No object detected in inference after fine-tuning on custom dataset

Dear all,
I am fine-tuning SAM3 on a custom astronomical dataset formatted in a COCO format. The dataset contains 5 object classes (custom naming), segmentation masks/bboxes and I have added a "noun_phrase" for each annotation.
I adapted the roboflow train configuration file, making these changes:

- set dataset & log paths
- enable segmentation (loss & metrics)
- adapted collator to perform runs with gradient accumulation >1
- add sam3.train.transforms.segmentation.DecodeRle in validation transforms
- set Slurm job parameters (batch=8, gradacc=8, 4 A100 GPUs)
- comment some roboflow settings (supercategory, task array)
- I have added in the code the possibility to freeze the backbone or other components (freeze_cfg config, commented out below)

I fine-tuned for 20 epochs both with all model components free (840M trainable pars) and also with backbone frozen (32.7M trainable pars). I set training configuration (learning rate, etc) to roboflow defaults. Below, I attach the training all loss and eval metrics in the two runs:

--> Full fine-tuning

Meters: {'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP': 0.6391414438821105, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_50': 0.8176683410036266, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_75': 0.7222655357848473, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_small': 0.6245980936200656, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_medium': 0.5391393291034561, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_large': 0.95, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_maxDets@1': 0.575984978215531, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_maxDets@10': 0.7667850931014953, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_maxDets@100': 0.790897661111249, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_small': 0.7862146778761182, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_medium': 0.686418844156647, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_large': 0.95, 'Losses/val_all_loss': 0, 'Losses/val_default_loss': 0, 'Losses/val_roboflow100_core_loss': 0.0, 'Trainer/where': 0.9997907949790795, 'Trainer/epoch': 19, 'Trainer/steps_val': 97090}

--> Backbone frozen

Meters: {'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP': 0.5608939549867914, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_50': 0.758768676001815, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_75': 0.6316128247121221, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_small': 0.5385709234878986, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_medium': 0.4265914293746788, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AP_large': 0.95, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_maxDets@1': 0.5454540602304996, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_maxDets@10': 0.7218796950563996, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_maxDets@100': 0.7489443844002187, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_small': 0.744400135157136, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_medium': 0.6562509361033513, 'Meters_train/val_roboflow100/detection/coco_eval_bbox_AR_large': 0.95, 'Losses/val_all_loss': 0, 'Losses/val_default_loss': 0, 'Losses/val_roboflow100_core_loss': 0.0, 'Trainer/where': 0.9997907949790795, 'Trainer/epoch': 19, 'Trainer/steps_val': 97090}

As far as I understood from metrics and loss, the model is indeed learning something, although for sure I need to train more and with optimized parameters.
Now I would like to run inference on a single image using the fine-tuning checkpoint and the example script [https://github.com/facebookresearch/sam3/blob/main/examples/sam3_image_predictor_example.ipynb](url). However, when I run the inference script on train/eval images using the same noun_phrase prompt and a low confidence score (0.1) no objects are detected.

When I load the model I see a log saying that many model component keys are missing:

`
loaded [RUN DIR]/checkpoints/checkpoint.pt and found missing and/or unexpected keys:
missing_keys=['backbone.vision_backbone.trunk.pos_embed', 'backbone.vision_backbone.trunk.patch_embed.proj.weight', 'backbone.vision_backbone.trunk.blocks.0.norm1.weight', 'backbone.vision_backbone.trunk.blocks.0.norm1.bias', 'backbone.vision_backbone.trunk.blocks.0.attn.freqs_cis', 'backbone.vision_backbone.trunk.blocks.0.attn.qkv.weight', 'backbone.vision_backbone.trunk.blocks.0.attn.qkv.bias', 'backbone.vision_backbone.trunk.blocks.0.attn.proj.weight', 'backbone.vision_backbone.trunk.blocks.0.attn.proj.bias', 'backbone.vision_backbone.trunk.blocks.0.norm2.weight', 'backbone.vision_backbone.trunk.blocks.0.norm2.bias', 'backbone.vision_backbone.trunk.blocks.0.mlp.fc1.weight',
...
...
`

Could someone give me some hint on what I am doing wrong? Is it a matter of fine-tuning (category embedding, hyperparameters, etc) or how I do the inference (input data normalization/transform) or both?

Thanks a lot.

