Datasets:
_id stringlengths 1 3 | text stringlengths 197 4.98k |
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1 | Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?/nThe SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it...
1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct
61 gttctctaaa cgaactttaa aatctgtgtg gctgtcactc ggctg... |
2 | What's the most efficient file format for the storage of DNA sequences?/nI'd like to learn which format is most commonly used for storing the full human genome sequence (4 letters without a quality score) and why.
I assume that storing it in plain-text format would be very inefficient. I expect a binary format would be... |
3 | Why sequence the human genome at 30x coverage?/nA bit of a historical question on a number, 30 times coverage, that's become so familiar in the field: why do we sequence the human genome at 30x coverage?
My question has two parts:
Who came up with the 30x value and why?
Does the value need to be updated to reflect toda... |
7 | How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq?/nIn single-cell RNA-seq data we have an inflated number of 0 (or near-zero) counts due to low mRNA capture rate and other inefficiencies.
How can we decide which genes are 0 due to gene dropout (lack of measurement sensitivity), an... |
9 | Difference between CPM and TPM and which one for downstream analysis?/nWhat the difference between TPM and CPM when dealing with RNA seq data?
What metrics would you use if you have to perform some down stream analysis other than Differential expression for eg.
Clustering analysis using Hclust function and then plottin... |
10 | How do I carry out an ancestry/admixture test on a single VCF file?/nThis is a question from /u/beneficii9 on reddit. The original post can be found here.
Through the Personal Genome Project, I have had my whole genome sequenced by Veritas, and have it in the form of a single VCF file for the whole genome and one BAS f... |
11 | Fast way to count number of reads and number of bases in a fastq file?/nI am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using zgrep and awk:
zgrep . foo.fastq.gz |
awk '... |
12 | How to simulate NGS reads, controlling sequence coverage?/nI have a FASTA file with 100+ sequences like this:
>Sequence1
GTGCCTATTGCTACTAAAA ...
>Sequence2
GCAATGCAAGGAAGTGATGGCGGAAATAGCGTTA
......
I also have a text file like this:
Sequence1 40
Sequence2 30
......
I would like to simulate next-generation paired-end re... |
13 | Generic HMM solvers in bioinformatics?/nHidden Markov models (HMMs) are used extensively in bioinformatics, and have been adapted for gene prediction, protein family classification, and a variety of other problems. Indeed, the treatise by Durbin, Eddy and colleagues is one of the defining volumes in this field.
Althoug... |
14 | Is there a standard k-mer count file format?/nI am doing a research project involving calculating k-mer frequencies and I am wondering if there is any standard file format for storing k-mer counts. |
15 | What to use to edit RNA alignments?/nI have many alignments from Rfam Database, and I would like to edit them. I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ?
e.g. Stockholm Alignment of Pistol (just few entries).
FP929053.1/1669026-1668956 AGUG... |
16 | Are there any databases of templates for common bioinformatic file formats?/nI want some templates of different file formats that I can use to test my scripts and identify possible bugs in my code.
For example, consider nucleotide FASTA, a simple but often abused format, I would want templates to capture regular and ir... |
17 | Normalization methods with RNA-Seq ERCC spike in?/nERCC spike-in is a set of synthetic controls developed for RNA-Seq. I'm interested in using it to normalize my RNA-Seq samples. In particular, I'd like to use the spike-ins to remove technical bias and any variation that should not be part of my analysis.
