A forensics software toolkit for DNA steganalysis.

Recent advances in genetic engineering have allowed the insertion of artificial DNA strands into the living cells of organisms. Several methods have been developed to insert information into a DNA sequence for the purpose of data storage, watermarking, or communication of secret messages. The ability to detect, extract, and decode messages from DNA is important for forensic data collection and for data security. We have developed a software toolkit that is able to detect the presence of a hidden message within a DNA sequence, extract that message, and then decode it. The toolkit is able to detect, extract, and decode messages that have been encoded with a variety of different coding schemes. The goal of this project is to enable our software toolkit to determine with which coding scheme a message has been encoded in DNA and then to decode it. The software package is able to decode messages that have been encoded with every variation of most of the coding schemes described in this document. The software toolkit has two different options for decoding that can be selected by the user. The first is a frequency analysis approach that is very commonly used in cryptanalysis. This approach is very fast, but is unable to decode messages shorter than 200 words accurately. The second option is using a Genetic Algorithm (GA) in combination with a Wisdom of Artificial Crowds (WoAC) technique. This approach is very time consuming, but can decode shorter messages with much higher accuracy

When in doubt ask the crowd : leveraging collective intelligence for improving event detection and machine learning

[no abstract

A Novel Evolutionary Algorithm with Column and Sub-Block Local Search for Sudoku Puzzles

Sudoku puzzles are not only popular intellectual games but also NP-hard combinatorial problems related to various real-world applications, which have attracted much attention worldwide. Although many efficient tools, such as evolutionary computation (EC) algorithms, have been proposed for solving Sudoku puzzles, they still face great challenges with regard to hard and large instances of Sudoku puzzles. Therefore, to efficiently solve Sudoku puzzles, this paper proposes a genetic algorithm (GA)-based method with a novel local search technology called local search-based GA (LSGA). The LSGA includes three novel design aspects. First, it adopts a matrix coding scheme to represent individuals and designs the corresponding crossover and mutation operations. Second, a novel local search strategy based on column search and sub-block search is proposed to increase the convergence speed of the GA. Third, an elite population learning mechanism is proposed to let the population evolve by learning the historical optimal solution. Based on the above technologies, LSGA can greatly improve the search ability for solving complex Sudoku puzzles. LSGA is compared with some state-of-the-art algorithms at Sudoku puzzles of different difficulty levels and the results show that LSGA performs well in terms of both convergence speed and success rates on the tested Sudoku puzzle instances

Multi-Agent Control in Sociotechnical Systems

Process control is essential in chemical engineering and has diverse applications in automation, manufacturing, scheduling, etc. In this cross-disciplinary work, we shift the domain focus from the control of machines to the control of multiple intelligent agents. Our goal is to improve the optimization problem-solving process, such as optimal regulation of emerging technologies, in a multi-agent system. Achieving that improvement would have potential value both within and outside the chemical engineering community. This work also illustrates the possibility of applying process systems engineering techniques, especially process control, beyond chemical plants. It is very common to observe crowds of individuals solving similar problems with similar information in a largely independent manner. We argue here that the crowds can become more efficient and robust problem-solvers, by partially following the average opinion. This observation runs counter to the widely accepted claim that the wisdom of crowds deteriorates with social influence. The key difference is that individuals are self-interested and hence will reject feedbacks that do not improve their performance. We propose a multi-agent control-theoretic methodology, soft regulation, to model the collective dynamics and compute the degree of social influence, i.e., the level to which one accepts the population feedback, that optimizes the problem-solving performance. Soft regulation is a modeling language for multi-agent sociotechnical systems. The state-space formulation captures the individual learning process (i.e., open loop dynamics) as well as the influence of the population feedback in a straightforward manner. It can model a diverse set of existing multi-agent dynamics. Through numerical analysis and linear algebra, we attempt to understand the role of feedback in multi-agent collective dynamics, thus achieving multi-agent control in sociotechnical systems. Our analysis through mathematical proofs, simulations, and a human subject experiment suggests that intelligent individuals, solving the same problem (or similar problems), could do much better by adaptively adjusting their decisions towards the population average. We even discover that the crowd of human subjects could self-organize into a near-optimal setting. This discovery suggests a new coordination mechanism for enhancing individual decision-making. Potential applications include mobile health, urban planning, and policymaking

