Protein annotation has long been a challenging task in computational biology. Gene Ontology (GO) has become one of the most popular frameworks to describe protein functions and their relationships. Prediction of a protein annotation with proper GO terms demands high-quality GO term representation learning, which aims to learn a low-dimensional dense vector representation with accompanying semantic meaning for each functional label, also known as embedding. However, existing GO term embedding methods, which mainly take into account ancestral co-occurrence information, have yet to capture the full topological information in the GO-directed acyclic graph (DAG). In this study, we propose a novel GO term representation learning method, PO2Vec, to utilize the partial order relationships to improve the GO term representations. Extensive evaluations show that PO2Vec achieves better outcomes than existing embedding methods in a variety of downstream biological tasks. Based on PO2Vec, we further developed a new protein function prediction method PO2GO, which demonstrates superior performance measured in multiple metrics and annotation specificity as well as few-shot prediction capability in the benchmarks. These results suggest that the high-quality representation of GO structure is critical for diverse biological tasks including computational protein annotation.

The IFDS algorithm can be compute-and memoryintensive for some large programs, often running for a long time (more than expected) or terminating prematurely after some time and/or memory budgets have been exhausted. In the latter case, the corresponding IFDS data-flow analyses may suffer from false negatives and/or false positives. To improve this, we introduce a sparse alternative to the traditional IFDS algorithm. Instead of propagating the data-flow facts across all the program points along the program’s (interprocedural) control flow graph, we propagate every data-flow fact directly to its next possible use points along its own sparse control flow graph constructed on the fly, thus reducing significantly both the time and memory requirements incurred by the traditional IFDS algorithm. In our evaluation, we compare FLOWDROID, a taint analysis performed by using the traditional IFDS algorithm, with our sparse incarnation, SPARSEDROID, on a set of 40 Android apps selected. For the time budget (5 hours) and memory budget (220GB) allocated per app, SPARSEDROID can run every app to completion but FLOWDROID terminates prematurely for 9 apps, resulting in an average speedup of 22.0x. This implies that when used as a market-level vetting tool, SPARSEDROID can finish analyzing these 40 apps in 2.13 hours (by issuing 228 leak warnings) while FLOWDROID manages to analyze only 30 apps in the same time period (by issuing only 147 leak warnings).