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Upload finetuned TabPFN-SDM models (nonspatial + spatial)

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+ ---------------------- ADDITIONAL PROVISION --------------------------
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README.md ADDED
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+ ---
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+ library_name: pytorch
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+ pipeline_tag: tabular-classification
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+ base_model: Prior-Labs/TabPFN-v2-clf
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+ license: other
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+ license_name: prior-labs-license-v1.1
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+ license_link: LICENSE
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+ tags:
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+ - pytorch
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+ - tabpfn
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+ - species-distribution-modeling
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+ - ecology
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+ - biodiversity
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+ - tabular-classification
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+ - finetuned
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+ metrics:
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+ - roc_auc
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+ - average_precision
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+ ---
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+
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+ # TabPFN-SDM: TabPFN Finetuned for Species Distribution Modeling
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+
23
+ **Built with PriorLabs-TabPFN**
24
+
25
+ Finetuned [TabPFN](https://huggingface.co/Prior-Labs/TabPFN-v2-clf) models for binary species distribution modeling (SDM). These models were adapted from the pretrained TabPFN foundation model to improve performance on presence/absence classification tasks common in ecology and conservation biology.
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+
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+ ## Model Variants
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+
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+ | File | Description | Epochs | Val ROC-AUC | Val PR-AUC |
30
+ |------|-------------|--------|-------------|------------|
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+ | `tabpfn-sdm-nonspatial.pt` | Standard (non-spatial) train/test evaluation | 100 | 0.747 | 0.261 |
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+ | `tabpfn-sdm-spatial.pt` | Spatially-separated train/test evaluation | 50 | 0.653 | 0.144 |
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+
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+ The **non-spatial** variant is trained and evaluated using standard random train/test splits. The **spatial** variant uses 10km buffer-based spatial separation between training and test data, which is more realistic for ecological applications but results in a harder prediction task.
35
+
36
+ ## Training Details
37
+
38
+ ### Two-Step Finetuning
39
+
40
+ Each model was finetuned in two steps:
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+
42
+ 1. **Step 1 (Cross-Validation):** Finetuned on CV-generated train/test splits from training data. Learning rate: 1e-5. Goal: adapt TabPFN to general SDM classification patterns.
43
+ 2. **Step 2 (Benchmark):** Further finetuned on actual benchmark train/test splits. Learning rate: 1e-6. Goal: refine for the specific evaluation setup.
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+
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+ ### Training Data
46
+
47
+ - **226 species** across **6 geographic regions**: AWT (Australia), NSW (New South Wales), CAN (Canada), NZ (New Zealand), SA (South Africa), SWI (Switzerland)
48
+ - Species split: 62.5% finetuning, 7.5% validation, 30% held-out test
49
+ - Data from the `disdat` R package (standardized presence-only and presence-absence datasets)
50
+ - Features include environmental covariates (7-12 per region) with native categorical variable support
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+
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+ ### Training Procedure
53
+
54
+ - **Base model:** TabPFN v2 classifier (`Prior-Labs/TabPFN-v2-clf`)
55
+ - **Optimizer:** AdamW
56
+ - **LR Schedule:** OneCycleLR
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+ - **Training approach:** Iterative R-Python epoch loop with smart sub-batching
58
+ - R generates cross-validation data (parallelized with 20 cores)
59
+ - Python trains one epoch on GPU
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+ - Smart sub-batching: keeps ALL presences (rare, valuable) in every sub-batch, partitions absences across sub-batches
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+ - **Max training samples per sub-batch:** 1,500
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+ - **Random seed:** 32639
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+
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+ ### Hardware
65
+
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+ - GPU: NVIDIA RTX 4000 ADA GPU with 20GB VRAM
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+ - Peak memory: ~14GB during training
