GAHLS: an optimized graph analytics based high level synthesis framework.

The urgent need for low latency, high-compute and low power on-board intelligence in autonomous systems, cyber-physical systems, robotics, edge computing, evolvable computing, and complex data science calls for determining the optimal amount and type of specialized hardware together with reconfigurability capabilities. With these goals in mind, we propose a novel comprehensive graph analytics based high level synthesis (GAHLS) framework that efficiently analyzes complex high level programs through a combined compiler-based approach and graph theoretic optimization and synthesizes them into message passing domain-specific accelerators. This GAHLS framework first constructs a compiler-assisted dependency graph (CaDG) from low level virtual machine (LLVM) intermediate representation (IR) of high level programs and converts it into a hardware friendly description representation. Next, the GAHLS framework performs a memory design space exploration while account for the identified computational properties from the CaDG and optimizing the system performance for higher bandwidth. The GAHLS framework also performs a robust optimization to identify the CaDG subgraphs with similar computational structures and aggregate them into intelligent processing clusters in order to optimize the usage of underlying hardware resources. Finally, the GAHLS framework synthesizes this compressed specialized CaDG into processing elements while optimizing the system performance and area metrics. Evaluations of the GAHLS framework on several real-life applications (e.g., deep learning, brain machine interfaces) demonstrate that it provides 14.27× performance improvements compared to state-of-the-art approaches such as LegUp 6.2.

In silico design and immunoinformatics analysis of a universal multi-epitope vaccine against monkeypox virus.

Monkeypox virus (MPXV) outbreaks have been reported in various countries worldwide; however, there is no specific vaccine against MPXV. In this study, therefore, we employed computational approaches to design a multi-epitope vaccine against MPXV. Initially, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), linear B lymphocytes (LBL) epitopes were predicted from the cell surface-binding protein and envelope protein A28 homolog, both of which play essential roles in MPXV pathogenesis. All of the predicted epitopes were evaluated using key parameters. A total of 7 CTL, 4 HTL, and 5 LBL epitopes were chosen and combined with appropriate linkers and adjuvant to construct a multi-epitope vaccine. The CTL and HTL epitopes of the vaccine construct cover 95.57% of the worldwide population. The designed vaccine construct was found to be highly antigenic, non-allergenic, soluble, and to have acceptable physicochemical properties. The 3D structure of the vaccine and its potential interaction with Toll-Like receptor-4 (TLR4) were predicted. Molecular dynamics (MD) simulation confirmed the vaccine's high stability in complex with TLR4. Finally, codon adaptation and in silico cloning confirmed the high expression rate of the vaccine constructs in strain K12 of Escherichia coli (E. coli). These findings are very encouraging; however, in vitro and animal studies are needed to ensure the potency and safety of this vaccine candidate.

Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins.

In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.

A stochastic quantum program synthesis framework based on Bayesian optimization.

Quantum computers and algorithms can offer exponential performance improvement over some NP-complete programs which cannot be run efficiently through a Von Neumann computing approach. In this paper, we present BayeSyn, which utilizes an enhanced stochastic program synthesis and Bayesian optimization to automatically generate quantum programs from high-level languages subject to certain constraints. We find that stochastic synthesis can comparatively and efficiently generate a program with a lower cost from the high dimensional program space. We also realize that hyperparameters used in stochastic synthesis play a significant role in determining the optimal program. Therefore, BayeSyn utilizes Bayesian optimization to fine-tune such parameters to generate a suitable quantum program.

Deciphering the laws of social network-transcendent COVID-19 misinformation dynamics and implications for combating misinformation phenomena.

The global rise of COVID-19 health risk has triggered the related misinformation infodemic. We present the first analysis of COVID-19 misinformation networks and determine few of its implications. Firstly, we analyze the spread trends of COVID-19 misinformation and discover that the COVID-19 misinformation statistics are well fitted by a log-normal distribution. Secondly, we form misinformation networks by taking individual misinformation as a node and similarity between misinformation nodes as links, and we decipher the laws of COVID-19 misinformation network evolution: (1) We discover that misinformation evolves to optimize the network information transfer over time with the sacrifice of robustness. (2) We demonstrate the co-existence of fit get richer and rich get richer phenomena in misinformation networks. (3) We show that a misinformation network evolution with node deletion mechanism captures well the public attention shift on social media. Lastly, we present a network science inspired deep learning framework to accurately predict which Twitter posts are likely to become central nodes (i.e., high centrality) in a misinformation network from only one sentence without the need to know the whole network topology. With the network analysis and the central node prediction, we propose that if we correctly suppress certain central nodes in the misinformation network, the information transfer of network would be severely impacted.

