Sequence-Aligned File Compression Using Warm-Start Consensus Pointers
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Solution Overview
Problem
Current data compression methods are inefficient in reducing storage and bandwidth requirements, particularly when dealing with large files, as they fail to effectively align and compress data sequences, leading to suboptimal compression ratios and increased computational resources.
Innovation Solution
A compression engine that utilizes multiple sequence alignment by splitting files into sequences, inserting gaps for alignment, and representing the input file as a list of pointer pairs into a consensus sequence, allowing for efficient compression and reconstruction of the original file.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If current data compression methods are used, then storage space and bandwidth are required, but compression ratios are suboptimal and computational resources are increased
Solution Approach 1:
The input file is divided into multiple sequences of fixed length, which are then processed independently through the alignment and compression workflow. This segmentation enables the system to handle large files efficiently by breaking them into manageable chunks that can be aligned and compressed separately, ultimately achieving better compression ratios while reducing the computational burden on any single processing step.
Solution Approach 2:
The system performs a warm start alignment using a first letter size to pre-process and align sequences before the actual compression step. This preliminary alignment creates a foundation that speeds up subsequent compression operations, allowing the system to achieve optimal compression ratios more quickly without redundant computation during the main compression phase.
2Quantity of substance
If current data compression methods are used, then bandwidth is required for data transmission, but compression ratios are suboptimal leading to increased transmission requirements
Solution Approach 1:
By segmenting the file into sequences and compressing each through aligned pointer representation, the system achieves superior compression ratios that directly reduce the amount of data transmitted over the network, thereby reducing bandwidth requirements for data transmission while maintaining optimal compression efficiency.
3Productivity
If files are split into sequences and aligned with gap insertion, then compression efficiency is improved, but computational complexity increases
Solution Approach 1:
The warm start alignment pre-processes sequences with a first letter size to establish initial alignments before the main compression step. This preliminary action reduces the computational complexity of the subsequent alignment and compression operations by pre-establishing the alignment framework, thereby improving overall compression efficiency without proportionally increasing total computational burden.
Solution Approach 2:
The system uses different letter sizes at different stages of the process (first letter size for warm start, second letter size for final compression). This local differentiation of processing parameters optimizes the balance between compression efficiency and computational complexity at each stage, applying more intensive processing only where necessary.
4Loss of time
If warm start alignment is performed with a first letter size, then computation time is reduced, but additional processing steps are required
Solution Approach 1:
The warm start alignment with first letter size is a preliminary action that reduces computation time for the main compression step by pre-establishing alignments. Although it adds an initial processing step, it eliminates redundant computation during the main compression phase, resulting in net reduction of total computation time while maintaining a manageable number of processing steps.
Data Source
AI summary
Compressing files is disclosed. An input file to be compressed is first aligned. Aligning the file includes splitting the file into sequences that can be aligned. The result is a compression matrix, where each row of the matrix corresponds to part of the file. The compression matrix may also serve as a warm start if additional compression is desired. Compression may be performed in stages, where an initial compression matrix is generated in a first stage using larger letter sizes for alignment and then a second compression stage is performed using smaller letter sizes. A consensus sequence id determined from the compression matrix. Using the consensus sequence, pointer pairs are generated. Each pointer pair identifies a subsequence of the consensus matrix. The compressed file includes the pointer pairs and the consensus sequence.