update README

README.md

@@ -3,36 +3,40 @@ license: cc-by-nc-sa-4.0
 language:
 - en
 tags:
-- biology
-- genomics
-pretty_name: Genomics Long Range Benchmark
+- Genomics
+- Benchmarks
+- Language Models
+- DNA
+pretty_name: Genomics Long-Range Benchmark
 viewer: false
 ---
 
 ## Summary
-The motivation of the genomics long range benchmark (LRB) is to compile a set of biologically relevant genomic tasks requiring long-range dependencies which will act as a robust evaluation tool for genomic language models. 
+The motivation of the genomics long-range benchmark (LRB) is to compile a set of 
+biologically relevant genomic tasks requiring long-range dependencies which will act as a robust evaluation tool for genomic language models. 
 While serving as a strong basis of evaluation, the benchmark must also be efficient and user-friendly. 
 To achieve this we strike a balance between task complexity and computational cost through strategic decisions, such as down-sampling or combining datasets.
 
-## Dataset Tasks
-The Genomics LRB is a collection of tasks which can be loaded by passing in the corresponding `task_name` into the `load_dataset` function. All of the following datasets 
+## Benchmark Tasks
+The Genomics LRB is a collection of nine tasks which can be loaded by passing in the 
+corresponding `task_name` into the `load_dataset` function. All of the following datasets 
 allow the user to specify an arbitrarily long sequence length, giving more context 
 to the task, by passing the `sequence_length` kwarg to `load_dataset`. Additional task 
 specific kwargs, if applicable, are mentioned in the sections below.<br>
 *Note that as you increase the context length to very large numbers you may start to reduce the size of the dataset since a large context size may 
 cause indexing outside the boundaries of chromosomes.
 
