Accurate identification of species in fine-grained, long-tailed datasets poses significant challenges due to imbalanced class distributions and the necessity for precise classification while minimizing confusion between dangerous and harmless species. This paper introduces a generalized training and inference methodology designed to tackle these challenges, demonstrated through competitive performance in both the SnakeCLEF and FungiCLEF 2024 challenges. While results for FungiCLEF 2024 are detailed in an accompanying paper, this work primarily explores the application and performance of the same techniques to the SnakeCLEF 2024 challenge. The proposed approach integrates a combination of augmentation techniques, specialized loss functions, and robust model architectures to enhance classification accuracy while jointly minimizing the asymmetric penalty for misclassification of venomous species. For both the public and private leaderboards, my approach achieved second place in all metrics. On the public leaderboard, it scored 81.2 for Track 1, 945 for Track 2, and 33.35 for the F1 score. On the private leaderboard, it scored 79.58 for Track 1, 2557 for Track 2, and 30.29 for the F1 score. These experimental results validate the efectiveness of this methodology, showcasing its robustness across diverse datasets and evaluation metrics. The versatility of this approach indicates its potential applicability to a wide range of similar image recognition tasks. Code and implementation details are available at https://github.com/Jack-Etheredge/snakeclef2024.
Venomous snake bites cause over half a million deaths and disabilities annually, highlighting the need
for an efective image-based snake identification system [
Fine-grained long-tailed image recognition is a challenging task due to the need for high granularity
in distinguishing between visually similar classes compounded by significant class imbalance.
Competitions like SnakeCLEF and FungiCLEF, both part of the LifeCLEF 2024 [
CEUR
ceur-ws.org
Many diferent techniques have been explored for the classification of fine-grained images of snakes
[
The SnakeCLEF dataset consists of 182,261 images across 1,784 snake species. The training data includes geographical location metadata. FungiCLEF’s dataset comprises 295,938 training images of 1,604 species with extensive metadata, including habitat and location. While the metadata was present in the test data for FungiCLEF 2024, it was absent from the test data for SnakeCLEF 2024.
Both competitions aim to enhance species recognition accuracy, albeit with difering focuses. SnakeCLEF
2024 evaluates class-balanced metrics, emphasizing the importance of correctly classifying venomous
vs. non-venomous species without leveraging metadata at inference time to blind the models to the
geographic region. FungiCLEF 2024 includes an open-set component for identifying unknown species
and penalizes misclassifications between edible and poisonous fungi. The venomous confusion loss for
SnakeCLEF is more complex than the poisonous confusion loss for FungiCLEF, with diferent costs for
misclassification between two venomous classes (2), between two nonvenomous classes (1), venomous
→ nonvenomous confusion (5), and nonvenomous → venomous confusion (2). Both competitions
report the macro-F1 score, but SnakeCLEF additionally incorporates it into the Track 1 score. Track 1 is
a weighted average of the accuracies for the four diferent confusion categories and the macro-averaged
F1. Accuracy is also reported for both competitions, but is largely ignored for the results shown in this
paper, as it is not reported for the granular results in the overview of either competition last year [
To address the long-tailed distribution and fine-grained nature of the datasets, I employed a combination of training techniques and test-time augmentations detailed below.
Training was performed with a resize to 768 with bicubic interpolation, square random crop of size 384,
TrivialAugment [20], horizontal flip with 50% probability, and random erasing [ 21] with a probability of
25%, applied in that order. MixUp augmentation [22] and augmentations inspired by it were intentionally
excluded due to the fine-grained nature of the dataset, which represents higher intra-class variability
and lower inter-class variability than standard classification tasks. However, mixing augmentations in
the form of CutMix [23] and RandoMix [24] were previously employed successfully by [
Multiple loss functions were evaluated for the classification loss. Seesaw loss [ 13] and a custom venom loss were used to train the models in the final ensemble. Seesaw loss was chosen since it is designed for long-tailed classification. Further, it achieves this without the need for class rebalancing through data sampling by adding additional terms to the standard cross-entropy loss. It employs a mitigation factor to reduce penalties for tail categories based on the ratio of training instances as well as a compensation factor to increase penalties for misclassified instances, thereby reducing the otherwise overwhelming efect of false positives in the tail classes.
A custom venom loss was added to seesaw loss to create the total loss during training. This cost function was formulated by creating a pairwise cost for the confusion for every combination of the target and predicted class. The vector corresponding to the target class was indexed from this cost matrix and the softmax probabilities were multiplied elementwise with the cost vector. The sum of these costs was used as the venom loss. This loss is similar to the real-world weighted cross entropy loss [14], but uses the costs directly instead of utilizing a weighted log loss. Future work could investigate the relative performance of these two loss functions. Since the venom confusion metric is calculated based on the percentage of misclassifications, it is a class-balanced metric. As such, I also experimented with the application of an inverse class weight to the venom loss to account for class imbalance (results shown in Table 5).