The site does... |
18 | Are fgsea and Broad Institute GSEA equivalent?/nSeveral gene set enrichment methods are available, the most famous/popular is the Broad Institute tool. Many other tools are available (See for example the biocView of GSE which list 82 different packages). There are several parameters in consideration :
the statistic use... |
19 | Compare alignment quality of multiple sequencing runs aligned against the same reference genome/nI have run Oxford Nanopore Technologies' MinION sequencing on the same DNA sample using three flowcells, each aligned against the same reference genome (E.coli K12 MG1655) using both BWA MEM and GraphMap and stored as BAM f... |
20 | How to download FASTA sequences from NCBI using the terminal?/nI have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
NC_030850.1
NC_030851.1
NC_030852.1
NC_030853.1
NC_030854.1
NC_030855.1
NC_030856.1
NC_030857.1
NC_030858.1
NC_030859.1
I need to download these FASTA files using the termin... |
21 | How to select high quality structures from the Protein Data Bank?/nModels of structures deposited in the Protein Data Bank vary in the quality, depending both on the data quality and expertise and patience of the person who built the model. Is there a well-accepted subset of the PDB entries that has only "high quality"... |
22 | Converting VCF file to PLINK bed/bim/fam files/nI am trying to find the best way to convert VCF files to PLINK binary bed/bim/fam files, but it seems like there are many varied ways to do this. (For example, using Plink 1.9 --vcf tag, bcftools, GATK, and vcftools).
Obviously they all probably have their uses and you co... |
23 | What is the best method to estimate a phylogenetic tree from a large dataset of >1000 loci and >100 species/nI have a large phylogenomic alignment of >1000 loci (each locus is ~1000bp), and >100 species. I have relatively little missing data (<10%).
I want to estimate a maximum-likelihood phylogenetic tree from this da... |
24 | Converting a VCF into a FASTA given a reference with Python, R/nI am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R.
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)
This script has been modified by oth... |
25 | How to quickly determine mutations in a read of a sam file?/nAfter DNA sequencing, I generated a sam file through alignment of a fastq file. Before using well known variant calling programs (eg. Annovar etc.), I want to pick some reads and know what kinds of mutations are there.
Is there any quick way of doing it? |
26 | Duplicate genes with RSEM counts: Which one to choose?/nI have Ensembl ids in the first column and samples with RSEM counts data in other columns. I converted Ensembl ids to gene symbols. Now I see there are three genes repeated twice.
Gene S1 S2 S3
COG8 804.07 1475.16 323.80
COG8 249.23 867.94 113... |
27 | What is deep sequencing?/nPeople talk about deep sequencing. Is there any way to calculate how deep the sequencing is ? What should be the optimum depth to get reliable data ?
I am doing whole genome sequencing of a virus genome which is 10 kb long. I got 80000 reads from Illumina sequencing. Is there any way to tell a... |
28 | Ultimate reproducibility in R?/nI'm looking for a convenient and reliable way to make an R analysis reproducible, either at different times or across collaborators.
Listing the package versions or a sessionInfo() output is not very helpful, as it leaves the work of re-creating the environment entirely to you.
As I see,... |
30 | Is there a standard definition for "assembly polishing"?/nIs there a standard definition for "assembly polishing" in the field?
Is there a standard definition for what polishing algorithms do?
My understanding of "polishing" is strongly influenced by Pilon:
Whereby users input a reference FASTA along with the BAM of al... |
31 | Convert R RNA-seq data object to a Python object/nI have done some work in R and would like to try a Python tool.
What is a good way to import the data (and its annotations etc) as a Python object?
I am particularly interested in converting a Seurat object into an AnnData object. (Either directly or as a Python object ... |
32 | How to count reads in bam per bed interval with bedtools/nI recently installed Ubuntu 16.04 (because I was still using 12.04). But it seems my bedtools scripts don't work properly anymore. I can't figure out how to use the new bedtools for my old ways. What I want to do is get the number of reads from a bam file, per i... |
33 | Are mitochondrial genes to exclude in scRNA-seq such as ribosomal genes?/nIn this answer, it is stated that ribosomal genes should be excluded prior to normalization in scRNA-seq as contaminants.
