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DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
A lexical database tool tailored for phonological research is described. Database fields include transcriptions, glosses and hyperlinks to speech files. Database queries are expressed using HTML forms, and these permit regular expression…
Since the birth of computer and networks, fuelled by pervasive computing and ubiquitous connectivity, the amount of data stored and transmitted has exponentially grown through the years. Due to this demand, new solutions for storing data…
Image compression techniques have made remarkable progress when it comes to file size reduction with a tolerable quality reduction; nonetheless, they are facing some challenges when it comes to applying more compression with the same…
Linked-Reads technologies, such as 10x Genomics, combine both the high-quality and low cost of short-reads sequencing and a long-range information, through the use of barcodes able to tag reads which originate from a common long DNA…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
The analysis of DNA sequences has become critical in numerous fields, from evolutionary biology to understanding gene regulation and disease mechanisms. While deep neural networks can achieve remarkable predictive performance, they…
Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative…
Multilingual dense retrieval aims to retrieve relevant documents across different languages based on a unified retriever model. The challenge lies in aligning representations of different languages in a shared vector space. The common…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
Compression techniques that support fast random access are a core component of any information system. Current state-of-the-art methods group documents into fixed-sized blocks and compress each block with a general-purpose adaptive…
Efficient similarity retrieval from large-scale multimodal database is pervasive in modern search engines and social networks. To support queries across content modalities, the system should enable cross-modal correlation and…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Information retrieval models that aim to search for documents relevant to a query have shown multiple successes, which have been applied to diverse tasks. Yet, the query from the user is oftentimes short, which challenges the retrievers to…
In this paper, we study methods for improving the efficiency and privacy of compressed DNA sequence comparison computations, under various querying scenarios. For instance, one scenario involves a querier, Bob, who wants to test if his DNA…
Multi-modal datasets, like those involving images, often miss the detailed descriptions that properly capture the rich information encoded in each item. This makes answering complex natural language queries a major challenge in this domain.…
We introduce SupercheQ, a family of quantum protocols that achieves asymptotic advantage over classical protocols for checking the equivalence of files, a task also known as fingerprinting. The first variant, SupercheQ-EE (Efficient…
Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the…
We present CREST (Compact Retrieval-Based Speculative Decoding), a redesign of REST that allows it to be effectively "compacted". REST is a drafting technique for speculative decoding based on retrieving exact n-gram matches of the most…