PS: My config file and inference script are reported below:

**CONFIG FILE**
```
# @package _global_
defaults:
- _self_

# ============================================================================
# Paths Configuration (Chage this to your own paths)
# ============================================================================
paths:
roboflow_vl_100_root: [DATASET ROOT DIR]
experiment_log_dir: [RUN LOG DIR]
bpe_path: [SAM PATH]/sam3/assets/bpe_simple_vocab_16e6.txt.gz

#freeze_cfg:
# backbone: true
# backbone_blocks: 0 # e.g. freeze first N blocks; 0 = none
# text_encoder: true
# transformer: false
# segmentation_head: false

# Roboflow dataset configuration
roboflow_train:
num_images: null # Note: This is the number of images used for training. If null, all images are used.

# Training transforms pipeline
train_transforms:
- _target_: sam3.train.transforms.basic_for_api.ComposeAPI
transforms:
- _target_: sam3.train.transforms.filter_query_transforms.FlexibleFilterFindGetQueries
query_filter:
_target_: sam3.train.transforms.filter_query_transforms.FilterCrowds
- _target_: sam3.train.transforms.point_sampling.RandomizeInputBbox
box_noise_std: 0.1
box_noise_max: 20
- _target_: sam3.train.transforms.segmentation.DecodeRle
- _target_: sam3.train.transforms.basic_for_api.RandomResizeAPI
sizes:
_target_: sam3.train.transforms.basic.get_random_resize_scales
size: ${scratch.resolution}
min_size: 480
rounded: false
max_size:
_target_: sam3.train.transforms.basic.get_random_resize_max_size
size: ${scratch.resolution}
square: true
consistent_transform: ${scratch.consistent_transform}
- _target_: sam3.train.transforms.basic_for_api.PadToSizeAPI
size: ${scratch.resolution}
consistent_transform: ${scratch.consistent_transform}
- _target_: sam3.train.transforms.basic_for_api.ToTensorAPI
- _target_: sam3.train.transforms.filter_query_transforms.FlexibleFilterFindGetQueries
query_filter:
_target_: sam3.train.transforms.filter_query_transforms.FilterEmptyTargets
- _target_: sam3.train.transforms.basic_for_api.NormalizeAPI
mean: ${scratch.train_norm_mean}
std: ${scratch.train_norm_std}
- _target_: sam3.train.transforms.filter_query_transforms.FlexibleFilterFindGetQueries
query_filter:
_target_: sam3.train.transforms.filter_query_transforms.FilterEmptyTargets
- _target_: sam3.train.transforms.filter_query_transforms.FlexibleFilterFindGetQueries
query_filter:
_target_: sam3.train.transforms.filter_query_transforms.FilterFindQueriesWithTooManyOut
max_num_objects: ${scratch.max_ann_per_img}

# Validation transforms pipeline
val_transforms:
- _target_: sam3.train.transforms.basic_for_api.ComposeAPI
transforms:
# 1) Decode COCO RLE/poly into mask tensors
- _target_: sam3.train.transforms.segmentation.DecodeRle

# 2) Resize image + masks
- _target_: sam3.train.transforms.basic_for_api.RandomResizeAPI
sizes: ${scratch.resolution}
max_size:
_target_: sam3.train.transforms.basic.get_random_resize_max_size
size: ${scratch.resolution}
square: true
consistent_transform: False

# 3) Convert to torch tensors
- _target_: sam3.train.transforms.basic_for_api.ToTensorAPI

# 4) Normalize
- _target_: sam3.train.transforms.basic_for_api.NormalizeAPI
mean: ${scratch.train_norm_mean}
std: ${scratch.train_norm_std}

# NOTE: Loss to be used for training in case of segmentation
loss:
_target_: sam3.train.loss.sam3_loss.Sam3LossWrapper
matcher: ${scratch.matcher}
o2m_weight: 2.0
o2m_matcher:
_target_: sam3.train.matcher.BinaryOneToManyMatcher
alpha: 0.3
threshold: 0.4
topk: 4
use_o2m_matcher_on_o2m_aux: false
loss_fns_find:
- _target_: sam3.train.loss.loss_fns.Boxes
weight_dict:
loss_bbox: 5.0
loss_giou: 2.0
- _target_: sam3.train.loss.loss_fns.IABCEMdetr
weak_loss: False
weight_dict:
loss_ce: 20.0 # Another option is 100.0
presence_loss: 20.0
pos_weight: 10.0 # Another option is 5.0
alpha: 0.25
gamma: 2
use_presence: True # Change
pos_focal: false
pad_n_queries: 200
pad_scale_pos: 1.0
- _target_: sam3.train.loss.loss_fns.Masks
focal_alpha: 0.25
focal_gamma: 2.0
weight_dict:
loss_mask: 200.0
loss_dice: 10.0
compute_aux: false
loss_fn_semantic_seg:
#_target_: sam3.losses.loss_fns.SemanticSegCriterion
_target_: sam3.train.loss.loss_fns.SemanticSegCriterion
presence_head: True