Model-agnostic network inference enhancement from noisy measurements via curriculum learning

Noise is a pervasive element within real-world measurement data, significantly undermining the performance of network inference models. However, the quest for a comprehensive enhancement framework capable of bolstering noise resistance across a diverse array of network inference models has remained elusive. Here, we present an elegant and efficient framework tailored to amplify the capabilities of network inference models in the presence of noise. Leveraging curriculum learning, we mitigate the deleterious impact of noisy samples on network inference models. Our proposed framework is model-agnostic, seamlessly integrable into a plethora of model-based and model-free network inference methods. Notably, we utilize one model-based and three model-free network inference methods as the foundation. Extensive experimentation across various synthetic and real-world networks, encapsulating diverse nonlinear dynamic processes, showcases substantial performance augmentation under varied noise types, particularly thriving in scenarios enriched with clean samples. This framework's adeptness in fortifying both model-free and model-based network inference methodologies paves the avenue towards a comprehensive and unified enhancement framework, encompassing the entire spectrum of network inference models. Available Code: https://github.com/xiaoyuans/MANIE

Learning And Decision Making In Groups

Many important real-world decision-making problems involve group interactions among individuals with purely informational interactions. Such situations arise for example in jury deliberations, expert committees, medical diagnoses, etc. We model the purely informational interactions of group members, where they receive private information and act based on that information while also observing other people\u27s beliefs or actions. In the first part of the thesis, we address the computations that a rational (Bayesian) decision-maker should undertake to realize her optimal actions, maximizing her expected utility given all available information at every decision epoch. We use an approach called iterated eliminations of infeasible signals (IEIS) to model the thinking process as well as the calculations of a Bayesian agent in a group decision scenario. Accordingly, as the Bayesian agent attempts to infer the true state of the world from her sequence of observations, she recursively refines her belief about the signals that other players could have observed and beliefs that they would have hold given the assumption that other players are also rational. We show that IEIS algorithm runs in exponential time; however, when the group structure is a partially ordered set the Bayesian calculations simplify and polynomial-time computation of the Bayesian recommendations is possible. We also analyze the computational complexity of the Bayesian belief formation in groups and show that it is NP-hard. We investigate the factors underlying this computational complexity and show how belief calculations simplify in special network structures or cases with strong inherent symmetries. We finally give insights about the statistical efficiency (optimality) of the beliefs and its relations to computational efficiency. In the second part, we propose the no-recall model of inference for heuristic decision-making that is rooted in the Bayes rule but avoids the complexities of rational inference in group interactions. Accordingly to this model, the group members behave rationally at the initiation of their interactions with each other; however, in the ensuing decision epochs, they rely on heuristics that replicate their experiences from the first stage and can be justified as optimal responses to simplified versions of their complex environments. We study the implications of the information structure, together with the properties of the probability distributions, which determine the structure of the so-called ``Bayesian heuristics\u27\u27 that the agents follow in this model. We also analyze the group decision outcomes in two classes of linear action updates and log-linear belief updates and show that many inefficiencies arise in group decisions as a result of repeated interactions between individuals, leading to overconfident beliefs as well as choice-shifts toward extreme actions. Nevertheless, balanced regular structures demonstrate a measure of efficiency in terms of aggregating the initial information of individuals. Finally, we extend this model to a case where agents are exposed to a stream of private data in addition to observing each other\u27s actions and analyze properties of learning and convergence under the no-recall framework

Toward human-like pathfinding with hierarchical approaches and the GPS of the brain theory

