BRAMAC: Compute-in-BRAM Architectures for Multiply-Accumulate on FPGAs

Deep neural network (DNN) inference using reduced integer precision has been shown to achieve significant improvements in memory utilization and compute throughput with little or no accuracy loss compared to full-precision floating-point. Modern FPGA-based DNN inference relies heavily on the on-chip block RAM (BRAM) for model storage and the digital signal processing (DSP) unit for implementing the multiply-accumulate (MAC) operation, a fundamental DNN primitive. In this paper, we enhance the existing BRAM to also compute MAC by proposing BRAMAC (Compute-in-$\underline{\text{BR}}$AM $\underline{\text{A}}$rchitectures for $\underline{\text{M}}$ultiply-$\underline{\text{Ac}}$cumulate). BRAMAC supports 2's complement 2- to 8-bit MAC in a small dummy BRAM array using a hybrid bit-serial & bit-parallel data flow. Unlike previous compute-in-BRAM architectures, BRAMAC allows read/write access to the main BRAM array while computing in the dummy BRAM array, enabling both persistent and tiling-based DNN inference. We explore two BRAMAC variants: BRAMAC-2SA (with 2 synchronous dummy arrays) and BRAMAC-1DA (with 1 double-pumped dummy array). BRAMAC-2SA/BRAMAC-1DA can boost the peak MAC throughput of a large Arria-10 FPGA by 2.6$\times$/2.1$\times$, 2.3$\times$/2.0$\times$, and 1.9$\times$/1.7$\times$ for 2-bit, 4-bit, and 8-bit precisions, respectively at the cost of 6.8%/3.4% increase in the FPGA core area. By adding BRAMAC-2SA/BRAMAC-1DA to a state-of-the-art tiling-based DNN accelerator, an average speedup of 2.05$\times$/1.7$\times$ and 1.33$\times$/1.52$\times$ can be achieved for AlexNet and ResNet-34, respectively across different model precisions.Comment: 11 pages, 13 figures, 3 tables, FCCM conference 202

Increasing The Odds Of Hit Iidentification By Screening Against Receptor Homologs

Increasing the odds of hit identification in screening is of significance for drug discovery. The odds for finding a hit are closely related either to the diversity of libraries or to the availability of focused libraries. There are no truly diverse libraries and it is difficult to design focused libraries without sufficient information. Hence it is helpful to consider alternative approaches that can enhance the odds using existing libraries. Multiple members of a protein family have been considered collectively in inhibitor design, on the basis of the correlation between protein families and ligands derived from specific compound classes. Such a correlation has been exploited in various drug discovery studies and a general receptor-homolog-based screening scheme may be devised. The feasibility of such a scheme in enhancing the odds of hit identification is discussed.Singapore-MIT Alliance (SMA

Computer-Aided Drug Target Search

Identification of the unknown targets of drugs, investigative drugs and herbal ingredients is an important task in drug discovery. It can potentially help in several aspects including: (1) determination of unknown therapeutic mechanism of certain drugs and medicinal herbs, (2) prediction of drug toxicity and side effect, and (3) analysis of protein-mediated pharmacokinetic properties of drugs. Here, a computer-aided drug target search method and its validation studies are presented.Singapore-MIT Alliance (SMA

Linear Thermodynamics of Rodlike DNA Filtration

Linear thermodynamics transportation theory is employed to study filtration of rodlike DNA molecules. Using the repeated nanoarray consisting of alternate deep and shallow regions, it is demonstrated that the complex partitioning of rodlike DNA molecules of different lengths can be described by traditional transport theory with the configurational entropy properly quantified. Unlike most studies at mesoscopic level, this theory focuses on the macroscopic group behavior of DNA transportation. It is therefore easier to conduct validation analysis through comparison with experimental results. It is also promising in design and optimization of DNA filtration devices through computer simulation.Singapore-MIT Alliance (SMA

Update of TTD: Therapeutic Target Database

Increasing numbers of proteins, nucleic acids and other molecular entities have been explored as therapeutic targets, hundreds of which are targets of approved and clinical trial drugs. Knowledge of these targets and corresponding drugs, particularly those in clinical uses and trials, is highly useful for facilitating drug discovery. Therapeutic Target Database (TTD) has been developed to provide information about therapeutic targets and corresponding drugs. In order to accommodate increasing demand for comprehensive knowledge about the primary targets of the approved, clinical trial and experimental drugs, numerous improvements and updates have been made to TTD. These updates include information about 348 successful, 292 clinical trial and 1254 research targets, 1514 approved, 1212 clinical trial and 2302 experimental drugs linked to their primary targets (3382 small molecule and 649 antisense drugs with available structure and sequence), new ways to access data by drug mode of action, recursive search of related targets or drugs, similarity target and drug searching, customized and whole data download, standardized target ID, and significant increase of data (1894 targets, 560 diseases and 5028 drugs compared with the 433 targets, 125 diseases and 809 drugs in the original release described in previous paper). This database can be accessed at http://bidd.nus.edu.sg/group/cjttd/TTD.asp

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

Sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) has emerged as one of the most popular techniques for label-free proteome quantification in current pharmacoproteomic research. It provides more comprehensive detection and more accurate quantitation of proteins comparing with the traditional techniques. The performance of SWATH-MS is highly susceptible to the selection of processing method. Till now, ≥27 methods (transformation, normalization, and missing-value imputation) are sequentially applied to construct numerous analysis chains for SWATH-MS, but it is still not clear which analysis chain gives the optimal quantification performance. Herein, the performances of 560 analysis chains for quantifying pharmacoproteomic data were comprehensively assessed. Firstly, the most complete set of the publicly available SWATH-MS based pharmacoproteomic data were collected by comprehensive literature review. Secondly, substantial variations among the performances of various analysis chains were observed, and the consistently well-performed analysis chains (CWPACs) across various datasets were for the first time generalized. Finally, the log and power transformations sequentially followed by the total ion current normalization were discovered as one of the best performed analysis chains for the quantification of SWATH-MS based pharmacoproteomic data. In sum, the CWPACs identified here provided important guidance to the quantification of proteomic data and could therefore facilitate the cutting-edge research in any pharmacoproteomic studies requiring SWATH-MS technique

A two-step target binding and selectivity support vector machines approach for virtual screening of dopamine receptor subtype-selective ligands

10.1371/journal.pone.0039076PLoS ONE76

In-memory computing

This report presents state-of-the-art In-memory Computing (IMC) works using SRAM. A brief introduction of static random access memory (SRAM) operation will be explained by introducing an intuitive method to analyze the circuits. Several state-of-the-art ultra-low-power (ULP) SRAM design techniques and IMC works will be discussed. A simple SRAM circuit simulation is carried out using Cadence and the circuit works correctly as expected. Compared to other FYP works, this report aims to analyze research papers from top circuit conferences such as International Solid-State Circuit Conference (ISSCC) and journals such as IEEE Journal of Solid-State Circuits (JSSC).Bachelor of Engineering (Electrical and Electronic Engineering