Pathways to cellular supremacy in biocomputing

Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems. We propose the notion of “cellular supremacy” to focus attention on domains in which biocomputing might offer superior performance over traditional computers. We consider potential pathways toward cellular supremacy, and suggest application areas in which it may be found.A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU grant number 820699). T.E.G. was supported by a Royal Society University Research Fellowship (grant UF160357) and BrisSynBio, a BBSRC/ EPSRC Synthetic Biology Research Centre (grant BB/L01386X/1). P.Z. was supported by the EPSRC Portabolomics project (grant EP/N031962/1). P.C. was supported by SynBioChem, a BBSRC/EPSRC Centre for Synthetic Biology of Fine and Specialty Chemicals (grant BB/M017702/1) and the ShikiFactory100 project of the European Union’s Horizon 2020 research and innovation programme under grant agreement 814408

Log-quantized stochastic computing for memory and computation efficient DNNs

For energy efficiency, many low-bit quantization methods for deep neural networks (DNNs) have been proposed. Among them, logarithmic quantization is being highlighted showing acceptable deep learning performance. It also simplifies high-cost multipliers as well as reducing memory footprint drastically. Meanwhile, stochastic computing (SC) was proposed for low-cost DNN acceleration and the recently proposed SC multiplier improved the accuracy and latency significantly which are main drawbacks of SC. However, in their binary-interfaced system which yet costs much less than storing all stochastic stream, quantization is basically linear as same as conventional fixed-point binary. We applied logarithmically quantized DNNs to the state-of-the-art SC multiplier and studied how it can benefit. We found that SC multiplication on logarithmically quantized input is more accurate and it can help fine-tuning process. Furthermore, we designed the much low-cost SC-DNN accelerator utilizing the reduced complexity of inputs. Finally, while logarithmic quantization benefits data flow, proposed architecture achieves 40% and 24% less area and power consumption than the previous SC-DNN accelerator. Its area ?? latency product is smaller even than the shifter based accelerator

Sign-Magnitude SC: Getting 10X Accuracy for Free in Stochastic Computing for Deep Neural Networks

Stochastic computing (SC) is a promising computing paradigm for applications with low precision requirement, stringent cost and power restriction. One known problem with SC, however, is the low accuracy especially with multiplication. In this paperwe propose a simple, yet very effective solution to the low-accuracy SC-multiplication problem, which is critical in many applications such as deep neural networks (DNNs). Our solution is based on an old concept of signmagnitude, which, when applied to SC, has unique advantages. Our experimental results using multiple DNN applications demonstrate that our technique can improve the efficiency of SC-based DNNs by about 32X in terms of latency over using bipolar SC, with very little area overhead (about 1%)

Exploiting Errors for Efficiency: A Survey from Circuits to Algorithms

When a computational task tolerates a relaxation of its specification or when an algorithm tolerates the effects of noise in its execution, hardware, programming languages, and system software can trade deviations from correct behavior for lower resource usage. We present, for the first time, a synthesis of research results on computing systems that only make as many errors as their users can tolerate, from across the disciplines of computer aided design of circuits, digital system design, computer architecture, programming languages, operating systems, and information theory. Rather than over-provisioning resources at each layer to avoid errors, it can be more efficient to exploit the masking of errors occurring at one layer which can prevent them from propagating to a higher layer. We survey tradeoffs for individual layers of computing systems from the circuit level to the operating system level and illustrate the potential benefits of end-to-end approaches using two illustrative examples. To tie together the survey, we present a consistent formalization of terminology, across the layers, which does not significantly deviate from the terminology traditionally used by research communities in their layer of focus

Administration of dietary antioxidants for patients with inflammatory bowel disease: A systematic review and meta-analysis of randomized controlled clinical trials

Objective: Accumulating evidence has been reported regarding the effect of dietary antioxidants on clinical variables in IBD patients, however, findings are controversial. This systematic review and meta-analysis aimed to investigate effect of dietary antioxidants on clinical variables in patients with IBD or its subtypes. Methods: We searched PubMed, Scopus, and ISI Web of Science from inception to January 2021 using relevant keywords. Data were pooled by using the random-effect model. All statistical analyses were done using STATA version 14. Results: Our meta-analysis was exclusively done on studies about the effect of curcumin on IBD patients, because limited studies were done on other antioxidants. Curcumin administration resulted in significant increment of clinical remission in patients with IBD (SMD: 0.86, 95 CI: 0.16, 1.56, p = 0.016), significant remission in clinical symptoms (SMD: �0.96 score, 95 CI: �1.34, �0.57, p < 0.001), and significant increment in endoscopic remission in IBD patients (SMD: 0.51, 95 CI: 0.16, 0.85, p = 0.004), comparing to control group. Curcumin supplementation also made better clinical response than control group (SMD: 0.74, 95 CI: 0.22, 1.26, p = 0.005) and also resulted in significant improvement in quality of life of patients with IBD, as compared to control group (SMD: 1.23 score, 95 CI: 0.72, 1.74, p < 0.001). Conclusions: Our meta-analysis showed that curcumin significantly improved clinical and endoscopic remissions in IBD patients. This supplementation also caused significant reduction in clinical symptoms of IBD patients along with better clinical response and the increased quality of life. Further researches with larger sample size and longer period of intervention are required to evaluate efficacy of dietary antioxidants on clinical variables in patients with IBD. © 202