A note on retrodiction and machine evolution

Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and transmitting meaning. Here I explore the need to dissect biomolecular communication with retrodiction approaches that make claims about the past given information that is available in the present. While the passage of time restricts the explanatory power of retrodiction, the use of molecular structure in biology offsets information erosion. This allows description of the gradual evolutionary rise of structural and functional innovations in RNA and proteins. The resulting chronologies can also describe the gradual rise of molecular machines of increasing complexity and computation capabilities. For example, the accretion of rRNA substructures and ribosomal proteins can be traced in time and placed within a geological timescale. Phylogenetic, algorithmic and theoretical-inspired accretion models can be reconciled into a congruent evolutionary model. Remarkably, the time of origin of enzymes, functional RNA, non-ribosomal peptide synthetase (NRPS) complexes, and ribosomes suggest they gradually climbed Chomsky's hierarchy of formal grammars, supporting the gradual complexification of machines and communication in molecular biology. Future retrodiction approaches and in-depth exploration of theoretical models of computation will need to confirm such evolutionary progression.Comment: 7 pages, 1 figur

Finite Computational Structures and Implementations

What is computable with limited resources? How can we verify the correctness of computations? How to measure computational power with precision? Despite the immense scientific and engineering progress in computing, we still have only partial answers to these questions. In order to make these problems more precise, we describe an abstract algebraic definition of classical computation, generalizing traditional models to semigroups. The mathematical abstraction also allows the investigation of different computing paradigms (e.g. cellular automata, reversible computing) in the same framework. Here we summarize the main questions and recent results of the research of finite computation.Comment: 12 pages, 3 figures, will be presented at CANDAR'16 and final version published by IEEE Computer Societ

VerSum: Verifiable Computations over Large Public Logs

VerSum allows lightweight clients to outsource expensive computations over large and frequently changing data structures, such as the Bitcoin or Namecoin blockchains, or a Certificate Transparency log. VerSum clients ensure that the output is correct by comparing the outputs from multiple servers. VerSum assumes that at least one server is honest, and crucially, when servers disagree, VerSum uses an efficient conflict resolution protocol to determine which server(s) made a mistake and thus obtain the correct output. VerSum's contribution lies in achieving low server-side overhead for both incremental re-computation and conflict resolution, using three key ideas: (1) representing the computation as a functional program, which allows memoization of previous results; (2) recording the evaluation trace of the functional program in a carefully designed computation history to help clients determine which server made a mistake; and (3) introducing a new authenticated data structure for sequences, called SeqHash, that makes it efficient for servers to construct summaries of computation histories in the presence of incremental re-computation. Experimental results with an implementation of VerSum show that VerSum can be used for a variety of computations, that it can support many clients, and that it can easily keep up with Bitcoin's rate of new blocks with transactions.United States. Defense Advanced Research Projects Agency. Clean-slate design of Resilient, Adaptive, Secure Hosts (CRASH) Program (Contract N66001-10-2-4089)National Science Foundation (U.S.) (Award CNS-1053143)National Science Foundation (U.S.) (Award CNS-1413920

Solving Partial Differential Equations with Monte Carlo / Random Walk on an Analog-Digital Hybrid Computer

Current digital computers are about to hit basic physical boundaries with respect to integration density, clock frequencies, and particularly energy consumption. This requires the application of new computing paradigms, such as quantum and analog computing in the near future. Although neither quantum nor analog computer are general purpose computers they will play an important role as co-processors to offload certain classes of compute intensive tasks from classic digital computers, thereby not only reducing run time but also and foremost power consumption. In this work, we describe a random walk approach to the solution of certain types of partial differential equations which is well suited for combinations of digital and analog computers (hybrid computers). The experiments were performed on an Analog Paradigm Model-1 analog computer attached to a digital computer by means of a hybrid interface. At the end we give some estimates of speedups and power consumption obtainable by using future analog computers on chip.Comment: 9 pages, 7 figures. Proceeding for the MikroSystemTechnik Kongress 2023 (VDE Verlag MST Kongress 2023

Computation Against a Neighbour

Recent works in contexts like the Internet of Things (IoT) and large-scale Cyber-Physical Systems (CPS) propose the idea of programming distributed systems by focussing on their global behaviour across space and time. In this view, a potentially vast and heterogeneous set of devices is considered as an "aggregate" to be programmed as a whole, while abstracting away the details of individual behaviour and exchange of messages, which are expressed declaratively. One such a paradigm, known as aggregate programming, builds on computational models inspired by field-based coordination. Existing models such as the field calculus capture interaction with neighbours by a so-called "neighbouring field" (a map from neighbours to values). This requires ad-hoc mechanisms to smoothly compose with standard values, thus complicating programming and introducing clutter in aggregate programs, libraries and domain-specific languages (DSLs). To address this key issue we introduce the novel notion of "computation against a neighbour", whereby the evaluation of certain subexpressions of the aggregate program are affected by recent corresponding evaluations in neighbours. We capture this notion in the neighbours calculus (NC), a new field calculus variant which is shown to smoothly support declarative specification of interaction with neighbours, and correspondingly facilitate the embedding of field computations as internal DSLs in common general-purpose programming languages -- as exemplified by a Scala implementation, called ScaFi. This paper formalises NC, thoroughly compares it with respect to the classic field calculus, and shows its expressiveness by means of a case study in edge computing, developed in ScaFi.Comment: 50 pages, 16 figure