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+ - Training time: ~188 hours total (Step 1 + Step 2) for non-spatial; ~178 hours for spatial
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+
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+ ## Usage
71
+
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+ ### Python
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+
74
+ ```python
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+ import torch
76
+ from tabpfn import TabPFNClassifier
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+ from huggingface_hub import hf_hub_download
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+
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+ # Download model
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+ model_path = hf_hub_download(
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+ repo_id="rdinnager/tabpfn-sdm-finetuned",
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+ filename="tabpfn-sdm-nonspatial.pt"
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+ )
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+
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+ # Load finetuned model
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+ device = "cuda" if torch.cuda.is_available() else "cpu"
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+ clf = TabPFNClassifier(
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+ ignore_pretraining_limits=True,
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+ device=device,
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+ n_estimators=8,
91
+ random_state=32639
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+ )
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+ clf._initialize_model_variables()
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+
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+ checkpoint = torch.load(model_path, map_location=device, weights_only=False)
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+ clf.models_[0].load_state_dict(checkpoint["model_state_dict"])
97
+ clf.models_[0].eval()
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+
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+ # Fit on training data and predict
100
+ clf.fit(X_train, y_train)
101
+ probs = clf.predict_proba(X_test)[:, 1] # Probability of presence
102
+ ```
103
+
104
+ ### R (via reticulate)
105
+
106
+ The companion R code provides inference wrappers. See the [TabPFN-SDM GitHub repository](https://github.com/rdinnager/TabPFN-SDM) for the full pipeline.
107
+
108
+ ```r
109
+ source("R/run_tabpfn_finetuned.R")
110
+
111
+ result <- run_tabpfn_finetuned_ensemble(
112
+ train_dat = train_data,
113
+ test_dat = test_data,
114
+ model_path = "tabpfn-sdm-nonspatial.pt",
115
+ max_train_size = 1000L,
116
+ n_estimators = 8L
117
+ )
118
+
119
+ # result$test contains y_truth and y_pred columns
120
+ ```
121
+
122
+ ### Ensemble Inference (Recommended)
123
+
124
+ For best results, use ensemble inference which matches the training procedure:
125
+ - Keeps ALL presences in every sub-batch
126
+ - Partitions absences across sub-batches for 100% data usage
127
+ - Averages predictions across sub-batches
128
+
129
+ This is implemented in `run_tabpfn_finetuned_ensemble()` (R) or can be replicated in Python using the utilities in the GitHub repo.
130
+
131
+ ## Checkpoint Contents
132
+
133
+ Each `.pt` file is a PyTorch checkpoint dictionary containing:
134
+
135
+ | Key | Description |
136
+ |-----|-------------|
137
+ | `model_state_dict` | Finetuned TabPFN model weights |
138
+ | `config` | Training configuration (hyperparameters, data settings) |
139
+ | `history` | Training history (loss, metrics per epoch) |
140
+ | `step1_path` | Path to the Step 1 model used as initialization |
141
+
142
+ ## Limitations
143
+
144
+ - Models were trained on species from 6 specific geographic regions and may not generalize to other regions without additional finetuning
145
+ - Performance varies by species; species with very few presences may have lower accuracy
146
+ - The spatial variant has lower validation metrics due to the inherently harder task of spatial extrapolation
147
+ - Requires the `tabpfn` Python package (v2) for inference
148
+ - Categorical variable handling requires proper setup (see project documentation)
149
+
150
+ ## Citation
151
+
152
+ If you use these models, please cite the accompanying paper:
153
+
154
+ ```bibtex
155
+ @article{dinnage2026niche,
156
+ title={A Niche in the Machine: The Promise of AI Foundation Models for Species Distribution Modeling},
157
+ author={Dinnage, Russell and Warren, Dan L.},
158
+ year={2026},
159
+ doi={10.32942/X2VQ10},
160
+ journal={EcoEvoRxiv},
161
+ url={https://ecoevorxiv.org/repository/view/11797/}
162
+ }
163
+ ```
164
+
165
+ Please also cite the original TabPFN paper:
166
+
167
+ ```bibtex
168
+ @article{hollmann2025tabpfn,
169
+ title={Accurate Predictions on Small Data with a Tabular Foundation Model},
170
+ author={Hollmann, Noah and M{\"u}ller, Samuel and Purucker, Lennart and
171
+ Krishnakumar, Arjun and K{\"o}rfer, Max and Hoo, Shi Bin and
172
+ Schirrmeister, Robin Tibor and Hutter, Frank},
173
+ journal={Nature},
174
+ year={2025},
175
+ publisher={Nature Publishing Group}
176
+ }
177
+ ```
178
+
179
+ ## License
180
+
181
+ These finetuned model weights are distributed under the [Prior Labs License v1.1](LICENSE), consistent with the base TabPFN model license. See the LICENSE file for full terms.
