Publications

Dynamic programming (DP) based algorithms are essential yet compute-intensive parts of numerous bioinformatics pipelines. This paper introduces DP-HLS, a novel framework based on High-Level Synthesis (HLS) that simplifies and accelerates the development of a broad set of bioinformatically relevant DP algorithms in hardware. DP-HLS features an easy-to-use template with integrated HLS directives, enabling efficient hardware solutions without requiring hardware design knowledge. We implemented 15 diverse DP kernels, achieving 1.3–32× improved throughput over state-of-the-art GPU and CPU baselines.

Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships. We present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. Using genomic datasets from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees comparable in quality to state-of-the-art approaches but in a fraction of the time.

The automatic surgical video processing for anomaly detection is becoming important since manual feedback from surgeons is subject to errors and time-consuming. In this paper, a convolutional neural network (CNN) is designed to evaluate laparoscopic and endoscopic surgical videos. The neural network will detect and localize the organs for the given videos, laying the path for automatic post-surgical processing.

The Clifford+T gate library consisting of Hadamard, T, and CNOT gates has attracted much interest in quantum circuit synthesis. Since fault-tolerant implementations of the T gate have very high latency, recent work aims at minimizing the T-depth. We present an approach to exploit additional ancilla qubits in the mapping of reversible circuits into Clifford+T quantum circuits with the primary objective to minimize the T-depth.