Do mitochondrial genes have to be excluded as well? I plotted the top 50 expressed genes for a specific dataset and they ten... |
34 | samtools depth print out all positions/nI am trying to use samtools depth (v1.4) with the -a option and a bed file listing the human chromosomes chr1-chr22, chrX, chrY, and chrM to print out the coverage at every position:
cat GRCh38.karyo.bed | awk '{print $3}' | datamash sum 1
3088286401
I would like to know how to r... |
35 | PDB format: remark number for free text/nI would like to add a text to PDB files that I'm processing with my tool, rna-pdb-tools. Someone points that the way I'm using it right now it's not correct (https://github.com/mmagnus/rna-pdb-tools/issues/48).
I use HEADER right now which is not correct.
HEADER Generated with r... |
38 | Least present k-mers in the human genome/nWhat are the least present k-mers in the human genome at different sizes?
Starting with k=4 and going up in size until k=10, what are the k-mers least seen (or not at all) in the human genome? I am only interested in the reference human genome, so I am discounting SNPs/Indels i... |
39 | What reasons are there to choose Illumina if PacBio provides longer and better reads?/nPacBio provides longer read length than Illumina's short-length reads. Longer reads offer better opportunity for genome assembly, structural variant calling. It is not worse than short reads for calling SNP/indels, quantifying transc... |
40 | What is 'k' in sequencing?/nWhen a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an answer for what 'k' represents but I don't quite recall. It can't just be an anomaly in tha... |
41 | How to manipulate a reference FASTA or bam to include variants from a VCF?/nI have some software which takes fastas as the input. I need to include SNVs and InDels from a VCF into the reference hg38 and then use this.
The problem is, I don't know of an algorithmically sound way to do this.
Are there any existing softwa... |
42 | How is the GT field in a VCF file defined?/nAs my question in SO was closed and asked to be posted in this forum, I am posting it here.
I am not from the bioinformatics domain. However, for the sake of analysis, I am trying to pick up certain basics related to the GT field in the VCF file.
I know we have a field called... |
44 | How should the popular press compare similarity of genomes?/nNote this is a question from a lay reader.
I've read in the popular press that ~1-4% of the genome of non-African Homo sapiens is inherited from Neanderthals, or that Melanesians derive a similar amount from the Denisovans.
This seems like a lot, until you re... |
45 | How can the cell line contribution be estimated from RNASeq data?/nUsing a laser-capture microdissection of cells a group of cells stained with the marker of interest was sequenced. In another cohort of patients (this is all human liver tissue) the whole tissue was sequenced (RNA-seq in both cases)
Can I estimate the c... |
47 | How GFF3 attributes (9th column) varies from one gene prediction algorithm to another/nGFF3 files are in tabular format with 9 fields per line, separated by tabs. The first 8 fields share almost same data structure, but the 9th field varies a lot depending on feature type and gene prediction algorithm.
Presently I am t... |
48 | estimate genome size: kmer-based approach from PacBio reads/nCan anyone suggest a software/method for kmer analysis using PacBio reads (RSII)?
Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. kmercounterexact from BBMapTools might also be an option, but again t... |
49 | Publicly available, free, complete database for antibiotics names and classes?/nThis is a tough one I think: is there a publicly available, up-to-date, free, complete database for antibiotics names and classes?
I am specifically looking for information like, e.g., cefpirome (is a) cephalosporin.
I've looked in a couple... |
50 | Tumor purity/contamination/admixture estimation/nCan anyone recommend a good tool for estimating the tumor content given a matched tumor and normal file for DNA NGS whole genome sequencing data or whole exome data?
Is it possible to estimate this without a normal sample as well? |
51 | Phyre2 vs ITasser, completely different models generated/nDoes anyone have experience generating pdb structures with Phyre and ITasser online tools. The results generated from each given the same amino acid sequence input are very different and I am wondering whether or not this is a usual experience. I know ITasser wa... |
52 | Understanding the significance of BLAT score calculations for read fragment alignment/nI'm attempting to reconstruct the read fragments that form a hit to a target, excluding/skipping gaps. BLAST's outfmt 6, and alternatives such as Diamond's M8 format only give the number of gap opens on the alignment. One can't just ... |
53 | What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line/nI have two DNA strings:
GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC
and
AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG
I want a tool that allows me to do something like this on the command line:
$ aligner GGAGGA... |
54 | How to concatenate "by chromosome"-VCFs?/nI have a several VCFs which are VCF which only contain information by chromosome. That is, there's a chromosome 1 VCF (with only chr1), a chromosome 2 VCF (with only chr2), etc.