-| Task                                 | `task_name`                            | Sample Output                                                                             | # Train Seqs | # Test Seqs |
-|--------------------------------------|----------------------------------------|-------------------------------------------------------------------------------------------| ------------ | ----------- |
-| Variant Effect Causal eQTL           | `variant_effect_causal_eqtl`           | {ref sequence, alt sequence, label, tissue, chromosome,position, distance to nearest TSS} |     88717  |     8846    |
-| Variant Effect Pathogenic Clinvar    | `variant_effect_pathogenic_clinvar`    | {ref sequence, alt sequence, label, chromosome, position}                                 |     38634  |     1018    |
-| Variant Effect Pathogenic OMIM       | `variant_effect_pathogenic_omim`       | {ref sequence, alt sequence, label,chromosome, position}                                  |     -  |     2321473    |
-| CAGE Prediction                      | `cage_prediction`                      | {sequence, labels, chromosome}                                                            |     33891        |     1922    |
-| Bulk RNA Expression                  | `bulk_rna_expression`                  | {sequence, labels, chromosome,position}                                                   |     22827       |     990     |
-| Chromatin Features Histone_Marks     | `chromatin_features_histone_marks`     | {sequence, labels,chromosome, position}                                                   |     2203689  |     227456    |
-| Chromatin Features DNA_Accessibility | `chromatin_features_dna_accessibility` | {sequence, labels,chromosome, position}                                                   |     2203689  |     227456    |
-| Regulatory Elements Promoter         | `regulatory_element_promoter`          | {sequence, label,chromosome, start, stop}                                                 |     953376  |     96240    |
-| Regulatory Elements Enhancer         | `regulatory_element_enhancer`          | {sequence, label,chromosome, start, stop}                                                 |     1914575  |     192201    |
+| Task  | `task_name` | Sample Output | ML Task Type            | # Outputs   | # Train Seqs | # Test Seqs | Data Source | 
+|-------|-------------|---------------|-------------------------|-------------|--------------|----------- |----------- |
+| Variant Effect Causal eQTL           | `variant_effect_causal_eqtl`           | {ref sequence, alt sequence, label, tissue, chromosome,position, distance to nearest TSS} | SNP Classification      | 1           | 88717        |     8846    | GTEx (via [Enformer](https://www.nature.com/articles/s41592-021-01252-x)) |
+| Variant Effect Pathogenic ClinVar    | `variant_effect_pathogenic_clinvar`    | {ref sequence, alt sequence, label, chromosome, position}                                | SNP Classification      | 1           | 38634        |     1018    | ClinVar, gnomAD (via [GPN-MSA](https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1)) |
+| Variant Effect Pathogenic OMIM       | `variant_effect_pathogenic_omim`       | {ref sequence, alt sequence, label,chromosome, position}                                 | SNP Classification      | 1           | -            |     2321473    |OMIM, gnomAD (via [GPN-MSA](https://www.biorxiv.org/content/10.1101/2023.10.10.561776v1))  |
+| CAGE Prediction                      | `cage_prediction`                      | {sequence, labels, chromosome}                                                           | Binned Regression       | 50 per bin  | 33891        |     1922    | FANTOM5 (via [Basenji](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008050)) |
+| Bulk RNA Expression                  | `bulk_rna_expression`                  | {sequence, labels, chromosome,position}                                              | Seq-wise Regression     | 218         | 22827        |     990     | GTEx, FANTOM5 (via [ExPecto](https://www.nature.com/articles/s41588-018-0160-6)) |
+| Chromatin Features Histone_Marks     | `chromatin_features_histone_marks`     | {sequence, labels,chromosome, position}                                              | Seq-wise Classification | 20          | 2203689      |     227456    | ENCODE, Roadmap Epigenomics (via [DeepSea](https://pubmed.ncbi.nlm.nih.gov/30013180/) |
+| Chromatin Features DNA_Accessibility | `chromatin_features_dna_accessibility` | {sequence, labels,chromosome, position}                                                  | Seq-wise Classification | 20          | 2203689      | 227456        | ENCODE, Roadmap Epigenomics (via [DeepSea](https://pubmed.ncbi.nlm.nih.gov/30013180/)) |
+| Regulatory Elements Promoter         | `regulatory_element_promoter`          | {sequence, label,chromosome, start, stop}                                                | Seq-wise Classification | 1|     953376   |     96240    | SCREEN |
+| Regulatory Elements Enhancer         | `regulatory_element_enhancer`          | {sequence, label,chromosome, start, stop}                                                | Seq-wise Classification | 1|     1914575  | 192201      | SCREEN |
 
 ## Usage Example
 ```python
@@ -57,190 +61,216 @@ dataset = load_dataset(
 
 ```
 
-
-
-### 1. CAGE Prediction
-Cap Analysis Gene Expression(CAGE) is a biological assay used to measure the level of mRNA production rather than steady state values, taking into account both production and 
-degradation. Being able to accurately predict mRNA levels as measured by CAGE is essential for deciphering tissue-specific expression patterns, transcriptional networks, and 
-identifying differentially expressed genes with functional significance. 
+### 1. Variant Effect Causal eQTL
+Predicting the effects of genetic variants, particularly expression quantitative trait loci (eQTLs), is essential for understanding the molecular basis of several diseases.
+eQTLs are genomic loci that are associated with variations in mRNA expression levels among individuals.
+By linking genetic variants to causal changes in mRNA expression, researchers can 
+uncover how certain variants contribute to disease development.
 
 #### Source
-Original CAGE data comes from FANTOM5. We used processed labeled data obtained from the [Basenji paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932613/) which also used to train Enformer and is located [here](https://console.cloud.google.com/storage/browser/basenji_barnyard/data/human?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false).
+Original data comes from GTEx. Processed data in the form of vcf files for positive 
+and negative variants across 49 different tissue types were obtained from the
+[Enformer paper](https://www.nature.com/articles/s41592-021-01252-x) located [here](https://console.cloud.google.com/storage/browser/dm-enformer/data/gtex_fine/vcf?pageState=%28%22StorageObjectListTable%22:%28%22f%22:%22%255B%255D%22%29%29&prefix=&forceOnObjectsSortingFiltering=false). 
 Sequence data originates from the GRCh38 genome assembly.
 