Enhancing Online Security with Image-based Captchas

Given the data loss, productivity, and financial risks posed by security breaches, there is a great need to protect online systems from automated attacks. Completely Automated Public Turing Tests to Tell Computers and Humans Apart, known as CAPTCHAs, are commonly used as one layer in providing online security. These tests are intended to be easily solvable by legitimate human users while being challenging for automated attackers to successfully complete. Traditionally, CAPTCHAs have asked users to perform tasks based on text recognition or categorization of discrete images to prove whether or not they are legitimate human users. Over time, the efficacy of these CAPTCHAs has been eroded by improved optical character recognition, image classification, and machine learning techniques that can accurately solve many CAPTCHAs at rates approaching those of humans. These CAPTCHAs can also be difficult to complete using the touch-based input methods found on widely used tablets and smartphones.;This research proposes the design of CAPTCHAs that address the shortcomings of existing implementations. These CAPTCHAs require users to perform different image-based tasks including face detection, face recognition, multimodal biometrics recognition, and object recognition to prove they are human. These are tasks that humans excel at but which remain difficult for computers to complete successfully. They can also be readily performed using click- or touch-based input methods, facilitating their use on both traditional computers and mobile devices.;Several strategies are utilized by the CAPTCHAs developed in this research to enable high human success rates while ensuring negligible automated attack success rates. One such technique, used by fgCAPTCHA, employs image quality metrics and face detection algorithms to calculate a fitness value representing the simulated performance of human users and automated attackers, respectively, at solving each generated CAPTCHA image. A genetic learning algorithm uses these fitness values to determine customized generation parameters for each CAPTCHA image. Other approaches, including gradient descent learning, artificial immune systems, and multi-stage performance-based filtering processes, are also proposed in this research to optimize the generated CAPTCHA images.;An extensive RESTful web service-based evaluation platform was developed to facilitate the testing and analysis of the CAPTCHAs developed in this research. Users recorded over 180,000 attempts at solving these CAPTCHAs using a variety of devices. The results show the designs created in this research offer high human success rates, up to 94.6\% in the case of aiCAPTCHA, while ensuring resilience against automated attacks

Mothers\u27 Adaptation to Caring for a New Baby

To date, most research on parents\u27 adjustment after adding a new baby to their family unit has focused on mothers\u27 initial transition to parenthood. This past research has examined changes in mothers\u27 marital satisfaction and perceived well-being across the transition, and has compared their prenatal expectations to their postnatal experiences. This project assessed first-time and experienced mothers\u27 stress and satisfaction associated with parenting, their adjustment to competing demands, and their perceived well-being longitudinally before and after the birth of a baby. Additionally, how maternal and child-related variables influenced the trajectory of mothers\u27 postnatal adaptation was assessed. These variables included mothers\u27 age, their education level, their prenatal expectations and postnatal experiences concerning shared infant care, their satisfaction with the division of infant caregiving, and their perceptions of their infant\u27s temperament. Mothers (N = 136) completed an online survey during their third trimester and additional online surveys when their baby was approximately 2, 4, 6, and 8 weeks old.;First-time mothers prenatally expected a more equal division of infant caregiving between themselves and their partners than did experienced mothers. Both first-time and experienced mothers reported less assistance from their partners than they had prenatally expected. Additionally, they experienced almost twice as many violated expectations than met expectations. Growth curve modeling revealed that a cubic function of time best fit the trajectory of mothers\u27 postnatal parenting satisfaction. Mothers reported less parenting satisfaction at 4 weeks, compared to 2 and 6 weeks, and reported stability in their satisfaction between 6 and 8 weeks. A quadratic function of time best fit the trajectories of mothers\u27 postnatal parenting stress and adjustment to the demands of their baby. Mothers reported more stress and difficulty adjusting to their baby\u27s demands at 4 and 6 weeks, compared to 2 and 8 weeks. A linear function of time best fit the trajectories of mothers\u27 adjustment to home demands, generalized state anxiety, and depressive symptoms. Mothers reported less difficulty meeting home demands, less generalized anxiety, and fewer depressive symptoms across the postnatal period. Mothers\u27 violated expectations were associated with level differences in all aspects of mothers\u27 postnatal adaptation except their adjustment to home demands. Specifically, more violated expectations, in number or in magnitude, were associated with poorer postnatal adaptation. Mothers\u27 violated expectations were not associated with the slope of mothers\u27 postnatal adaptation trajectories. Exploratory models revealed that other maternal and child-related variables also impacted the level and slope of mothers\u27 postnatal adaptation.;Overall, first-time and experienced mothers were more similar than different in regards to their postnatal adaptation. This study suggests that prior findings concerning adults\u27 initial transition to parenthood may also apply to adults during each addition of a new baby into the family unit. Additionally, mothers who reported less of a mismatch between their expectations and experiences concerning shared infant care had fewer issues adapting the postnatal period. Thus, methods to increase the assistance mothers receive from their partner should be sought. Limitations of this study and suggestions for future research are also discussed