presence_loss: False # Change
focal: True
focal_alpha: 0.6
focal_gamma: 2.0
downsample: False
weight_dict:
loss_semantic_seg: 20.0
loss_semantic_presence: 1.0
loss_semantic_dice: 30.0
scale_by_find_batch_size: ${scratch.scale_by_find_batch_size}

# ============================================================================
# Different helper parameters and functions
# ============================================================================
scratch:
enable_segmentation: True # NOTE: This is the number of queries used for segmentation
# Model parameters
d_model: 256
pos_embed:
_target_: sam3.model.position_encoding.PositionEmbeddingSine
num_pos_feats: ${scratch.d_model}
normalize: true
scale: null
temperature: 10000

# Box processing
use_presence_eval: True
original_box_postprocessor:
_target_: sam3.eval.postprocessors.PostProcessImage
max_dets_per_img: -1 # infinite detections
use_original_ids: true
use_original_sizes_box: true
use_presence: ${scratch.use_presence_eval}

# Matcher configuration
matcher:
_target_: sam3.train.matcher.BinaryHungarianMatcherV2
focal: true # with `focal: true` it is equivalent to BinaryFocalHungarianMatcher
cost_class: 2.0
cost_bbox: 5.0
cost_giou: 2.0
alpha: 0.25
gamma: 2
stable: False
scale_by_find_batch_size: True

# Image processing parameters
resolution: 1008
consistent_transform: False
max_ann_per_img: 200

# Normalization parameters
train_norm_mean: [0.5, 0.5, 0.5]
train_norm_std: [0.5, 0.5, 0.5]
val_norm_mean: [0.5, 0.5, 0.5]
val_norm_std: [0.5, 0.5, 0.5]

# Training parameters
num_train_workers: 10
num_val_workers: 0
max_data_epochs: 20
target_epoch_size: 1500
hybrid_repeats: 1
context_length: 2
gather_pred_via_filesys: false

# Learning rate and scheduler parameters
lr_scale: 0.1
lr_transformer: ${times:8e-4,${scratch.lr_scale}}
lr_vision_backbone: ${times:2.5e-4,${scratch.lr_scale}}
lr_language_backbone: ${times:5e-5,${scratch.lr_scale}}
lrd_vision_backbone: 0.9
wd: 0.1
scheduler_timescale: 20
scheduler_warmup: 20
scheduler_cooldown: 20

val_batch_size: 1
collate_fn_val:
_target_: sam3.train.data.collator.collate_fn_api
_partial_: true
repeats: ${scratch.hybrid_repeats}
dict_key: roboflow100
with_seg_masks: ${scratch.enable_segmentation} # Note: Set this to true if using segmentation masks!

gradient_accumulation_steps: 8
train_batch_size: 8

## USE THIS WITH GRAD ACC=1
#collate_fn:
# _target_: sam3.train.data.collator.collate_fn_api
# _partial_: true
# repeats: ${scratch.hybrid_repeats}
# dict_key: all
# with_seg_masks: ${scratch.enable_segmentation} # Note: Set this to true if using segmentation masks!

## USE THIS WITH GRAD ACC>1
collate_fn:
_target_: sam3.train.data.collator.collate_fn_api_with_chunking
_partial_: true
repeats: ${scratch.hybrid_repeats}
dict_key: all
with_seg_masks: ${scratch.enable_segmentation}
num_chunks: ${scratch.gradient_accumulation_steps}

# ============================================================================
# Trainer Configuration
# ============================================================================

trainer:

_target_: sam3.train.trainer.Trainer
skip_saving_ckpts: false
empty_gpu_mem_cache_after_eval: True
skip_first_val: True
max_epochs: 20
accelerator: cuda
seed_value: 123
val_epoch_freq: 1
mode: train
gradient_accumulation_steps: ${scratch.gradient_accumulation_steps}

distributed:
backend: nccl
find_unused_parameters: True
gradient_as_bucket_view: True

loss:
all: ${roboflow_train.loss}
default:
_target_: sam3.train.loss.sam3_loss.DummyLoss

data:

train:
_target_: sam3.train.data.torch_dataset.TorchDataset
dataset:
_target_: sam3.train.data.sam3_image_dataset.Sam3ImageDataset
limit_ids: ${roboflow_train.num_images}
transforms: ${roboflow_train.train_transforms}
load_segmentation: ${scratch.enable_segmentation}
max_ann_per_img: 500000
multiplier: 1
max_train_queries: 50000
max_val_queries: 50000
training: true
use_caching: False
img_folder: ${paths.roboflow_vl_100_root}
ann_file: ${paths.roboflow_vl_100_root}/dataset_sam_train.json

shuffle: True
batch_size: ${scratch.train_batch_size}
num_workers: ${scratch.num_train_workers}
pin_memory: True
drop_last: True
collate_fn: ${scratch.collate_fn}

val:
_target_: sam3.train.data.torch_dataset.TorchDataset
