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Asam deoksiribonukleat
Asam deoksiribonukleat, lebih dikenal dengan singkatan DNA (bahasa Inggris: "deoxyribonucleic acid"), adalah sejenis biomolekul yang menyimpan dan menyandi instruksi-instruksi genetika setiap organisme dan banyak jenis virus. Instruksi-instruksi genetika ini berperan penting dalam pertumbuhan, perkembangan, dan fungsi organisme dan virus. DNA merupakan asam nukleat; bersamaan dengan protein dan karbohidrat, asam nukleat adalah makromolekul esensial bagi seluruh makhluk hidup yang diketahui. Kebanyakan molekul DNA terdiri dari dua unting biopolimer yang berpilin satu sama lainnya membentuk heliks ganda. Dua unting DNA ini dikenal sebagai polinukleotida karena keduanya terdiri dari satuan-satuan molekul yang disebut nukleotida. Tiap-tiap nukleotida terdiri atas salah satu jenis basa nitrogen (guanina (G), adenina (A), timina (T), atau sitosina (C)), gula monosakarida yang disebut deoksiribosa, dan gugus fosfat. Nukleotida-nukelotida ini kemudian tersambung dalam satu rantai ikatan kovalen antara gula satu nukleotida dengan fosfat nukelotida lainnya. Hasilnya adalah rantai punggung gula-fosfat yang berselang-seling. Menurut kaidah pasangan basa (A dengan T dan C dengan G), ikatan hidrogen mengikat basa-basa dari kedua unting polinukleotida membentuk DNA unting ganda
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1#1
Asam deoksiribonukleat
Dua unting DNA bersifat anti-paralel, yang berarti bahwa keduanya berpasangan secara berlawanan. Pada setiap gugus gula, terikat salah satu dari empat jenis nukleobasa. Urutan-urutan empat nukleobasa di sepanjang rantai punggung DNA inilah yang menyimpan kode informasi biologis. Melalui proses biokimia yang disebut transkripsi, unting DNA digunakan sebagai templat untuk membuat unting RNA. Unting RNA ini kemudian ditranslasikan untuk menentukan urutan asam amino protein yang dibangun.
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1#2
Asam deoksiribonukleat
Struktur kimia DNA yang ada membuatnya sangat cocok untuk menyimpan informasi biologis setiap makhluk hidup. Rantai punggung DNA resisten terhadap pembelahan kimia, dan kedua-dua unting dalam struktur unting ganda DNA menyimpan informasi biologis yang sama. Karenanya, informasi biologis ini akan direplikasi ketika dua unting DNA dipisahkan. Sebagian besar DNA (lebih dari 98% pada manusia) bersifat non-kode, yang berarti bagian ini tidak berfungsi menyandikan protein.
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1#3
Asam deoksiribonukleat
Dalam sel, DNA tersusun dalam kromosom. Semasa pembelahan sel, kromosom-kromosom ini diduplikasi dalam proses yang disebut replikasi DNA. Organisme eukariotik (hewan, tumbuhan, fungi, dan protista) menyimpan kebanyakan DNA-nya dalam inti sel dan sebagian kecil sisanya dalam organel seperti mitokondria ataupun kloroplas. Sebaliknya organisme prokariotik (bakteri dan arkaea) menyimpan DNA-nya hanya dalam sitoplasma. Dalam kromosom, protein kromatin seperti histon berperan dalam penyusunan DNA menjadi struktur kompak. Struktur kompak inilah yang kemudian berinteraksi antara DNA dengan protein lainnya, sehingga membantu kontrol bagian-bagian DNA mana sajakah yang dapat ditranskripsikan.
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1#4
Asam deoksiribonukleat
Para ilmuwan menggunakan DNA sebagai alat molekuler untuk menyingkap teori-teori dan hukum-hukum fisika, seperti misalnya teorema ergodik dan teori elastisitas. Sifat-sifat materi DNA yang khas membuatnya sangat menarik untuk diteliti bagi ilmuwan dan insinyur yang bekerja di bidang mikrofabrikasi dan nanofabrikasi material. Beberapa kemajuan di bidang material ini misalnya origami DNA dan material hibrida berbasis DNA.
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1#5
Asam deoksiribonukleat
DNA merupakan sebuah polimer yang terdiri dari satuan-satuan berulang yang disebut nukleotida. Tiap-tiap nukleotida terdiri dari tiga komponen utama, yakni gugus fosfat, gula deoksiribosa, dan basa nitrogen (nukleobasa). Pada DNA, nukleobasa yang ditemukan adalah Adenina (A), Guanina (G), Sitosina (C) dan Timina (T). Nukleobasa yang terhubung dengan sebuah gugus gula disebut sebagai nukleosida, dan nukleosida yang terhubung dengan satu atau lebih gugus fosfat disebut sebagai nukleotida. Polimer yang terdiri dari nukleotida yang saling terhubung menjadi satu rantai disebut sebagai polinukleotida. Sehingga DNA termasuk pula ke dalam polinukleotida.