I checked to make sure that these VCFs were valid via VCFtools, i.e.
$ vcf-validator chr1.vcf
which ... |
55 | A good tool for gene locus visualization/nDoes anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to plug it into and get an image of the locus to compare.
I'm talking something b... |
56 | Is there a way to retrieve several SAM fields faster than `samtools view | cut -f`?/nI am constructing a bit of software which pipes the outputs of the bam file via samtools view into a script for parsing. My goal is to (somehow) make this process more efficient, and faster than samtools view.
I am only using 3-4 field... |
58 | Importing GFF file with Biopython/nIs there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?
For example,
from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)
This wi... |
59 | How to release an R package with several bed files?/nI'm currently creating an R package, and my scripts require before any analysis is done that 1-2 bed files be loaded. Normally, I would run the scripts with the following:
library(data.table)
session_bed = read.table("/path/name/to/bedfile.bed")
and then refer to ses... |
60 | Is there a command line tool to split a SAM/BAM file by CB (cell barcode) tag?/nI have a BAM file from a single cell sequencing experiment. Each read has had the cell barcode annotated in the CB tag. Some reads do not have a CB tag. For each of an arbitrary set of barcodes, I would like to split out the reads for each ... |
61 | Visualization tools for 3C/Hi-C long-range interaction data?/nI have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.
After viewing it in the UCSC genome browser, I have confirmed that it does not overlap any annotated gene promoters, gene bo... |
62 | visualisation of genome alignment/nI was asked to check the synteny of some genes in two genome assemblies of the same species (PacBio & Illumina). I was given two scaffolds couples (so 4 scaffolds total) in the Illumina genome and asked if they were assembled together in the PacBio assembly.
So, I proceeded with a DNA... |
64 | Multithread fastq processing with kseq.h in C++11?/nBackground
I am using the wonderful kseq.h as my fastq/fasta parser for a C++ project. My actual implementation uses something like this, where I am counting kmers of each sequence and performing a bunch of other processing on every read pair.
Thanks to @user1782818's... |
65 | How to represent a deletion at position 1 in a VCF file?/nI am writing a small script to write a VCF file from short multiple sequence alignments, and stumbled into an interesting corner case.
This is the way a deletion should be represented in VCF format (I assume version 4+):
NC_000016.9 2138199 rs1799758 GTGAG ... |
67 | What's a template switching site?/nReading Islam et al. (2011):
From each transcript, a single read is obtained, corresponding to a template-switching site located preferentially at the 59 end of the mRNA.
By reading this page I think that a template switching site is an additional set of nucleotides added at the 3' en... |
69 | How to make chromosome color maps for bed ranges/nI have genomic .bed file data of 4 different types; type A,B,C,D. These are some examples-
Type A:
1 101380000 101710000 A
1 110085000 110320000 A
Type B:
1 100930000 101335000 B
1 10430000 10560000 B
Type C:
1 101775000 101825000 C
1 1... |
73 | validating identified sub-populations of cells in scRNA-seq/nIn the analyses of single-cell RNA-seq data there are different unsupervised approaches to identify putative subpopulations (e.g. as available with Suerat or SCDE packages).
Is there a good way of computationally validating the cluster solutions? Different me... |
74 | Convert rs ID of one hg build to rs IDs of another build/nI have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150 as of the time of this post). Is there any ID mapping available? If not, are there any tools I can use? |
76 | What is this 5-column sequencing format from 2009?/nThere is high throughput sequencing data here, and I don't know what format it is in.