dataset:
_target_: sam3.train.data.sam3_image_dataset.Sam3ImageDataset
load_segmentation: ${scratch.enable_segmentation}
coco_json_loader:
_target_: sam3.train.data.coco_json_loaders.COCO_FROM_JSON
include_negatives: true
category_chunk_size: 2 # Note: You can increase this based on the memory of your GPU.
_partial_: true
img_folder: ${paths.roboflow_vl_100_root}
ann_file: ${paths.roboflow_vl_100_root}/dataset_sam_val.json
transforms: ${roboflow_train.val_transforms}
max_ann_per_img: 100000
multiplier: 1
training: false

shuffle: False
batch_size: ${scratch.val_batch_size}
num_workers: ${scratch.num_val_workers}
pin_memory: True
drop_last: False
collate_fn: ${scratch.collate_fn_val}

model:
_target_: sam3.model_builder.build_sam3_image_model
bpe_path: ${paths.bpe_path}
device: cpus
eval_mode: false
enable_segmentation: ${scratch.enable_segmentation} # Warning: Enable this if using segmentation.
checkpoint_path: [HF_HOME]/models/huggingface/hub/models--facebook--sam3/snapshots/3c879f39826c281e95690f02c7821c4de09afae7/sam3.pt

freeze_cfg: ${freeze_cfg}

meters:
val:
roboflow100:
detection:
_target_: sam3.eval.coco_writer.PredictionDumper
iou_type: "bbox"
dump_dir: ${launcher.experiment_log_dir}/dumps
merge_predictions: True
postprocessor: ${scratch.original_box_postprocessor}
gather_pred_via_filesys: ${scratch.gather_pred_via_filesys}
maxdets: 100
pred_file_evaluators:
- _target_: sam3.eval.coco_eval_offline.CocoEvaluatorOfflineWithPredFileEvaluators
gt_path: ${paths.roboflow_vl_100_root}/dataset_sam_val.json
tide: False
iou_type: "bbox"

optim:
amp:
enabled: True
amp_dtype: bfloat16

optimizer:
_target_: torch.optim.AdamW

gradient_clip:
_target_: sam3.train.optim.optimizer.GradientClipper
max_norm: 0.1
norm_type: 2

param_group_modifiers:
- _target_: sam3.train.optim.optimizer.layer_decay_param_modifier
_partial_: True
layer_decay_value: ${scratch.lrd_vision_backbone}
apply_to: 'backbone.vision_backbone.trunk'
overrides:
- pattern: '*pos_embed*'
value: 1.0

options:
lr:
- scheduler: # transformer and class_embed
_target_: sam3.train.optim.schedulers.InverseSquareRootParamScheduler
base_lr: ${scratch.lr_transformer}
timescale: ${scratch.scheduler_timescale}
warmup_steps: ${scratch.scheduler_warmup}
cooldown_steps: ${scratch.scheduler_cooldown}
- scheduler:
_target_: sam3.train.optim.schedulers.InverseSquareRootParamScheduler
base_lr: ${scratch.lr_vision_backbone}
timescale: ${scratch.scheduler_timescale}
warmup_steps: ${scratch.scheduler_warmup}
cooldown_steps: ${scratch.scheduler_cooldown}
param_names:
- 'backbone.vision_backbone.*'
- scheduler:
_target_: sam3.train.optim.schedulers.InverseSquareRootParamScheduler
base_lr: ${scratch.lr_language_backbone}
timescale: ${scratch.scheduler_timescale}
warmup_steps: ${scratch.scheduler_warmup}
cooldown_steps: ${scratch.scheduler_cooldown}
param_names:
- 'backbone.language_backbone.*'

weight_decay:
- scheduler:
_target_: fvcore.common.param_scheduler.ConstantParamScheduler
value: ${scratch.wd}
- scheduler:
_target_: fvcore.common.param_scheduler.ConstantParamScheduler
value: 0.0
param_names:
- '*bias*'
module_cls_names: ['torch.nn.LayerNorm']

checkpoint:
save_dir: ${launcher.experiment_log_dir}/checkpoints
save_freq: 0 # 0 only last checkpoint is saved.

logging:
tensorboard_writer:
_target_: sam3.train.utils.logger.make_tensorboard_logger
log_dir: ${launcher.experiment_log_dir}/tensorboard
flush_secs: 120
should_log: True
wandb_writer: null
log_dir: ${launcher.experiment_log_dir}/logs
log_freq: 10

# ============================================================================
# Launcher and Submitit Configuration
# ============================================================================

launcher:
num_nodes: 1
gpus_per_node: 4
experiment_log_dir: ${paths.experiment_log_dir}

submitit:
use_cluster: True
account: XXX
partition: XXX
qos: XXX
timeout_hour: 96
name: sam3
cpus_per_task: 8
port_range: [10000, 65000]

# ============================================================================
# Available Roboflow Supercategories (for reference)
# ============================================================================

all_roboflow_supercategories:
- -grccs
- zebrasatasturias
...
...
```