 #### Data Processing
-The original dataset from the Basenji paper includes labels for 638 CAGE total tracks over 896 bins (each bin corresponding to 128 base pairs) 
-totaling over ~70 GB. In the interest of dataset size and user-friendliness, only a 
-subset of the labels are selected. 
-From the 638 CAGE tracks, 50 of these tracks are selected with the following criteria:
-
-  1. Only select one cell line
-  2. Only keep mock treated and remove other treatments
-  3. Only select one donor
-     
-The [896 bins, 50 tracks] labels total in at ~7 GB. A description of the 50 included CAGE tracks can be found here `cage_prediction/label_mapping.csv`.
+Fine-mapped GTEx eQTLs originate from [Wang et al](https://www.nature.com/articles/s41467-021-23134-8), while the negative matched set of 
+variants comes from [Avsec et al](https://www.nature.com/articles/s41592-021-01252-x)
+. The statistical fine-mapping tool SuSiE was used to label variants. 
+Variants from the fine-mapped eQTL set were selected and given positive labels if 
+their posterior inclusion probability was > 0.9,
+as assigned by SuSiE. Variants from the matched negative set were given negative labels if their
+posterior inclusion probability was < 0.01.
 
 #### Task Structure
 
-Type: Multi-variable regression<br>
-Because this task involves predicting expression levels for 128bp bins and there are 896 total bins in the dataset, there are in essence labels for 896 * 128 = 114,688 basepair sequences. If
-you request a sequence length smaller than 114,688 bps than the labels will be subsetted.
+Type: Binary classification<br>
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length, *must be a multiple of 128 given the binned nature of labels<br>
+`sequence_length`: an integer type, the desired final sequence length<br>
 
-Input: a genomic nucleotide sequence<br>
-Output: a variable length vector depending on the requested sequence length [requested_sequence_length / 128, 50]
+Input: a genomic nucleotide sequence centered on the SNP with the reference allele at the SNP location, a genomic nucleotide sequence centered on the SNP with the alternative allele at the SNP location, and tissue type<br>
+Output: a binary value referring to whether the variant has a causal effect on gene 
+expression
 
 #### Splits
-Train/Test splits were maintained from Basenji and Enformer where randomly sampling was used to generate the splits. Note that for this dataset a validation set is also returned. In practice we merged the validation 
-set with the train set and use cross validation to select a new train and validation set from this combined set.
-
+Train: chromosomes 1-8, 11-22, X, Y<br>
+Test: chromosomes 9,10
 
 ---
 
-### 2. Bulk RNA Expression
-In comparison to CAGE, bulk RNA sequencing assays measure the steady state level (both transription and degradation) of mRNA in a population of cells.
+### 2. Variant Effect Pathogenic ClinVar
+A coding variant refers to a genetic alteration that occurs within the protein-coding regions of the genome, also known as exons.
+Such alterations can impact protein structure, function, stability, and interactions 
+with other molecules, ultimately influencing cellular processes and potentially contributing to the development of genetic diseases. 
+Predicting variant pathogenicity is crucial for guiding research into disease mechanisms and personalized treatment strategies, enhancing our ability to understand and manage genetic disorders effectively.
 
 #### Source
-Original data comes from GTEx. We use processed data files from the [ExPecto paper](https://www.nature.com/articles/s41588-018-0160-6) found 
-[here](https://github.com/FunctionLab/ExPecto/tree/master/resources). Sequence data originates from the GRCh37/hg19 genome assembly.
+Original data comes from ClinVar and gnomAD. However, we use processed data files 
+from the [GPN-MSA paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592768/) 
+located [here](https://huggingface.co/datasets/songlab/human_variants/blob/main/test.parquet).
+Sequence data originates from the GRCh38 genome assembly.
 