Pathfinding for autonomous agents and robots has been traditionally driven by finding optimal paths. Where typically optimality means finding the shortest path between two points in a given environment. However, optimality may not always be strictly necessary. For example, in the case of video games, often computing the paths for non-player characters (NPC) must be done under strict time constraints to guarantee real time simulation. In those cases, performance is more important than finding the shortest path, specially because often a sub-optimal path can be just as convincing from the point of view of the player. When simulating virtual humanoids, pathfinding has also been used with the same goal: finding the shortest path. However, humans very rarely follow precise shortest paths, and thus there are other aspects of human decision making and path planning strategies that should be incorporated in current simulation models. In this thesis we first focus on improving performance optimallity to handle as many virtual agents as possible, and then introduce neuroscience research to propose pathfinding algorithms that attempt to mimic humans in a more realistic manner.In the case of simulating NPCs for video games, one of the main challenges is to compute paths as efficiently as possible for groups of agents. As both the size of the environments and the number of autonomous agents increase, it becomes harder to obtain results in real time under the constraints of memory and computing resources. For this purpose we explored hierarchical approaches for two reasons: (1) they have shown important performance improvements for regular grids and other abstract problems, and (2) humans tend to plan trajectories also following an topbottom abstraction, focusing first on high level location and then refining the path as they move between those high level locations. Therefore, we believe that hierarchical approaches combine the best of our two goals: improving performance for multi-agent pathfinding and achieving more human-like pathfinding. Hierarchical approaches, such as HNA* (Hierarchical A* for Navigation Meshes) can compute paths more efficiently, although only for certain configurations of the hierarchy. For other configurations, the method suffers from a bottleneck in the step that connects the Start and Goal positions with the hierarchy. This bottleneck can drop performance drastically.In this thesis we present different approaches to solve the HNA* bottleneck and thus obtain a performance boost for all hierarchical configurations. The first method relies on further memory storage, and the second one uses parallelism on the GPU. Our comparative evaluation shows that both approaches offer speed-ups as high as 9x faster than A*, and show no limitations based on hierarchical configuration. Then we further exploit the potential of CUDA parallelism, to extend our implementation to HNA* for multi-agent path finding. Our method can now compute paths for over 500K agents simultaneously in real-time, with speed-ups above 15x faster than a parallel multi-agent implementation using A*. We then focus on studying neurosience research to learn about the way that humans build mental maps, in order to propose novel algorithms that take those finding into account when simulating virtual humans. We propose a novel algorithm for path finding that is inspired by neuroscience research on how the brain learns and builds cognitive maps. Our method represents the space as a hexagonal grid, based on the GPS of the brain theory, and fires memory cells as counters. Our path finder then combines a method for exploring unknown environments while building such a cognitive map, with an A* search using a modified heuristic that takes into account the GPS of the brain cognitive map.El problema de Pathfinding para agentes autónomos o robots, ha consistido tradicionalmente en encontrar un camino óptimo, donde por óptimo se entiende el camino de distancia mínima entre dos posiciones de un entorno. Sin embargo, en ocasiones puede que no sea estrictamente necesario encontrar una solución óptima. Para ofrecer la simulación de multitudes de agentes autónomos moviéndose en tiempo real, es necesario calcular sus trayectorias bajo condiciones estrictas de tiempo de computación, pero no es fundamental que las soluciones sean las de distancia mínima ya que, con frecuencia, el observador no apreciará la diferencia entre un camino óptimo y un sub-óptimo. Por tanto, suele ser suficiente con que la solución encontrada sea visualmente creíble para el observado. Cuando se simulan humanoides virtuales en aplicaciones de realidad virtual que requieren avatares que simulen el comportamiento de los humanos, se tiende a emplear los mismos algoritmos que en video juegos, con el objetivo de encontrar caminos de distancia mínima. Pero si realmente queremos que los avatares imiten el comportamiento humano, tenemos que tener en cuenta que, en el mundo real, los humanos rara vez seguimos precisamente el camino más corto, y por tanto se deben considerar otros aspectos que influyen en la toma de decisiones de los humanos y la selección de rutas en el mundo real. En esta tesis nos centraremos primero en mejorar el rendimiento de la búsqueda de caminos para poder simular grandes números de humanoides virtuales autónomos, y a continuación introduciremos conceptos de investigación con mamíferos en neurociencia, para proponer soluciones al problema de pathfinding que intenten imitar con mayor realismo, el modo en el que los humanos navegan el entorno que les rodea. A medida que aumentan tanto el tamaño de los entornos virtuales como el número de agentes autónomos, resulta más difícil obtener soluciones en tiempo real, debido a las limitaciones de memoria y recursos informáticos. Para resolver este problema, en esta tesis exploramos enfoques jerárquicos porque consideramos que combinan dos objetivos fundamentales: mejorar el rendimiento en la búsqueda de caminos para multitudes de agentes y lograr una búsqueda de caminos similar a la de los humanos. El primer método presentado en esta tesis se basa en mejorar el rendimiento del algoritmo HNA* (Hierarchical A* for Navigation Meshes) incrementando almacenamiento de datos en memoria, y el segundo utiliza el paralelismo para mejorar drásticamente el rendimiento. La evaluación cuantitativa realizada en esta tesis, muestra que ambos enfoques ofrecen aceleraciones que pueden llegar a ser hasta 9 veces más rápidas que el algoritmo A* y no presentan limitaciones debidas a la configuración jerárquica. A continuación, aprovechamos aún más el potencial del paralelismo ofrecido por CUDA para extender nuestra implementación de HNA* a sistemas multi-agentes. Nuestro método permite calcular caminos simultáneamente y en tiempo real para más de 500.000 agentes, con una aceleración superior a 15 veces la obtenida por una implementación paralela del algoritmo A*. Por último, en esta tesis nos hemos centrado en estudiar los últimos avances realizados en el ámbito de la neurociencia, para comprender la manera en la que los humanos construyen mapas mentales y poder así proponer nuevos algoritmos que imiten de forma más real el modo en el que navegamos los humanos. Nuestro método representa el espacio como una red hexagonal, basada en la distribución de ¿place cells¿ existente en el cerebro, e imita las activaciones neuronales como contadores en dichas celdas. Nuestro buscador de rutas combina un método para explorar entornos desconocidos mientras construye un mapa cognitivo hexagonal, utilizando una búsqueda A* con una nueva heurística adaptada al mapa cognitivo del cerebro y sus contadores