Balanced sampling is a simpler alternative to seesaw loss for mitigating the efect of class imbalance. For each epoch, samples were drawn with replacement from the training data with a probability inversely proportional to the number of samples belonging to that class. Focal loss [15] penalizes misclassifications for dificult to classify samples by reducing the loss for well-classified examples (high predicted probability for the correct class) relative to standard cross entropy loss. This is done in an attempt to put more focus on dificult examples dynamically during training. Since the tail classes will likely be more dificult to classify, focal loss should in theory work in conjunction with balanced sampling to improve tail class classification.
Another loss that was evaluated was sub-center ArcFace loss [25]. Sub-center ArcFace loss is a refinement to ArcFace that allows multiple cluster centers per class, which seemed better suited to snake classification than the original ArcFace loss since snakes of the same species can vary widely in their appearance due to age and other factors. Losses that operate directly on the embedding of the model rather than a dense classification are typically used in conjunction with clustering or a distance-based classification relative to ground truth embeddings per class. Instead, I tested the addition of sub-center ArcFace loss to the seesaw and custom venom losses.
LogitNorm [26] was applied to the logits during training before seesaw loss or venom loss were applied. This was done for parity with the models used for the FungiCLEF 2024 challenge [27]. LogitNorm increases class separation in the embedding space of the classifier as well as calibrating the model probabilities. Since the class with the highest predicted probability was selected as the classification in every case, probability calibration was assumed to be of no consequence for individual model classifications. However, since the probabilities are averaged in the model ensembles, it is possible that probability calibration could have an impact on the performance of ensembles.
The training paradigm used for the SnakeCLEF competition involved several key techniques and methodologies. The dataset was augmented using Trivial Augment and Random Erasing to improve the models’ robustness. The AdamW optimizer [28] was used with a weight decay of 0.05. The learning rate was initially set to 1e-3 for the classification output dense layer with the pretrained model frozen for the ifrst 5 epochs, then reduced to 5e-5. Training was conducted with a batch size of 40 for CAFormer-S18, 32 for Metaformer-0, and 24 for CAFormer-S36. CAFormer models were were used with weights pretrained on ImageNet-21K [29] while Metaformer-0 was used with weights pretrained on iNaturalist2021 [30]. A dropout rate of 0.2 was implemented between the dense output classification layer and the penultimate layer to prevent overfitting in all cases unless otherwise stated. Learning rate scheduling was employed, reducing the rate by a factor of 0.1 if the model did not improve the validation loss for 5 consecutive epochs. Early stopping was implemented to prevent overfitting and conserve computational resources. The models were fine-tuned using CAFormer-S18, and a 4x ensemble approach was adopted, utilizing diferent data splits to improve generalization.
During inference, several techniques were applied to maximize performance. Test-time augmentations were used, including horizontal flips and multi-instance averaging, to increase the robustness of predictions. The resolution of CAFormer-S18 and CAFormer-S36 models was adjusted by resizing from 384x384 to 576x576 for higher resolution inference. Additionally, ensemble averaging was employed, combining predictions from multiple models to improve overall accuracy. Models were ensembled by simple averaging of the prediction probabilities before selecting the class with the highest predicted probability as the prediction. These strategies collectively enhanced the model’s performance during the inference phase as shown in Section 4.
Multi-crop refers to the generation and use of three overlapping crops that collectively ensure complete coverage of the entire image. The predicted class probabilities for each of these crops are then averaged to generate the final maximum probability classification. Horizontal flipping (hflip) augmentation involves taking the average predicted class probabilities from both the original and horizontally flipped version of each image in the same manner as multi-crop. Multi-instance refers to averaging the probabilities for each instance in cases where an observation has more than a single instance. In cases where multi-instance is not used, only the first instance for each observation is used to make each prediction. Image size refers to the inference image size that the image was resized to before a square center crop (or multiple square crops in the case of multi-crop) of the same resolution are taken.
Taken collectively, if multi-instance and hflip test time augmentations are both used with an ensemble of CAFormer models, the inference procedure would be as follows: Every image (instance) belonging to each observation would be 1) resized and center cropped to 576x576, and 2) horizontally flipped to keep both the original and mirrored image. Then, probabilities would be generated for each model for both flips of every instance. Finally, the simple average of all of these probabilities would be calculated to determine the class prediction based on the maximum class probability after averaging.
An ensemble of CAFormer models [19] were used in the best-performing solution for this competition. These models balance computational eficiency and classification accuracy, making them suitable for both competitions. Notably, the CAFormer models performed consistently well across diverse datasets. A dropout rate of 0.2 was used between the dense output classification layer and the penultimate layer of the network.