It was submitted in 2009, and the description says the following:
Library strategy: ncRNA-Seq
Library source: transcriptomic
Library selection: size fractionation
Instrument model: I... |
77 | Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?/nI'm working with scATAC-Seq data on the K562 cell line, which is supposed to be derived from a female patient. While following the scATAC-seq data analysis pipeline, after performing bowtie alignment they recommend filtering out all reads a... |
78 | Human Cell Atlas - Data availability/nA news item from 2017-10-18 on the website of the Human Cell Atlas states:
In addition, the consortium today also announced the impending release of gene expression profiles from the first one million immune cells collected under the HCA, toward an initial milestone of collecting a... |
79 | What are some good practices to follow during EPIC DNA methylation data analysis?/nI recently got some EPIC DNA methylation data and I was wondering what are some good practices to follow? I am interested in knowing about normalization and differential analysis. Thank you. |
81 | Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?/nI believe that the human genome reference took DNA samples from different people and that some natural variation is included in extra contigs.
However, the human reference genome comes from a limited number of peo... |
83 | Searching for gene expression data by cell line/nI have two cancer cell lines (OCI-Ly18 & riva) that I want to find gene expression data for, but I'm not aware of many gene expression databases that allow searching by cell-line without searching by gene.
I tried Genevestigator on the recommendation of this thread but f... |
87 | Where can I find a database that has phenotype information together with associated SNPs?/nI have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association. Moreover, for some species,... |
88 | What does "fetching by region is not available for SAM files" mean?/nI am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant pysam. So I looked at the manual, but ran into quite bizarre troubles with the first couple of lines using my bam file
import pysam
samfi... |
90 | Error creating indices using STAR/nI am trying to index wheat genome using STAR through following command
STAR --runMode genomeGenerate --genomeFastaFiles Triticum_aestivum.TGACv1.dna_sm.toplevel.fa --runThreadN 28
But getting following error,
terminate called after throwing an instance of 'std::bad_alloc'
what(): st... |
91 | What are the ways to process a list of differentially expressed genes?/nWe are studying six different human macrophage/dendritic cell types isolated from healthy skin. They all differ from each other in a few cell surface markers.
We are interested in the characteristics of each cell type ("marker" genes or biological ... |
92 | Why are Minimap2 alignments different with CIGAR generation flag?/nI am using Minimap2 (v2.26-r1175) in Linux to generate a sequence alignment between the Streptomyces coelicolor A3(2) chromosome (ref.fa) and the Mycobacterium tuberculosis chromosome (query.fa). My desired output is a PAF (Pairwise mApping Format) file... |
93 | Major variability in speed of BLAST between proteins/nI'm running blast+ searches for a list of proteins using specific parameters.
This is my search
blastp -query protein.fasta -remote -db refseq_protein -out
protein_refseq_blast.txt -outfmt '6 qseqid sseqid qstart qend length evalue' -
entrez_query 'txid2 [ORGN] or... |
94 | Smallest group size for differential expression in limma (bulk RNA-Seq)/nI am reading Smyth et al. (ref. 1). I want to run differential expression analysis on a bulk RNA-Seq dataset in which each group is composed by 2 samples. In the paper previously cited it is written that:
Genes must be expressed in at least one gr... |
96 | Fasta Sequence Identifier format?/nI have been analyzing some virus DNA from the NCBI databases. The fasta sequences that I recieve from them have header lines that look like this:
>gi|61393989|gb|AY848686.1|
I think that the second number is the GenBank ID, but I have several questions:
1) What does the "gi" in the fi... |
99 | Which are the use cases for the methods for DE in Seurat/nIn Seurat we can specify multiple methods for finding DE genes.
I am wondering when should we use which one, the use cases. As I understand, whole Seurat package is used for single cell sequencing analysis. I ran different methods for my dataset that was produce... |
101 | Are there certain alignment methods/tools which perform better with a high density of indels?/nI have a set of experiments which should result in WGS reads with a high density of indels.
Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? I'm not very interested in ... |
102 | Can I index a compressed FASTA file using STAR?/nI am using STAR to align RNA-seq reads to a reference genome. Before the alignment, I need to generate an index of the reference genome. I use the following code to generate the index successfully:
STAR --runThreadN 8 --runMode genomeGenerate --genomeDir output/index/sta... |
103 | Can index hopping lead to more reads in samples?/nWe run multiple samples for sequencing on an Illumina NovaSeq machine. After converting the files to fastq format using bcl2fastq, we can see that we have some trouble with index hopping.
The image attached here shows the structure of the indices, how they are supposed ... |
104 | How to use SBOL (Synthetic Biology Open Language)?/nOne of my students is working on the development of a SynBio tool to design and represent genetic circuits in a standardized format. I know there are some libraries out there.
What I am interested in finding out is to have a hands-on tutorial how to use an SBOL librar... |
NanoR2MED
This dataset is a Nano-style retrieval dataset for HAKARI-bench.
NanoR2MED contains 8 Nano retrieval splits derived from R2MED. Each split keeps up to 200 eligible queries and up to 10000 corpus documents, with exact duplicate query and document text removed where the generator records that policy.
Usage
from datasets import load_dataset
dataset_id = "hakari-bench/NanoR2MED"
split = "NanoR2MEDBioinformatics"
queries = load_dataset(dataset_id, "queries", split=split)
corpus = load_dataset(dataset_id, "corpus", split=split)
qrels = load_dataset(dataset_id, "qrels", split=split)
reranking_candidates = load_dataset(dataset_id, "reranking_hybrid", split=split)
Data Layout
This dataset uses six Hugging Face Datasets configs:
corpus: documents with_idandtextqueries: queries with_idandtextqrels: positive relevance labels withquery-idandcorpus-idbm25: BM25 candidate lists withquery-idandcorpus-idsharrier_oss_v1_270m: dense candidate lists frommicrosoft/harrier-oss-v1-270mreranking_hybrid: RRF candidate lists built frombm25andharrier_oss_v1_270m
Each config has the same Nano split names.
Candidate Construction
bm25: local BM25 top-500 with automatic language-aware tokenization. The resolved tokenizer is shown in the Candidate Quality table, for examplewordseg@ja.harrier_oss_v1_270m: dense top-500 frommicrosoft/harrier-oss-v1-270m. In tables this is shown asDense; Dense meansmicrosoft/harrier-oss-v1-270mwith theweb_search_queryprompt for queries and cosine similarity over normalized embeddings.reranking_hybrid: RRF overbm25andharrier_oss_v1_270musingrrf_k=100, keeping the RRF top-100.
Safeguard means rank 101 is appended only when RRF top-100 contains no qrels-positive document.
Split Statistics
Length statistics are character counts computed with len(str(text)).
| Nano split | Queries | Corpus | Qrels | Query chars avg | Query chars p50 | Query chars p75 | Doc chars avg | Doc chars p50 | Doc chars p75 |
|---|---|---|---|---|---|---|---|---|---|
| NanoR2MEDBioinformatics | 77 | 10000 | 226 | 890.3 | 727.0 | 1016.0 | 666.8 | 679.0 | 798.0 |
| NanoR2MEDBiology | 103 | 10000 | 374 | 523.0 | 440.0 | 627.5 | 474.1 | 397.0 | 556.0 |
| NanoR2MEDIIYiClinical | 129 | 10000 | 457 | 2584.1 | 2523.0 | 3306.0 | 5042.3 | 4280.5 | 6809.5 |
| NanoR2MEDMedQADiag | 118 | 10000 | 522 | 706.7 | 630.0 | 884.0 | 791.4 | 882.0 | 989.0 |
| NanoR2MEDMedXpertQAExam | 97 | 10000 | 292 | 928.4 | 879.0 | 1086.0 | 723.9 | 767.0 | 922.0 |
| NanoR2MEDMedicalSciences | 88 | 10000 | 244 | 477.6 | 378.0 | 596.8 | 678.6 | 679.0 | 801.0 |
| NanoR2MEDPMCClinical | 114 | 10000 | 248 | 827.7 | 832.0 | 956.8 | 2103.5 | 2131.0 | 2724.0 |
| NanoR2MEDPMCTreatment | 150 | 10000 | 315 | 1755.8 | 1750.5 | 1980.8 | 726.6 | 608.0 | 928.0 |
Candidate Quality
nDCG@10 and Recall@100 are computed from the included candidate rankings against the included qrels, then reported as 0-100 scores such as 52.45. Recall@100 uses only the top 100 candidates; an optional rank-101 safeguard positive is not counted in Recall@100.