Bayesian Decision Process for Cost-Efficient Dynamic Ranking via Crowdsourcing

Abstract Rank aggregation based on pairwise comparisons over a set of items has a wide range of applications. Although considerable research has been devoted to the development of rank aggregation algorithms, one basic question is how to efficiently collect a large amount of high-quality pairwise comparisons for the ranking purpose. Because of the advent of many crowdsourcing services, a crowd of workers are often hired to conduct pairwise comparisons with a small monetary reward for each pair they compare. Since different workers have different levels of reliability and different pairs have different levels of ambiguity, it is desirable to wisely allocate the limited budget for comparisons among the pairs of items and workers so that the global ranking can be accurately inferred from the comparison results. To this end, we model the active sampling problem in crowdsourced ranking as a Bayesian Markov decision process, which dynamically selects item pairs and workers to improve the ranking accuracy under a budget constraint. We further develop a computationally efficient sampling policy based on knowledge gradient as well as a moment matching technique for posterior approximation. Experimental evaluations on both synthetic and real data show that the proposed policy achieves high ranking accuracy with a lower labeling cost

Changing the focus: worker-centric optimization in human-in-the-loop computations

A myriad of emerging applications from simple to complex ones involve human cognizance in the computation loop. Using the wisdom of human workers, researchers have solved a variety of problems, termed as “micro-tasks” such as, captcha recognition, sentiment analysis, image categorization, query processing, as well as “complex tasks” that are often collaborative, such as, classifying craters on planetary surfaces, discovering new galaxies (Galaxyzoo), performing text translation. The current view of “humans-in-the-loop” tends to see humans as machines, robots, or low-level agents used or exploited in the service of broader computation goals. This dissertation is developed to shift the focus back to humans, and study different data analytics problems, by recognizing characteristics of the human workers, and how to incorporate those in a principled fashion inside the computation loop. The first contribution of this dissertation is to propose an optimization framework and a real world system to personalize worker’s behavior by developing a worker model and using that to better understand and estimate task completion time. The framework judiciously frames questions and solicits worker feedback on those to update the worker model. Next, improving workers skills through peer interaction during collaborative task completion is studied. A suite of optimization problems are identified in that context considering collaborativeness between the members as it plays a major role in peer learning. Finally, “diversified” sequence of work sessions for human workers is designed to improve worker satisfaction and engagement while completing tasks