Models were trained on four diferent training-validation data splits to increase diversity and decrease correlation between the errors of the models comprising the ensemble. The dataset is originally provided as three collections of observations: training, validation, and additional training observations for rare classes. In all cases, the additional training observations are considered part of the original training set. As such, the original dataset can be considered as being provided as a single training and validation split. The A, B, and C data splits were constructed by first combining the original training and validation data for the competition. The A split used the first 90% of the observations per class as the training samples and the remaining 10% of the observations per class as the validation samples. In cases where there were fewer than 4 observations per class, all observations were used for training. The B split used the last 90% of samples for training and the C split used the middle 90% of samples for training, both with the same exception regarding tail classes with very few observations. Since the original training observations come before the original validation observations in this combined dataset, the A split is most similar of these 3 splits to the original training and validation split. The D split is the original training and validation split provided by the competition.
All experiments were conducted on a single NVIDIA RTX 4090 graphics card, emphasizing the eficiency of our methodology given limited computational resources.
My methodology demonstrated competitive performance in both SnakeCLEF and FungiCLEF 2024. For SnakeCLEF, my model achieved second place in all competition metrics on the public and private leaderboards, successfully diferentiating between venomous and non-venomous species without the ability to overfit to geographic regions utilizing the metadata. For FungiCLEF, my approach excelled in recognizing unknown species while minimizing edible-poisonous misclassifications. My models achieved 1st place for Track1 classification score, macro F1, and Accuracy, while achieving competitive performance in the other two metrics [27].
FixRes involves not only inference at a higher resolution relative to training, but also fine-tuning the ifnal layers of the model at the desired inference resolution without training augmentations. FixRes ifne-tuning did not improve performance on any metric when inference was performed on a resolution of 576, as can be seen in Table 1.
Multiple loss functions were evaluated in addition to seesaw loss and the custom venom loss. One of the losses that was evaluated in addition to seesaw loss was sub-center ArcFace loss. Table 2 shows the addition of sub-center ArcFace loss to the training of one of the models in the ensemble. CAFormer-S18 with data split A was trained both with and without the sub-center ArcFace loss. In both cases, the classifications from the dense layer were used for predictions rather than utilizing the embeddings directly. The ensemble that contained a model with sub-center ArcFace loss had poorer performance across all metrics. This suggests that the addition of sub-center ArcFace loss to the seesaw and custom venom losses did not further mitigate the impact of the tail classes with very few observations despite the loss optimizing the separation of classes in the pre-classification model embedding.
Another loss that was evaluated for the multiclass classification was focal loss, which was paired with balanced sampling to directly address class imbalance. Focal loss with balanced sampling did not perform as well as seesaw loss, as can be seen in Table 3. Increasing the dropout rate for the penultimate layer may be slightly beneficial, with the greatest percent improvement in metrics being the F1 score (which increased 0.99), but this diference is trivial compared to the diference across all metrics for seesaw loss vs focal loss with balanced sampling. F1 increases nearly 7 points when focal loss with balanced sampling is replaced with seesaw loss.
Initial experiments with Metaformer-0 [19] showed that CAFormer-S18 gave better performance across all metrics. While Metaformer shows remarkable performance on fine-grained datasets, particularly when metadata is available, it appears that CAFormer models may be more performant when metadata is unavailable.
Class weighted venom loss was evaluated as an alternative to the venom loss, since the custom venom loss did not account for class imbalance. In the case of two diferent data splits, the addition of this weight term to the venom loss negatively impacted all metrics. Results are shown in Table 5. Weighted venom loss did not improve the generalizability of the Track 2 score.
Several diferent model ensembles were evaluated based on diferent splits of the dataset, the inclusion of random erasing, and the CAFormer-S18 vs CAFormer-S36 architecture. Results are shown in Table 6. The best performing ensemble of models included on the private leaderboard comprised a CAFormer-S36 model trained on split D without random erasing, and three CAFormer-S18 models trained on splits B and C with random erasing and on split D without random erasing. The private leaderboard Track1 score of 79.96, Track 2 score of 2481, and F1 score of 30.2 achieved second place for all three metrics. An ensemble of all CAFormer-S18 models slightly outperformed this ensemble for private leaderboard F1 score (30.29 vs 30.2). Interestingly, this ensemble comprisingly solely CAFormer-S18 models performed best across all public leaderboard metrics. The all CAFormer-S18 ensemble has the same composition as the ensemble mentioned above with the exception of replacing the CAFormer-S36 model with a CAFormer-S18 model trained on data split A without random erasing. In all cases, there was a large disparity between the public and private leaderboard performance, particularly with respect to the Track 2 venomous → harmless confusion loss. In all cases, the private Track 2 loss was over two fold higher than the public Track 2 loss.
