Describe the bug
Error: UserWarning: X does not have valid feature names, but TabPFNClassifier was fitted with feature names
It seems that calling .fit() with X_val and y_val converts the training data to tensors early, which deletes the Pandas feature names.
If X_val is omitted, the model remembers the feature names.
If X_val is included, it forgets them. Calling .predict_proba(X_test) with a DataFrame later throws a UserWarning about missing feature names.
The Workaround:
Cast test data to numpy (X_test.to_numpy()) during inference.
With X_val...
finetuned_clf.fit(X_train, y_train, X_val=X_val, y_val=y_val)
finetuned_clf.predict_proba(X_test.to_numpy())
Without...
finetuned_clf.fit(X_train, y_train)
finetuned_clf.predict_proba(X_test)
Steps/Code to Reproduce
from sklearn.datasets import make_classification
from sklearn.model_selection import train_test_split
from tabpfn.finetuning.finetuned_classifier import FinetunedTabPFNClassifier
# 1. Create dummy Pandas DataFrame with feature names
X, y = make_classification(n_samples=500, n_features=10, random_state=42)
X_df = pd.DataFrame(X, columns=[f"feature_{i}" for i in range(10)])
X_train, X_temp, y_train, y_temp = train_test_split(X_df, y, test_size=0.4, random_state=42)
X_val, X_test, y_val, y_test = train_test_split(X_temp, y_temp, test_size=0.5, random_state=42)
clf = FinetunedTabPFNClassifier(
device="cuda",
epochs=2,
n_estimators_finetune=2,
n_estimators_final_inference=2
)
# 2. Fit WITH validation sets
clf.fit(X_train, y_train, X_val=X_val, y_val=y_val)
# 3. Predict with a DataFrame (Triggers Warning)
preds = clf.predict_proba(X_test)```
### Expected Results
Warning is thrown, but does not stop the run.
### Actual Results
`Error: UserWarning: X does not have valid feature names, but TabPFNClassifier was fitted with feature names`
### Versions
```shell
Collecting system and dependency information...
PyTorch version: 2.6.0+cu124
CUDA used to build PyTorch: 12.4
ROCM used to build PyTorch: N/A
OS: Ubuntu 20.04.6 LTS (x86_64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
Clang version: Could not collect
CMake version: Could not collect
Libc version: glibc-2.31
Python version: 3.11.15 (main, Mar 11 2026, 17:20:07) [GCC 14.3.0] (64-bit runtime)
Python platform: Linux-5.15.0-139-generic-x86_64-with-glibc2.31
Is CUDA available: True
CUDA runtime version: Could not collect
CUDA_MODULE_LOADING set to: LAZY
GPU models and configuration: GPU 0: NVIDIA A100-SXM4-80GB
Nvidia driver version: 570.133.20
cuDNN version: Could not collect
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True
CPU:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 48 bits physical, 48 bits virtual
CPU(s): 64
On-line CPU(s) list: 0-63
Thread(s) per core: 1
Core(s) per socket: 32
Socket(s): 2
NUMA node(s): 8
Vendor ID: AuthenticAMD
CPU family: 25
Model: 1
Model name: AMD EPYC 7543 32-Core Processor
Stepping: 1
CPU MHz: 2794.685
BogoMIPS: 5589.37
Virtualization: AMD-V
L1d cache: 2 MiB
L1i cache: 2 MiB
L2 cache: 32 MiB
L3 cache: 512 MiB
NUMA node0 CPU(s): 0-7
NUMA node1 CPU(s): 8-15
NUMA node2 CPU(s): 16-23
NUMA node3 CPU(s): 24-31
NUMA node4 CPU(s): 32-39
NUMA node5 CPU(s): 40-47
NUMA node6 CPU(s): 48-55
NUMA node7 CPU(s): 56-63
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit: Not affected
Vulnerability L1tf: Not affected
Vulnerability Mds: Not affected
Vulnerability Meltdown: Not affected
Vulnerability Mmio stale data: Not affected
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Not affected
Vulnerability Spec rstack overflow: Mitigation; safe RET
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2: Mitigation; Retpolines; IBPB conditional; IBRS_FW; STIBP disabled; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Not affected
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf rapl pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 invpcid cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd amd_ppin arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload vgif v_spec_ctrl umip pku ospke vaes vpclmulqdq rdpid overflow_recov succor smca
Dependency Versions:
--------------------
tabpfn: 7.0.1
torch: 2.6.0+cu124
numpy: 2.1.3
scipy: 1.16.3
pandas: 2.3.3
scikit-learn: 1.7.2
typing_extensions: 4.15.0
einops: 0.8.2
huggingface-hub: 0.36.2
Describe the bug
Error: UserWarning: X does not have valid feature names, but TabPFNClassifier was fitted with feature names
It seems that calling .fit() with X_val and y_val converts the training data to tensors early, which deletes the Pandas feature names.
If X_val is omitted, the model remembers the feature names.
If X_val is included, it forgets them. Calling .predict_proba(X_test) with a DataFrame later throws a UserWarning about missing feature names.
The Workaround:
Cast test data to numpy (X_test.to_numpy()) during inference.
With X_val...
finetuned_clf.fit(X_train, y_train, X_val=X_val, y_val=y_val)finetuned_clf.predict_proba(X_test.to_numpy())Without...
finetuned_clf.fit(X_train, y_train)finetuned_clf.predict_proba(X_test)Steps/Code to Reproduce