Dense means microsoft/harrier-oss-v1-270m with the web_search_query prompt and cosine similarity.
| Nano split | BM25 tokenizer | BM25 nDCG@10 | Dense nDCG@10 | Hybrid nDCG@10 | BM25 Recall@100 | Dense Recall@100 | Hybrid Recall@100 | Hybrid candidates | Safeguard positives |
|---|---|---|---|---|---|---|---|---|---|
| Mean | - | 20.94 | 30.07 | 28.82 | 55.11 | 68.46 | 70.40 | - | 122 |
| NanoR2MEDBioinformatics | english_porter_stop | 21.89 | 34.25 | 26.23 | 67.34 | 75.92 | 80.48 | 100-101 | 6 |
| NanoR2MEDBiology | english_porter_stop | 34.55 | 49.53 | 47.22 | 70.56 | 82.57 | 85.61 | 100-101 | 3 |
| NanoR2MEDIIYiClinical | english_porter_stop | 14.82 | 18.70 | 19.75 | 47.30 | 66.15 | 67.21 | 100-101 | 14 |
| NanoR2MEDMedQADiag | english_porter_stop | 7.00 | 12.54 | 14.06 | 25.10 | 46.74 | 42.14 | 100-101 | 34 |
| NanoR2MEDMedXpertQAExam | english_porter_stop | 2.77 | 15.99 | 9.79 | 19.94 | 47.09 | 43.55 | 100-101 | 33 |
| NanoR2MEDMedicalSciences | english_porter_stop | 21.40 | 35.67 | 33.20 | 74.86 | 85.61 | 85.66 | 100-101 | 3 |
| NanoR2MEDPMCClinical | english_porter_stop | 39.33 | 35.84 | 44.77 | 81.58 | 76.61 | 86.48 | 100-101 | 6 |
| NanoR2MEDPMCTreatment | english_porter_stop | 25.80 | 38.01 | 35.55 | 54.18 | 66.97 | 72.04 | 100-101 | 23 |
Hybrid Safeguard Summary
- Safeguard positives: 122
- Rows limited by corpus size: 0
- Metadata file:
reranking_hybrid_metadata.json
Source Links
- Source benchmark:
R2MED R2MED/Bioinformatics: https://huggingface.co/datasets/R2MED/BioinformaticsR2MED/Biology: https://huggingface.co/datasets/R2MED/BiologyR2MED/IIYi-Clinical: https://huggingface.co/datasets/R2MED/IIYi-ClinicalR2MED/MedQA-Diag: https://huggingface.co/datasets/R2MED/MedQA-DiagR2MED/MedXpertQA-Exam: https://huggingface.co/datasets/R2MED/MedXpertQA-ExamR2MED/Medical-Sciences: https://huggingface.co/datasets/R2MED/Medical-SciencesR2MED/PMC-Clinical: https://huggingface.co/datasets/R2MED/PMC-ClinicalR2MED/PMC-Treatment: https://huggingface.co/datasets/R2MED/PMC-Treatment
License
NanoR2MED is a derived dataset. Users must comply with the licenses, terms, and attribution requirements of the upstream datasets and benchmarks.
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