 #### Data Processing
-The continuous labels were log(1+x) transformed and standardized. A list of names of tissues corresponding to the labels can be found here: `bulk_rna_expression/label_mapping.csv`.
+Positive labels correspond to pathogenic variants originating from ClinVar whose review status was
+described as having at least a single submitted record with a classification but without assertion criteria.
+The negative set are variants that are defined as common from gnomAD. gnomAD version 3.1.2 was downloaded and filtered to variants with allele number of at least 25,000. Common
+variants were defined as those with MAF > 5%.
 
 #### Task Structure
 
-Type: Multi-variable regression<br>
+Type: Binary classification<br>
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length<br>
+`sequence_length`: an integer type, the desired final sequence length<br>
 
-Input: a genomic nucleotide sequence centered around the CAGE representative trancription start site<br>
-Output: a 218 length vector of continuous values corresponding to the bulk RNA expression levels in 218 different tissue types
+Input: a genomic nucleotide sequence centered on the SNP with the reference allele at the SNP location, a genomic nucleotide sequence centered on the SNP with the alternative allele at the SNP location<br>
+Output: a binary value referring to whether the variant is pathogenic or not
 
 #### Splits
-Train: chromosomes 1-7,9-22,X,Y<br>
-Test: chromosome 8
-
-#### Metrics
-Mean Spearman correlation across tissues <br>
-Mean Spearman correlation across genes <br>
-R<sup>2</sup>
+Train: chromosomes 1-7, 9-22, X, Y<br>
+Test: chromosomes 8
 
 ---
 
-### 3. Variant Effect Causal eQTL
-In genomics, a key objective is to predict how genetic variants affect gene expression in specific cell types.
+### 3. Variant Effect Pathogenic OMIM
+Predicting the effects of regulatory variants on pathogenicity is crucial for understanding disease mechanisms.
+Elements that regulate gene expression are often located in non-coding regions, and variants in these areas can disrupt normal cellular function, leading to disease.
+Accurate predictions can identify biomarkers and therapeutic targets, enhancing personalized medicine and genetic risk assessment. 
 
 #### Source
-Original data comes from GTEx. However, we used processed data files from the [Enformer paper](https://www.nature.com/articles/s41592-021-01252-x) located [here](https://console.cloud.google.com/storage/browser/dm-enformer/data/gtex_fine/vcf?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false). 
+Original data comes from the Online Mendelian Inheritance in Man (OMIM) and gnomAD 
+databases. 
+However, we use processed data files from the 
+[GPN-MSA paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592768/) located [here](
+https://huggingface.co/datasets/songlab/omim/blob/main/test.parquet).
 Sequence data originates from the GRCh38 genome assembly.
 
 #### Data Processing
-In Enformer the datasets were partitioned in 48 different sets based on the tissue types. In our framing of the task we combine all samples across all tissues into one set 
-and provide the tissue type along with each sample.
-
-As data files were used from Enformer, the labels were constructed according to their methodology - variants were labeled as 1 if their posterior inclusion probability was greater than 0.9 as 
-assigned by the population-based fine-mapping tool SuSiE, while a matched set of negative variants was built with posterior inclusion probabilities of less than .01.
+Positive labeled data originates from a curated set of pathogenic variants located 
+in the Online Mendelian Inheritance in Man (OMIM) catalog. The negative set is 
+composed of variants that are defined as common from gnomAD. gnomAD version 3.1.2 was downloaded and filtered to variants with
+allele number of at least 25,000. Common variants were defined as those with minor allele frequency
+(MAF) > 5%. 
 