Several test-time augmentations were evaluated including horizontal flipping (hflip), averaging multiple crops (multi-crop), multi-instance averaging, and inference at a higher resolution than the training resolution. The results for all of these augmentations are summarized in Table 7 with the exception of increasing the inference image resolution, the results of which are shown in Table 8. Each of the averaging-based test-time augmentations improve performance, in isolation or in combination. Multi-instance is the most computationally demanding, but also provides the greatest lift in performance of hflip, multi-crop, and multi-instance. Hflip provides a similar lift to multi-crop, but involves doubling rather than tripling the number of images that must pass through the models. The most impactful augmentation for is inference at 576 image resolution instead of inference at the training resolution of 384, as shown in Table 8.
Random erasing was included in many of the models in an efort to increase the generalizability of the models. It appears that too much of the class-specific information was obscured by the erasure leading to a slight degradation in performance. As shown in Table 9, the public Track 1 score is worse by 0.87 while the private Track 1 score is worse by 2.31 when random erasing is included in the training augmentations.
Since the learning rate reduction and early stopping was decided based on validation loss, it was necessary to perform all training with a training-validation split. In order to utilize all the available data and to increase the diversity of the models in the final ensemble, diferent training-validation splits of the data were used to train otherwise identical models. Table 10 shows the impact of these diferent splits on the performance of the models. The diference between the best and worst performing splits is greater than the diferences between the inclusion of LogitNorm (Table 12), random erasing (Table 9), horizontal flipping (Table 7), or multiple crops (Table 7). The diference was also greater than the diference between a larger ensemble and averaging multiple image resolutions (Table 11). This suggests that diferent splits of the data can have a significant impact on final performance of the models, particularly if individual models are used instead of being combined into an ensemble.
Averaging the predicted probabilities from multiple image (multi-res) resolutions was investigated as a test-time augmentation. However, since this requires performing inference through the same model for n resolutions, the increased performance must be weighted against this increase in compute cost. Since multi-res requires inference through the same model n resolutions number of times, the compute cost should be comparable between an ensemble that is twice as large vs averaging two resolutions. Better performance is achieved across all metrics using a larger ensemble, as shown in Table 11.
All final models were trained with LogitNorm. To determine whether its inclusion was beneficial, an identical model was trained without LogitNorm and evaluated using the same settings. The inclusion of LogitNorm may slightly degrade performance of the models as shown in Table 12. Since it significantly improves performance on FungiCLEF [27], it may be of greater benefit to open-set classification, and thus if the task will never be open-set, it seems that LogitNorm can be safely excluded from the training.
All final models were trained with venom loss. To determine whether its inclusion was beneficial, an identical model was trained without venom loss and evaluated using the same settings. As shown in Table 13, the custom venom loss improves performance on the Track2 metric as expected. Since the Track1 metric is also influenced by the venomous → harmless confusion, it is unsurprising that Track1 would improve with the inclusion of venom loss. What is more surprising is that the F1 score was improved by the venom loss. This shows that a real-world cost matrix for pairwise class confusion can be utilized without sacrificing overall classification performance. Future work could investigate how broadly applicable this is beyond this specific dataset.
The best performing ensembles both utilized horizontal flipping, multi-instance averaging, and a higher resolution image of 576x576 relative to the training resolution of 384x384. An ensemble of CAFormerS18 models trained on data splits A and D without random erasing and data splits B and C with random erasing performed best for all public leaderboard metrics as well as F1 on the private leaderboard. However, this ensemble was outperformed for Track 1 and Track 2 on the private leaderboard by swapping the CAFormer-S18 model trained on data split A for a CAFormer-S36 model trained on data split D as shown in Table 6 and described previously in Section 4.
Table 14 shows the public leaderboard performance of each team and Table 15 shows the private leaderboard performance. In both cases, my method achieves 2nd place across all metrics. Notably, there is a larger gap between the performance of my models and 3rd place than the diference in performance of my models relative to 1st place for all metrics. Interestingly, there is a large disparity in the performance of Track2 between the public leaderboard and the private leaderboard for all participants. This suggests that either the public and private leaderboard have diferent data distributions or all competitors overfit their solutions to the public leaderboard. Since the other metrics do not show such a large disparity, this suggests that the ratio of dificult to classify venomous species may be greater in the private leaderboard test set.
I presented in this work a robust training and inference methodology that generalizes well across diferent fine-grained long-tailed image recognition tasks. The similarities between SnakeCLEF and FungiCLEF, such as asymmetric penalties for misclassification, highlight the efectiveness and generalizability of my approach. Diferences, such as the lack of metadata in SnakeCLEF and the presence of unknowns in FungiCLEF, necessitated specific adjustments. Future work could explore few-shot learning techniques to further enhance performance for classes with few examples. Additional future work could investigate the potential for geographic metadata to increase model bias against the successful identification of invasive snake species in comparison to models not using that metadata. My approach’s competitive performance on both SnakeCLEF and FungiCLEF 2024 suggests its potential applicability to other similar challenges.
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