**INFERENCE SCRIPT**
```
import os
import sys
import matplotlib.pyplot as plt
import numpy as np

import sam3
from PIL import Image
from sam3 import build_sam3_image_model
from sam3.model.box_ops import box_xywh_to_cxcywh
from sam3.model.sam3_image_processor import Sam3Processor
from sam3.visualization_utils import draw_box_on_image, normalize_bbox, plot_results
from sam3.train.transforms.basic_for_api import ComposeAPI, RandomResizeAPI, ToTensorAPI, NormalizeAPI
from sam3.model.position_encoding import PositionEmbeddingSine
from sam3.eval.postprocessors import PostProcessImage

import torch
import torchvision
torch.backends.cuda.matmul.allow_tf32 = True
torch.backends.cudnn.allow_tf32 = True

#########################
## MAIN
#########################
sam3_root = os.path.join(os.path.dirname(sam3.__file__), "..")
print("sam3_root")
print(sam3_root)
device = "cuda" if torch.cuda.is_available() else "cpu"

# - Build model
print("Loading model ...")
bpe_path = f"{sam3_root}/assets/bpe_simple_vocab_16e6.txt.gz"
checkpoint_path= "[RUN DIR]/checkpoints/checkpoint.pt"

model= build_sam3_image_model(
bpe_path=bpe_path,
device=device,
eval_mode=True,
checkpoint_path=checkpoint_path,
load_from_HF=False,
enable_segmentation=True,
enable_inst_interactivity=False,
compile=False,
)

# - Load image
print("Loading image ...")
image_path= "sidelobe0001.png"
image = Image.open(image_path).convert('RGB')
width, height = image.size
print(f"Image width={width}, height={height}")

# - Transform image
print("Transforming image ...")
resize_size= 1008
processor = Sam3Processor(model, resolution=resize_size, confidence_threshold=0.0)
inference_state = processor.set_image(image) ## Looking at the code, image is resized inside set_image method

# - Inference
prompt= "spurious source, imaging artefact, sidelobe"
processor.reset_all_prompts(inference_state)
inference_state= processor.set_text_prompt(state=inference_state, prompt=prompt)

masks, boxes, scores = inference_state["masks"], inference_state["boxes"], inference_state["scores"]

# - Draw results
img0 = Image.open(image_path)
plot_results(img0, inference_state)
plt.show()
```

Start with the linked sam3_image_predictor_example.ipynb and compare its model-loading and image preprocessing with the reported training config and inference script. Check why checkpoint.pt reports missing component keys, then verify inference on a train or evaluation image with the same noun_phrase prompt. Done means the fine-tuned checkpoint loads the intended weights and produces detections on those images.

Written by the indexing model from the issue text.