 #### Task Structure
 
 Type: Binary classification<br>
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length<br>
+`sequence_length`: an integer type, the desired final sequence length<br>
+`subset`: a boolean type, whether to use the full dataset or a subset of the dataset (we provide this option as the full dataset has millions of samples)
 
-Input: a genomic nucleotide sequence centered on the SNP with the reference allele at the SNP location, a genomic nucleotide sequence centered on the SNP with the alternative allele at the SNP location, and tissue type<br>
-Output: a binary value refering to whether the variant has an effect on gene expression 
+Input: a genomic nucleotide sequence centered on the SNP with the reference allele at the SNP location, a genomic nucleotide sequence centered on the SNP with the alternative allele at the SNP location<br>
+Output: a binary value referring to whether the variant is pathogenic or not
 
 #### Splits
-Train: chromosomes 1-8, 11-22, X, Y<br>
-Test: chromosomes 9,10
+Test: all chromosomes
 
 ---
 
-### 4. Variant Effect Pathogenic ClinVar
-This task differs from the above in that variants in this datasets are linked to disease pathogenicity rather than effect on gene expression. Specifically, this tasks involves
-predicting whether a variant located in a coding region is pathogenic or is a common missense variant.
+### 4. CAGE Prediction
+CAGE provides accurate high-throughput measurements of RNA expression by mapping TSSs at a nucleotide-level resolution.
+This is vital for detailed mapping of TSSs, understanding gene regulation mechanisms, and obtaining quantitative expression data to study gene activity comprehensively.
 
 #### Source
-Original data comes from ClinVar and gnomAD. However, we use processed data files from the [GPN-MSA paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592768/) located here :https://huggingface.co/datasets/songlab/human_variants/blob/main/test.parquet .
+Original CAGE data comes from FANTOM5. We used processed labeled data obtained from 
+the [Basenji paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932613/) which 
+also used to train Enformer and is located [here](https://console.cloud.google.com/storage/browser/basenji_barnyard/data/human?pageState=%28%22StorageObjectListTable%22:%28%22f%22:%22%255B%255D%22%29%29&prefix=&forceOnObjectsSortingFiltering=false).
 Sequence data originates from the GRCh38 genome assembly.
 
 #### Data Processing
-Human labelers generated the pathogenic missense set from ClinVar. The non-pathogenic set comes from common missense variants in gnomAD.
+The original dataset from the Basenji paper includes labels for 638 CAGE total tracks over 896 bins (each bin corresponding to 128 base pairs) 
+totaling over ~70 GB. In the interest of dataset size and user-friendliness, only a 
+subset of the labels are selected. 
+From the 638 CAGE tracks, 50 of these tracks are selected with the following criteria:
+
+  1. Only select one cell line
+  2. Only keep mock treated and remove other treatments
+  3. Only select one donor
+     
+The [896 bins, 50 tracks] labels total in at ~7 GB. A description of the 50 included CAGE tracks can be found here `cage_prediction/label_mapping.csv`.
+*Note the data in this repository for this task has not already been log(1+x) normalized. 
 
 #### Task Structure
 
-Type: Binary classification<br>
+Type: Multi-variable regression<br>
+Because this task involves predicting expression levels for 128bp bins and there are 896 total bins in the dataset, there are in essence labels for 896 * 128 = 114,688 basepair sequences. If
+you request a sequence length smaller than 114,688 bps than the labels will be subsetted.
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length<br>
+`sequence_length`: an integer type, the desired final sequence length, *must be a multiple of 128 given the binned nature of labels<br>
 
-Input: a genomic nucleotide sequence centered on the SNP with the reference allele at the SNP location, a genomic nucleotide sequence centered on the SNP with the alternative allele at the SNP location<br>
-Output: a binary value referring to whether the variant is pathogenic or not
+Input: a genomic nucleotide sequence<br>
+Output: a variable length vector depending on the requested sequence length [requested_sequence_length / 128, 50]
 
 #### Splits
-Train: chromosomes 1-7, 9-22, X, Y<br>
-Test: chromosomes 8
+Train/Test splits were maintained from Basenji and Enformer where randomly sampling was used to generate the splits. Note that for this dataset a validation set is also returned. In practice we merged the validation 
+set with the train set and use cross validation to select a new train and validation set from this combined set.
+
 
 ---
 
-### 5. Variant Effect Pathogenic OMIM
-This tasks involves predicting whether a variant located in a regulatory region is 
-implicated in a mendelian disease or is a common missense variant.
+### 5. Bulk RNA Expression
+Gene expression involves the process by which information encoded in a gene directs the synthesis of a functional gene product, typically a protein, through transcription and translation.
+Transcriptional regulation determines the amount of mRNA produced, which is then translated into proteins. Developing a model that can predict RNA expression levels solely from sequence 
+data is crucial for advancing our understanding of gene regulation, elucidating disease mechanisms, and identifying functional sequence variants.
 
