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README.md

@@ -56,47 +56,56 @@ This is an UNOFFICIAL release of the [RYOS](https://www.kaggle.com/competitions/
 
 ## Example Entry
 
-| ID      | design_name | sequence      | structure     | reactivity                    | errors_reactivity            | signal_to_noise_reactivity | deg_pH10                      | errors_deg_pH10              | signal_to_noise_deg_pH10 | deg_50C                     | errors_deg_50C | signal_to_noise_deg_50C            | deg_Mg_pH10                   | errors_deg_Mg_pH10           | signal_to_noise_deg_Mg_pH10 | deg_Mg_50C                  | errors_deg_Mg_50C            | signal_to_noise_deg_Mg_50C | SN_filter |
-| ------- | ----------- | ------------- | ------------- | ----------------------------- | ---------------------------- | -------------------------- | ----------------------------- | ---------------------------- | ------------------------ | --------------------------- | -------------- | ---------------------------------- | ----------------------------- | ---------------------------- | --------------------------- | --------------------------- | ---------------------------- | -------------------------- | --------- |
-| 9830366 | testing     | GGAAAUUUGC... | .......(((... | [0.4167, 1.5941, 1.2359, ...] | [0.1689, 0.2323, 0.193, ...] | 5.326                      | [1.5966, 2.6482, 1.3761, ...] | [0.3058, 0.3294, 0.233, ...] | 4.198                    | [0.7885, 1.93, 2.0423, ...] |                | 3.746 [0.2773, 0.328, 0.3048, ...] | [1.5966, 2.6482, 1.3761, ...] | [0.3058, 0.3294, 0.233, ...] | 4.198                       | [0.7885, 1.93, 2.0423, ...] | [0.2773, 0.328, 0.3048, ...] | 3.746                      | True      |
+| id      | design  | sequence      | secondary_structure | reactivity                    | errors_reactivity            | signal_to_noise_reactivity | deg_pH10                      | errors_deg_pH10              | signal_to_noise_deg_pH10 | deg_50C                     | errors_deg_50C | signal_to_noise_deg_50C            | deg_Mg_pH10                   | errors_deg_Mg_pH10           | signal_to_noise_deg_Mg_pH10 | deg_Mg_50C                  | errors_deg_Mg_50C            | signal_to_noise_deg_Mg_50C | SN_filter |
+| ------- | ------- | ------------- | ------------------- | ----------------------------- | ---------------------------- | -------------------------- | ----------------------------- | ---------------------------- | ------------------------ | --------------------------- | -------------- | ---------------------------------- | ----------------------------- | ---------------------------- | --------------------------- | --------------------------- | ---------------------------- | -------------------------- | --------- |
+| 9830366 | testing | GGAAAUUUGC... | .......(((...       | [0.4167, 1.5941, 1.2359, ...] | [0.1689, 0.2323, 0.193, ...] | 5.326                      | [1.5966, 2.6482, 1.3761, ...] | [0.3058, 0.3294, 0.233, ...] | 4.198                    | [0.7885, 1.93, 2.0423, ...] |                | 3.746 [0.2773, 0.328, 0.3048, ...] | [1.5966, 2.6482, 1.3761, ...] | [0.3058, 0.3294, 0.233, ...] | 4.198                       | [0.7885, 1.93, 2.0423, ...] | [0.2773, 0.328, 0.3048, ...] | 3.746                      | True      |
 
 ## Column Description
 
 The RYOS dataset consists of the following columns, providing crucial insights for understanding RNA stability for vaccine design:
 
-- **ID**:
-  A unique identifier for each RNA sequence entry.
+- **id**:
+    A unique identifier for each RNA sequence entry.
 
-- **design_name**:
-  The name given to each RNA design by contributors, used for easy reference.
+- **design**:
+    The name given to each RNA design by contributors, used for easy reference.
 
 - **sequence**:
-  The nucleotide sequence of the RNA, using standard bases.
+    The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:
 
-- **structure**:
-  The predicted secondary structure of the RNA, represented using dot-bracket notation.
-  The structure helps determine the likely secondary interactions within each RNA molecule.
+    - **A**: Adenine
+    - **C**: Cytosine
+    - **G**: Guanine
+    - **U**: Uracil
+
+- **secondary_structure**:
+    The secondary structure of the RNA represented in dot-bracket notation, using up to three types of symbols to indicate base pairing and unpaired regions, as per bpRNA's standard:
+
+    - **Dots (`.`)**: Represent unpaired nucleotides.
+    - **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1).
+    - **Square Brackets (`[` and `]`)**: Represent base pairs in pseudoknots (page 2).
+    - **Curly Braces (`{` and `}`)**: Represent base pairs in additional pseudoknots (page 3).
 
 - **reactivity**:
-  A list of floating-point values that provide an estimate of the likelihood of the RNA backbone being cut at each nucleotide position.
-  These values help determine the stability of the RNA structure under various experimental conditions.
+    A list of floating-point values that provide an estimate of the likelihood of the RNA backbone being cut at each nucleotide position.
+    These values help determine the stability of the RNA structure under various experimental conditions.
 
 - **deg_pH10** and **deg_Mg_pH10**:
-  Arrays of degradation rates observed under two conditions: incubation at pH 10 without and with magnesium, respectively.
-  These values provide insight into how different conditions affect the stability of RNA molecules.
+    Arrays of degradation rates observed under two conditions: incubation at pH 10 without and with magnesium, respectively.
+    These values provide insight into how different conditions affect the stability of RNA molecules.
 
 - **deg_50C** and **deg_Mg_50C**:
-  Arrays of degradation rates after incubation at 50°C, without and with magnesium.
-  These values capture how RNA sequences respond to elevated temperatures, which is relevant for storage and transportation conditions.
+    Arrays of degradation rates after incubation at 50°C, without and with magnesium.
+    These values capture how RNA sequences respond to elevated temperatures, which is relevant for storage and transportation conditions.
 
 - **\*\_error\_\* Columns**:
-  Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the **reactivity** and **deg\_** columns.
-  These values help quantify the uncertainty in the degradation rates and reactivity measurements.
+    Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the **reactivity** and **deg\_** columns.
+    These values help quantify the uncertainty in the degradation rates and reactivity measurements.
 
 - **SN_filter**:
-  A filter applied to the dataset based on the signal-to-noise ratio, indicating whether a specific sequence meets the dataset’s quality criteria.
+    A filter applied to the dataset based on the signal-to-noise ratio, indicating whether a specific sequence meets the dataset’s quality criteria.
 
-  If the SN_filter is `True`, the sequence meets the quality criteria; otherwise, it does not.
+    If the SN_filter is `True`, the sequence meets the quality criteria; otherwise, it does not.
 
 Note that due to technical limitations, the ground truth measurements are not available for the final bases of each RNA sequence, resulting in a shorter length for the provided labels compared to the full sequence.
 

test.parquet

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train.parquet

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