Compressed sensing for simultaneous measurement of multiple different biological molecule types in a sample

An apparatus comprising:

• at least one processor;
• and
• at least one memory including one or more sequences of instructions,
• the at least one memory and the one or more sequences of instructions configured to, with the at least one processor, cause the apparatus to perform at least the following,
• determine a set of L different labels for each of which abundance can be measured;
• determine a set of M different biological molecule types to be detected, wherein M is greater than L;
• determine an assignment matrix A suitable for compressed sensing that indicates a unique combination of a plurality of labels for each molecule type so that A is a matrix of size L rows by M columns;
• cause the different biological molecule types to be physically labeled according to the assignment matrix by presenting data that indicates the assignment matrix;
• after presenting data that indicates the assignment matrix, obtain measurements of abundance of labels in a biological sample represented by a vector o of L rows by 1 column, wherein the measurements are based on the assignment matrix;
• and
• determine abundances for up to M different molecule types in the biological sample represented by a vector x of M rows by 1 column, based on techniques of compressed sensing to solve for x by minimizing a penalty based at least in part on a magnitude of a vector given by A x−o.

An apparatus comprising:

• means for physically labeling a plurality of M different biological molecule types in a biological sample, each different biological molecule type with a unique combination of a plurality of labels, according to by an assignment matrix A suitable for compressed sensing, wherein
• each different biological molecule type is selected from a population of M different biological molecules types,
• the plurality of labels is selected from a population of L different labels so that A is a matrix of size L rows by M columns, and
• M is greater than L;
• means for obtaining measurements of relative abundance of the L different labels in the sample represented by a vector o of L rows by 1 column;
• and
• means for determining relative abundance of up to M different molecule types in the sample, represented by a vector x of M rows by 1 column, based on a method of compressed sensing to solve for x by minimizing a penalty based at least in part on a magnitude of a vector given by A x−o.

A non-transitory computer-readable medium carrying one or more sequences of instructions, wherein execution of the one or more sequences of instructions by one or more processors causes the one or more processors to perform to:

• determine a set of L different labels for each of which abundance can be measured;
• determine a set of M different biological molecule types to be detected;
• determine an assignment matrix A suitable for compressed sensing that indicates a unique combination of a plurality of labels for each molecule type so that A is a matrix of size L rows by M columns;
• cause the different biological molecule types to be physically labeled according to the assignment matrix by presenting data that indicates the assignment matrix;
• after presenting data that indicates the assignment matrix, obtain measurements of abundance of labels in a biological sample represented by a vector o of L rows by 1 column, wherein the measurements are based on the assignment matrix;
• and
• determine abundances for up to M different molecule types in the biological sample represented by a vector x of M rows by 1 column, based on techniques of compressed sensing to solve for x by minimizing a penalty based at least in part on a magnitude of a vector given by A x−o.