 #### Source
-Original data comes from the Online Mendelian Inheritance in Man (OMIM) and gnomAD 
-databases. 
-However, we use processed data files from the 
-[GPN-MSA paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592768/) located here :https://huggingface.co/datasets/songlab/omim/blob/main/test.parquet.
-Sequence data originates from the GRCh38 genome assembly.
+Original data comes from GTEx. We use processed data files from the [ExPecto paper](https://www.nature.com/articles/s41588-018-0160-6) found 
+[here](https://github.com/FunctionLab/ExPecto/tree/master/resources). Sequence data originates from the GRCh37/hg19 genome assembly.
 
 #### Data Processing
-Pathogenic variants originate from OMIM. The non-pathogenic set comes 
-from common missense variants in gnomAD.
+The authors of ExPecto determined representative TSS for Pol II transcribed genes 
+based on quantification of CAGE reads from the FANTOM5 project. The specific procedure they used is as
+follows, a CAGE peak was associated to a GENCODE gene if it was withing 1000 bps from a
+GENCODE v24 annotated TSS. The most abundant CAGE peak for each gene was then selected
+as the representative TSS. When no CAGE peak could be assigned to a gene, the annotated gene
+start position was used as the representative TSS. We log(1 + x) normalized then standardized the
+RNA-seq counts before training models. A list of names of tissues corresponding to 
+the labels can be found here: `bulk_rna_expression/label_mapping.csv`. *Note the 
+data in this repository for this task has already been log(1+x) normalized and 
+standardized to mean 0 and unit variance.
 
 #### Task Structure
 
-Type: Binary classification<br>
+Type: Multi-variable regression<br>
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length<br>
-`subset`: a boolean type, whether to use the full dataset or a subset of the dataset (we provide this option as the full dataset has millions of samples)
+`sequence_length`: an integer type, the desired final sequence length<br>
 
-Input: a genomic nucleotide sequence centered on the SNP with the reference allele at the SNP location, a genomic nucleotide sequence centered on the SNP with the alternative allele at the SNP location<br>
-Output: a binary value referring to whether the variant is pathogenic or not
+Input: a genomic nucleotide sequence centered around the CAGE representative trancription start site<br>
+Output: a 218 length vector of continuous values corresponding to the bulk RNA expression levels in 218 different tissue types
 
 #### Splits
-Test: all chromosomes
+Train: chromosomes 1-7,9-22,X,Y<br>
+Test: chromosome 8
 
 ---
 ### 6. Chromatin Features 
-Chromatin refers to the mixture of DNA and proteins that form the chromosomes and allow the DNA to exist in a compact structure. There are many factors describing the state of
-chromatin which play important roles in regulating the cell. In this task we present two features which represent chromatin state, histone marks and DNA accessibility. Histones are proteins which in combination with 
-a short strand of DNA form the basic unit of chromatin called the nucleosome. Histone marks correspond to the chemical modifications of histones which include methylation, acetylation,
-phosphorylation, and ubiquitination. DNA accessibility as measured through DNase I–hypersensitive sites refers to regions of the chromosome where DNA is not bound in a nucleosome but 
-rather is open and accessible for other proteins such as transcription factors to bind.
+Predicting chromatin features, such as histone marks and DNA accessibility, is crucial for understanding gene regulation, as these features indicate chromatin state and are essential for transcription activation.
 