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1#6
Asam deoksiribonukleat
Rantai punggung unting DNA terdiri dari gugus fosfat dan gula yang berselang-seling. Gula pada DNA adalah gula pentosa (berkarbon lima), yaitu 2-deoksiribosa. Dua gugus gula terhubung dengan fosfat melalui ikatan fosfodiester antara atom karbon ketiga pada cincin satu gula dan atom karbon kelima pada gula lainnya. Ikatan yang tidak simetris ini membuat DNA memiliki arah atau orientasi tertentu. Pada struktur heliks ganda, orientasi rantai nukleotida pada satu unting berlawanan dengan orientasi nukleotida unting lainnya. Hal ini disebut sebagai "antiparalel". Kedua ujung asimetris DNA disebut sebagai 5' (lima prima) dan 3' (tiga prima). Ujung 5' memiliki gugus fosfat terminus, sedangkan ujung 3' memiliki gugus hidroksi terminus. Salah satu perbedaan utama DNA dan RNA adalah gula penyusunnya, yakni gula 2-deoksiribosa pada DNA digantikan gula ribosa pada RNA.
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1#7
Asam deoksiribonukleat
Dalam organisme hidup, DNA biasanya ditemukan dalam bentuk berpasangan dan terikat kuat. Dua unting DNA saling berpilin membentuk heliks ganda. Heliks ganda ini distabilisasi oleh dua gaya utama: ikatan hidrogen antar nukleotida dan interaksi tumpukan antar nukleobasa aromatik. Dalam lingkungan sel yang berair, ikatan π konjugasi antar basa nukleotida tersusun tegak lurus terhadap sumbu pilinan DNA. Hal ini meminimalisasi interaksi dengan cangkang solvasi, dan sehingganya menurunkan energi bebas Gibbs.
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1#8
Asam deoksiribonukleat
Struktur DNA semua jenis spesies terdiri dari dua rantai heliks yang berpilin dengan jarak antar putaran heliks 34 Å (3,4 nanometer) dan jari-jari 10 Å (1.0 nanometer). Menurut kajian lainnya, ketika diukur menggunakan larutan tertentu, rantai DNA memiliki lebar 22-26 Å (2,2-2,6 nanometer) sedangkan satu satuan nukleotida memiliki panjang 33 Å (0,33 nm). Walaupun satuan nukleotida ini sangatlah kecil, polimer DNA dapat memiliki jutaan nukleotida yang terangkai seperti rantai. Misalnya, kromosom 1 yang merupakan kromosom terbesar pada manusia mengandung sekitar 220 juta pasangan basa.
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1#9
Asam deoksiribonukleat
Nukleobasa diklasifikasikan ke dalam dua jenis: purina (A dan G) yang berupa fusi senyawa heterolingkar beranggota lima dengan senyawa heterolingkar beranggota enam, dan pirimidina (C dan T) yang berupa cincin beranggota enam. Pirimidina lainnya, urasil (U), biasanya menggantikan timina pada DNA. Perbedaan urasil dengan timina terletak pada ketiadaan gugus metil pada cincin urasil. Selain kelima nukleobasa tersebut, terdapat pula sejumlah besar analog asam nukleat buatan yang telah disintesis untuk mengkaji sifat-sifat asam nukleat dan digunakan dalam bioteknologi.
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1#10
Asam deoksiribonukleat
Urasil biasanya tidak ditemukan dalam DNA (ditemukan dalam sel hanya sebagai produk uraian sitosina). Namun pada sejumlah bakteriofag– bakteriofag PBS1 dan PBS2 "Bacillus subtilis" dan bakteriofag piR1-37 "Yersinia"– timina telah digantikan oleh urasil. Fag lainnya - fag S6 Staphylococcus - juga telah diidentifikasi mempunyai urasil pada genomnya.
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1#11
Asam deoksiribonukleat
Basa J (beta-d-glukopiranosiloksimetilurasil) yang merupakan bentuk modifikasi dari urasil juga dapat ditemukan pada sejumlah organisme: flagellata "Diplonema" dan "Euglena", dan seluruh organisme marga kinetoplastid Biosintesis basa J terjadi dalam dua tahap: pada tahap pertama, basa timina spesifik pada DNA diubah menjadi hidroksimetildeoksiuridina (HOMedU); pada tahap kedua HOMedU diglikosilasi menjadi basa J. Protein-protein yang mengikat basa J ini juga telah berhasil diidentifikasi. Protein-protein ini tampaknya merupakan kerabat jauh dari onkogen Tet1 yang terlibat dalam patogenesis leukimia myeloid akut. Basa J tampaknya bekerja sebagai sinyal terminasi untuk RNA polimerase II.
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MIRACL (id) embedded with cohere.ai multilingual-22-12 encoder

