Update README.md

README.md

@@ -44,6 +44,7 @@ python bin/PhaStyle.py \
 
 ```
 
+
 ### Datasets Used:
 
 - **BACPHLIP (without E. coli)**: 1,868 training sequences and 246 validation sequences.
@@ -53,18 +54,55 @@ python bin/PhaStyle.py \
 Each dataset was processed using **512bp segment lengths** to simulate fragmented metagenomic assemblies.
 
 ---
+## Performance Results
+
+The performance of ProkBERT PhaStyle was evaluated on various datasets, including *Escherichia* and EXTREMOPHILE phages, using segment lengths of 512bp and 1022bp. The results are summarized below:
+
+### Performance on *Escherichia* Dataset (512bp and 1022bp segments)
+
+| Method                   | Balanced Accuracy | MCC   | Sensitivity | Specificity |
+|--------------------------|-------------------|-------|-------------|-------------|
+| **ProkBERT-mini (512bp)** | 0.91              | 0.83  | 0.94        | 0.89        |
+| ProkBERT-mini-long (512bp)| 0.90              | 0.82  | 0.96        | 0.85        |
+| ProkBERT-mini-c (512bp)   | 0.89              | 0.80  | 0.95        | 0.84        |
+| DNABERT-2-117M (512bp)    | 0.84              | 0.72  | 0.95        | 0.74        |
+| Nuc. Trans.-50m (512bp)   | 0.85              | 0.72  | 0.92        | 0.78        |
+| **ProkBERT-mini (1022bp)**| **0.94**          | **0.88** | **0.97**    | **0.91**    |
+| ProkBERT-mini-long (1022bp)| 0.94             | 0.89  | 0.97        | 0.91        |
 
-## Performance
+### Performance on EXTREMOPHILE Dataset (512bp and 1022bp segments)
 
-ProkBERT PhaStyle outperforms state-of-the-art models, especially in generalization and speed. It has been benchmarked on **short fragments** (512bp) and **phages from unseen environments**, demonstrating its robustness for both environmental and clinical datasets.
+| Method                   | Balanced Accuracy | MCC   | Sensitivity | Specificity |
+|--------------------------|-------------------|-------|-------------|-------------|
+| **ProkBERT-mini (512bp)** | 0.93              | 0.83  | 0.99        | 0.87        |
+| ProkBERT-mini-long (512bp)| 0.93              | 0.82  | **1.00**    | 0.86        |
+| ProkBERT-mini-c (512bp)   | 0.92              | 0.80  | 0.99        | 0.84        |
+| DNABERT-2-117M (512bp)    | 0.89              | 0.74  | 0.99        | 0.79        |
+| **ProkBERT-mini (1022bp)**| **0.96**          | **0.91** | **1.00**    | **0.93**    |
+| ProkBERT-mini-long (1022bp)| 0.96             | 0.90  | 1.00        | 0.92        |
 
-### Key Metrics:
-- **Balanced Accuracy**: 0.94 (on 1022bp fragments from the *Escherichia* dataset)
-- **MCC (Matthews Correlation Coefficient)**: 0.91
-- **Sensitivity**: 0.97
-- **Specificity**: 0.91
+These tables highlight the high accuracy, MCC, and generalization capability of ProkBERT models, particularly on challenging datasets like *Escherichia* and extremophile phages. The ProkBERT-mini and ProkBERT-mini-long models consistently performed well on both datasets.
 
+For more detailed results, including additional metrics, please refer to the original research paper.
 ---
+## Inference Speed and Running Times
+
+The computational performance of ProkBERT PhaStyle was evaluated using 1,000 randomly selected sequences from the BACPHLIP dataset. The evaluation was performed on a consistent hardware setup with NVIDIA Tesla A100 GPUs. The execution times and inference speeds of various models are summarized below:
+
+### Execution Times (in seconds)
+
+| Model                   | Execution Time (seconds) | Inference Speed (MB/sec) |
+|--------------------------|--------------------------|--------------------------|
+| **ProkBERT-mini-long**    | **132**                  | **0.52**                 |
+| ProkBERT-mini             | 141                      | 0.49                     |
+| ProkBERT-mini-c           | 146                      | 0.47                     |
+| DNABERT-2-117M            | 248                      | 0.25                     |
+| Nucleotide Transformer-50m| 342                      | 0.18                     |
+| Nucleotide Transformer-500m| 502                     | 0.12                     |
+| DeePhage                  | 159                      | 0.43                     |
+| PhaTYP                    | 2,718                    | 0.03                     |
+| BACPHLIP                  | 7,125                    | 0.01                     |
+
 
 ## Limitations