 #### Source
 Original data used to generate labels for histone marks and DNase profiles comes from the ENCODE and Roadmap Epigenomics project. We used processed data files from the [Deep Sea paper](https://www.nature.com/articles/nmeth.3547) to build this dataset.
 Sequence data originates from the GRCh37/hg19 genome assembly.
 
 #### Data Processing
-As we use the data from Deep Sea the labels were generated according to the their following procedure - the genome was split into 200 base pairs bins and bins were labeled
- as 1 if more than half of the bin overlapped with the peak region of the chromatin feature annotations and 0 otherwise.
-
-Data from Deep Sea contains 919 labels for various chromatin features - 690 TF binding profiles, 125 DNase profiles and 104 histone-mark profiles. To make the dataset more accessible 
-while still providing a representative set, we randomly sampled 20 histone marks and 20 DNase tissues.
+The authors of DeepSea processed the data by chunking the human genome
+into 200 bp bins where for each bin labels were determined for hundreds of different chromatin
+features. Only bins with at least one transcription factor binding event were 
+considered for the dataset. If the bin overlapped with a peak region of the specific 
+chromatin profile by more than half of the
+sequence, a positive label was assigned. DNA sequences were obtained from the human reference
+genome assembly GRCh37. To make the dataset more accessible, we randomly sub-sampled the
+chromatin profiles from 125 to 20 tracks for the histones dataset and from 104 to 20 tracks for the
+DNA accessibility dataset.
 
 #### Task Structure
 
 Type: Multi-label binary classification
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length<br>
+`sequence_length`: an integer type, the desired final sequence length<br>
 `subset`: a boolean type, whether to use the full dataset or a subset of the dataset (we provide this option as the full dataset has millions of samples)
 
 Input: a genomic nucleotide sequence centered on the 200 base pair bin that is associated with the labels<br>
@@ -251,26 +281,29 @@ Train set: chromosomes 1-7,10-22<br>
 Test set: chromosomes 8,9
 
 ---
-### 7. Regulatory Element 
-Regulatory elements are segments of DNA that play a pivotal role in controlling gene expression and cellular processes. 
-These elements include promoters, enhancers, and other regions that interact with transcription factors and other proteins 
-to modulate the activity of genes. Identifying regulatory elements is essential for understanding the complex regulatory 
-networks governing cellular functions. 
+### 7. Regulatory Elements
+Cis-regulatory elements, such as promoters and enhancers, control the spatial and temporal expression of genes. 
+These elements are essential for understanding gene regulation mechanisms and how genetic variations can lead to differences in gene expression.
 
 #### Source
 Original data annotations to build labels came from the Search Candidate cis-Regulatory Elements by ENCODE project. Sequence data originates from the GRCh38 
 genome assembly.
 
 #### Data Processing
-To generate labels from the annotations we first split the genome into 200 base pairs bins. We label a bin as 1 if more than half of the bin overlaps with any regulatory
-element given in the annotations and 0 otherwise.
+The data is processed as follows, we break the human
+reference genome into 200 bp non-overlapping chunks. If the 200 bp chunk overlaps by at least 50%
+or more with a contiguous region from the set of annotated cis-regulatory elements (promoters or
+enhancers), we label them as positive, else the chunk is labeled as negative. The resulting dataset
+was composed of ∼15M negative samples and ∼50k positive promoter samples and ∼1M positive
+enhancer samples We randomly sub-sampled the negative set to 1M samples, and kept all positive
+samples, to make this dataset more manageable in size.
 
 #### Task Structure
 
 Type: Binary classification
 
 Task Args:<br>
-`sequence_length`: an interger type, the desired final sequence length<br>
+`sequence_length`: an integer type, the desired final sequence length<br>
 `subset`: a boolean type, whether to use the full dataset or a subset of the dataset (we provide this option as the full dataset has millions of samples)
 
 Input: a genomic nucleotide sequence centered on the 200 base pair bin that is associated with the label<br>