We encoded the MIRACL dataset using the cohere.ai multilingual-22-12 embedding model.

The query embeddings can be found in Cohere/miracl-id-queries-22-12 and the corpus embeddings can be found in Cohere/miracl-id-corpus-22-12.

For the orginal datasets, see miracl/miracl and miracl/miracl-corpus.

Dataset info:

MIRACL 🌍🙌🌏 (Multilingual Information Retrieval Across a Continuum of Languages) is a multilingual retrieval dataset that focuses on search across 18 different languages, which collectively encompass over three billion native speakers around the world.

The corpus for each language is prepared from a Wikipedia dump, where we keep only the plain text and discard images, tables, etc. Each article is segmented into multiple passages using WikiExtractor based on natural discourse units (e.g., \n\n in the wiki markup). Each of these passages comprises a "document" or unit of retrieval. We preserve the Wikipedia article title of each passage.

Embeddings

We compute for title+" "+text the embeddings using our multilingual-22-12 embedding model, a state-of-the-art model that works for semantic search in 100 languages. If you want to learn more about this model, have a look at cohere.ai multilingual embedding model.

Loading the dataset

In miracl-id-corpus-22-12 we provide the corpus embeddings. Note, depending on the selected split, the respective files can be quite large.

You can either load the dataset like this:

from datasets import load_dataset
docs = load_dataset(f"Cohere/miracl-id-corpus-22-12", split="train")

Or you can also stream it without downloading it before:

from datasets import load_dataset
docs = load_dataset(f"Cohere/miracl-id-corpus-22-12", split="train", streaming=True)

for doc in docs:
    docid = doc['docid']
    title = doc['title']
    text = doc['text']
    emb = doc['emb']

Search

Have a look at miracl-id-queries-22-12 where we provide the query embeddings for the MIRACL dataset.

To search in the documents, you must use dot-product.

And then compare this query embeddings either with a vector database (recommended) or directly computing the dot product.

A full search example:

# Attention! For large datasets, this requires a lot of memory to store
# all document embeddings and to compute the dot product scores.
# Only use this for smaller datasets. For large datasets, use a vector DB

from datasets import load_dataset
import torch

#Load documents + embeddings
docs = load_dataset(f"Cohere/miracl-id-corpus-22-12", split="train")
doc_embeddings = torch.tensor(docs['emb'])

# Load queries 
queries = load_dataset(f"Cohere/miracl-id-queries-22-12", split="dev")

# Select the first query as example
qid = 0
query = queries[qid]
query_embedding = torch.tensor(queries['emb'])

# Compute dot score between query embedding and document embeddings
dot_scores = torch.mm(query_embedding, doc_embeddings.transpose(0, 1))
top_k = torch.topk(dot_scores, k=3)

# Print results
print("Query:", query['query'])
for doc_id in top_k.indices[0].tolist():
    print(docs[doc_id]['title'])
    print(docs[doc_id]['text'])

You can get embeddings for new queries using our API:

#Run: pip install cohere
import cohere
co = cohere.Client(f"{api_key}")  # You should add your cohere API Key here :))
texts = ['my search query']
response = co.embed(texts=texts, model='multilingual-22-12')
query_embedding = response.embeddings[0] # Get the embedding for the first text

Performance

In the following table we compare the cohere multilingual-22-12 model with Elasticsearch version 8.6.0 lexical search (title and passage indexed as independent fields). Note that Elasticsearch doesn't support all languages that are part of the MIRACL dataset.

We compute nDCG@10 (a ranking based loss), as well as hit@3: Is at least one relevant document in the top-3 results. We find that hit@3 is easier to interpret, as it presents the number of queries for which a relevant document is found among the top-3 results.

Note: MIRACL only annotated a small fraction of passages (10 per query) for relevancy. Especially for larger Wikipedias (like English), we often found many more relevant passages. This is know as annotation holes. Real nDCG@10 and hit@3 performance is likely higher than depicted.

Model cohere multilingual-22-12 nDCG@10 cohere multilingual-22-12 hit@3 ES 8.6.0 nDCG@10 ES 8.6.0 acc@3
miracl-ar 64.2 75.2 46.8 56.2
miracl-bn 61.5 75.7 49.2 60.1
miracl-de 44.4 60.7 19.6 29.8
miracl-en 44.6 62.2 30.2 43.2
miracl-es 47.0 74.1 27.0 47.2
miracl-fi 63.7 76.2 51.4 61.6
miracl-fr 46.8 57.1 17.0 21.6
miracl-hi 50.7 62.9 41.0 48.9
miracl-id 44.8 63.8 39.2 54.7
miracl-ru 49.2 66.9 25.4 36.7
Avg 51.7 67.5 34.7 46.0

Further languages (not supported by Elasticsearch):

Model cohere multilingual-22-12 nDCG@10 cohere multilingual-22-12 hit@3
miracl-fa 44.8 53.6
miracl-ja 49.0 61.0
miracl-ko 50.9 64.8
miracl-sw 61.4 74.5
miracl-te 67.8 72.3
miracl-th 60.2 71.9
miracl-yo 56.4 62.2
miracl-zh 43.8 56.5
Avg 54.3 64.6
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