0.0,0.0,0.0,2.0
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+QUKE (114),0.6,0.75,0.6667,4.0
+QULA2 (115),0.3226,0.4545,0.3774,22.0
+QULA3 (116),0.5,0.3333,0.4,3.0
+QULY (117),0.3333,0.25,0.2857,4.0
+QUMA13 (118),0.0,0.0,0.0,7.0
+QUMA2 (119),0.0,0.0,0.0,1.0
+QUMA3 (120),0.3,0.2727,0.2857,11.0
+QUMI (121),0.0,0.0,0.0,5.0
+QUMO4 (122),0.1739,0.25,0.2051,16.0
+QUMU (123),0.4,0.4,0.4,5.0
+QUNI (124),0.2222,0.1538,0.1818,13.0
+QUPA5 (125),0.1111,0.1429,0.125,7.0
+QUPH (126),0.0,0.0,0.0,2.0
+QURU (127),0.4156,0.3855,0.4,83.0
+QUSH (128),0.0,0.0,0.0,1.0
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+QUVI (131),0.0,0.0,0.0,1.0
+QUWI2 (132),1.0,0.6667,0.8,3.0
+ROPS (133),0.0,0.0,0.0,5.0
+SAAL5 (134),0.1667,0.1667,0.1667,6.0
+SILA20 (135),0.0,0.0,0.0,1.0
+SYOR (136),0.0,0.0,0.0,2.0
+TABR2 (137),0.0,0.0,0.0,4.0
+THPL (138),0.0,0.0,0.0,6.0
+TIAM (139),0.0,0.0,0.0,2.0
+TRSE6 (140),0.0,0.0,0.0,2.0
+TSCA (141),0.4957,0.4161,0.4524,137.0
+TSHE (142),0.43,0.5443,0.4804,79.0
+ULAL (143),0.2,0.25,0.2222,4.0
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+ULCR (145),0.0,0.0,0.0,5.0
+ULMUS (146),0.0,0.0,0.0,3.0
+ULRU (147),0.0,0.0,0.0,5.0
+accuracy,0.393,0.393,0.393,0.393
+macro avg,0.2471,0.2507,0.2323,2453.0
+weighted avg,0.4046,0.393,0.387,2453.0

config.json

@@ -0,0 +1,178 @@
+{
+  "cropmodel": {
+    "architecture": "resnet18",
+    "batch_size": 4,
+    "num_workers": 0,
+    "lr": 0.0001,
+    "scheduler": {
+      "type": "ReduceLROnPlateau",
+      "params": {
+        "mode": "min",
+        "factor": 0.5,
+        "patience": 5,
+        "threshold": 0.0001,
+        "threshold_mode": "rel",
+        "cooldown": 0,
+        "min_lr": 0,
+        "eps": 1e-08
+      }
+    },
+    "balance_classes": false,
+    "resize": [
+      224,
+      224
+    ],
+    "resize_interpolation": "nearest",
+    "expand": 0,
+    "label_dict": {
+      "2PLANT": 0,
+      "2PLANT-S": 1,
+      "ABAM": 2,
+      "ABBA": 3,
+      "ABCO": 4,
+      "ABFR": 5,
+      "ABIES": 6,
+      "ABLAL": 7,
+      "ABLO": 8,
+      "ABMA": 9,
+      "ACBA3": 10,
+      "ACCI": 11,
+      "ACNE2": 12,
+      "ACNEN": 13,
+      "ACPE": 14,
+      "ACRU": 15,
+      "ACRUR": 16,
+      "ACSA2": 17,
+      "ACSA3": 18,
+      "ACSAS": 19,
+      "ALRU2": 20,
+      "AMLA": 21,
+      "ARVIM": 22,
+      "BEAL2": 23,
+      "BELE": 24,
+      "BENE4": 25,
+      "BEPA": 26,
+      "BEPAP": 27,
+      "BEPO": 28,
+      "BOSU2": 29,
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+      "CADE27": 34,
+      "CAGL8": 35,
+      "CAIL2": 36,
+      "CAOV2": 37,
+      "CATO6": 38,
+      "CECA4": 39,
+      "CECAC": 40,
+      "CELA": 41,
+      "CEOC": 42,
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+      "DIVI5": 44,
+      "FAGR": 45,
+      "FRAM2": 46,
+      "FRAXI": 47,
+      "FRNI": 48,
+      "FRPE": 49,
+      "GLTR": 50,
+      "GYDI": 51,
+      "HATE3": 52,
+      "ILOP": 53,
+      "JUNI": 54,
+      "JUOS": 55,
+      "JUVI": 56,
+      "LALA": 57,
+      "LIST2": 58,
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+      "MAFR": 61,
+      "MAPO": 62,
+      "MEPO5": 63,
+      "MORU2": 64,
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+      "NYSY": 67,
+      "OSVI": 68,
+      "OXAR": 69,
+      "PIAB": 70,
+      "PIAL3": 71,
+      "PICO": 72,
+      "PICOL": 73,
+      "PIEC2": 74,
+      "PIED": 75,
+      "PIEL": 76,
+      "PIEN": 77,
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+      "PIGL": 79,
+      "PIJE": 80,
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+      "PIMO3": 82,
+      "PINACE": 83,
+      "PINUS": 84,
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+      "PIPO": 86,
+      "PIPOS": 87,
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+      "PIRE": 89,
+      "PIRI": 90,
+      "PIRU": 91,
+      "PISA2": 92,
+      "PIST": 93,
+      "PITA": 94,
+      "PLOC": 95,
+      "PODE3": 96,
+      "POGR4": 97,
+      "POTR5": 98,
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+      "PRSES": 103,
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+      "QUMA3": 120,
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+      "QUMO4": 122,
+      "QUMU": 123,
+      "QUNI": 124,
+      "QUPA5": 125,
+      "QUPH": 126,
+      "QURU": 127,
+      "QUSH": 128,
+      "QUST": 129,
+      "QUVE": 130,
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+      "SAAL5": 134,
+      "SILA20": 135,
+      "SYOR": 136,
+      "TABR2": 137,
+      "THPL": 138,
+      "TIAM": 139,
+      "TRSE6": 140,
+      "TSCA": 141,
+      "TSHE": 142,
+      "ULAL": 143,
+      "ULAM": 144,
+      "ULCR": 145,
+      "ULMUS": 146,
+      "ULRU": 147
+    }
+  }
+}

model.safetensors

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