182
+
183
+ ## Links
184
+
185
+ - [TabPFN-SDM GitHub Repository](https://github.com/rdinnager/TabPFN-SDM)
186
+ - [Base TabPFN Model](https://huggingface.co/Prior-Labs/TabPFN-v2-clf)
187
+ - [TabPFN GitHub](https://github.com/PriorLabs/TabPFN)
config.json ADDED
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+ {
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+ "model_type": "tabpfn-finetuned",
3
+ "base_model": "Prior-Labs/TabPFN-v2-clf",
4
+ "task": "binary-classification",
5
+ "domain": "species-distribution-modeling",
6
+ "variants": {
7
+ "nonspatial": {
8
+ "filename": "tabpfn-sdm-nonspatial.pt",
9
+ "description": "Standard train/test split evaluation",
10
+ "step1_epochs": 40,
11
+ "step2_epochs": 100,
12
+ "final_val_roc_auc": 0.747,
13
+ "final_val_pr_auc": 0.261,
14
+ "final_train_loss": 0.460,
15
+ "final_val_loss": 3.429
16
+ },
17
+ "spatial": {
18
+ "filename": "tabpfn-sdm-spatial.pt",
19
+ "description": "Spatially-separated (10km buffer) evaluation",
20
+ "step1_epochs": 25,
21
+ "step2_epochs": 50,
22
+ "final_val_roc_auc": 0.653,
23
+ "final_val_pr_auc": 0.144,
24
+ "final_train_loss": 0.470,
25
+ "final_val_loss": 5.469
26
+ }
27
+ },
28
+ "training": {
29
+ "optimizer": "AdamW",
30
+ "lr_schedule": "OneCycleLR",
31
+ "step1_learning_rate": 1e-5,
32
+ "step2_learning_rate": 1e-6,
33
+ "max_train_size_per_subbatch": 1500,
34
+ "max_test_size": 1500,
35
+ "n_estimators_training": 2,
36
+ "n_estimators_inference": 8,
37
+ "seed": 32639,
38
+ "species_split_seed": 12345
39
+ },
40
+ "data": {
41
+ "total_species": 226,
42
+ "finetune_species_fraction": 0.625,
43
+ "validation_species_fraction": 0.075,
44
+ "test_species_fraction": 0.30,
45
+ "regions": ["AWT", "NSW", "CAN", "NZ", "SA", "SWI"],
46
+ "categorical_variables": {
47
+ "CAN": ["ontveg"],
48
+ "NSW": ["vegsys"],
49
+ "NZ": ["age", "toxicats"],
50
+ "SWI": ["calc"]
51
+ }
52
+ },
53
+ "checkpoint_format": {
54
+ "keys": ["model_state_dict", "config", "history", "step1_path"],
55
+ "framework": "pytorch"
56
+ }
57
+ }
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Git LFS Details

  • SHA256: bd469523a48df19ba6c336c31831ceadf5c0a699ab4b309751686108d8c56492
  • Pointer size: 131 Bytes
  • Size of remote file: 317 kB
training_logs/tabpfn-sdm-spatial_training_log.csv ADDED
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training_logs/tabpfn-sdm-spatial_training_plot.png ADDED

Git LFS Details

  • SHA256: b7ba2076be3d7bc60635cb0ab66515d103871468a3ef3d7c977294c0667bb9cd
  • Pointer size: 131 Bytes
  • Size of remote file: 361 kB