From rumor to genetic mutation detection with explanations: a GAN approach.

Social media have emerged as increasingly popular means and environments for information gathering and propagation. This vigorous growth of social media contributed not only to a pandemic (fast-spreading and far-reaching) of rumors and misinformation, but also to an urgent need for text-based rumor detection strategies. To speed up the detection of misinformation, traditional rumor detection methods based on hand-crafted feature selection need to be replaced by automatic artificial intelligence (AI) approaches. AI decision making systems require to provide explanations in order to assure users of their trustworthiness. Inspired by the thriving development of generative adversarial networks (GANs) on text applications, we propose a GAN-based layered model for rumor detection with explanations. To demonstrate the universality of the proposed approach, we demonstrate its benefits on a gene classification with mutation detection case study. Similarly to the rumor detection, the gene classification can also be formulated as a text-based classification problem. Unlike fake news detection that needs a previously collected verified news database, our model provides explanations in rumor detection based on tweet-level texts only without referring to a verified news database. The layered structure of both generative and discriminative models contributes to the outstanding performance. The layered generators produce rumors by intelligently inserting controversial information in non-rumors, and force the layered discriminators to detect detailed glitches and deduce exactly which parts in the sentence are problematic. On average, in the rumor detection task, our proposed model outperforms state-of-the-art baselines on PHEME dataset by [Formula: see text] in terms of macro-f1. The excellent performance of our model for textural sequences is also demonstrated by the gene mutation case study on which it achieves [Formula: see text] macro-f1 score.

An in silico deep learning approach to multi-epitope vaccine design: a SARS-CoV-2 case study.

The rampant spread of COVID-19, an infectious disease caused by SARS-CoV-2, all over the world has led to over millions of deaths, and devastated the social, financial and political entities around the world. Without an existing effective medical therapy, vaccines are urgently needed to avoid the spread of this disease. In this study, we propose an in silico deep learning approach for prediction and design of a multi-epitope vaccine (DeepVacPred). By combining the in silico immunoinformatics and deep neural network strategies, the DeepVacPred computational framework directly predicts 26 potential vaccine subunits from the available SARS-CoV-2 spike protein sequence. We further use in silico methods to investigate the linear B-cell epitopes, Cytotoxic T Lymphocytes (CTL) epitopes, Helper T Lymphocytes (HTL) epitopes in the 26 subunit candidates and identify the best 11 of them to construct a multi-epitope vaccine for SARS-CoV-2 virus. The human population coverage, antigenicity, allergenicity, toxicity, physicochemical properties and secondary structure of the designed vaccine are evaluated via state-of-the-art bioinformatic approaches, showing good quality of the designed vaccine. The 3D structure of the designed vaccine is predicted, refined and validated by in silico tools. Finally, we optimize and insert the codon sequence into a plasmid to ensure the cloning and expression efficiency. In conclusion, this proposed artificial intelligence (AI) based vaccine discovery framework accelerates the vaccine design process and constructs a 694aa multi-epitope vaccine containing 16 B-cell epitopes, 82 CTL epitopes and 89 HTL epitopes, which is promising to fight the SARS-CoV-2 viral infection and can be further evaluated in clinical studies. Moreover, we trace the RNA mutations of the SARS-CoV-2 and ensure that the designed vaccine can tackle the recent RNA mutations of the virus.

There Is Hope After All: Quantifying Opinion and Trustworthiness in Neural Networks.

Artificial Intelligence (AI) plays a fundamental role in the modern world, especially when used as an autonomous decision maker. One common concern nowadays is "how trustworthy the AIs are." Human operators follow a strict educational curriculum and performance assessment that could be exploited to quantify how much we entrust them. To quantify the trust of AI decision makers, we must go beyond task accuracy especially when facing limited, incomplete, misleading, controversial or noisy datasets. Toward addressing these challenges, we describe DeepTrust, a Subjective Logic (SL) inspired framework that constructs a probabilistic logic description of an AI algorithm and takes into account the trustworthiness of both dataset and inner algorithmic workings. DeepTrust identifies proper multi-layered neural network (NN) topologies that have high projected trust probabilities, even when trained with untrusted data. We show that uncertain opinion of data is not always malicious while evaluating NN's opinion and trustworthiness, whereas the disbelief opinion hurts trust the most. Also trust probability does not necessarily correlate with accuracy. DeepTrust also provides a projected trust probability of NN's prediction, which is useful when the NN generates an over-confident output under problematic datasets. These findings open new analytical avenues for designing and improving the NN topology by optimizing opinion and trustworthiness, along with accuracy, in a multi-objective optimization formulation, subject to space and time constraints.