Luís C. Lamb

Three-dimensional protein structure prediction

A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction.

Connectionist modal logic: Representing modalities in neural networks

Modal logics are amongst the most successful applied logical systems. Neural networks were proved to be effective learning systems. In this paper, we propose to combine the strengths of modal logics and neural networks by introducing Connectionist Modal Logics (CML). CML belongs to the domain of neural-symbolic integration, which concerns the application of problem-specific symbolic knowledge within the neurocomputing paradigm. In CML, one may represent, reason or learn modal logics using a neural network. This is achieved by a Modalities Algorithm that translates modal logic programs into neural network ensembles. We show that the translation is sound, i.e. the network ensemble computes a fixed-point meaning of the original modal program, acting as a distributed computational model for modal logic. We also show that the fixed-point computation terminates whenever the modal program is well-behaved. Finally, we validate CML as a computational model for integrated knowledge representation and learning by applying it to a well-known testbed for distributed knowledge representation. This paves the way for a range of applications on integrated knowledge representation and learning, from practical reasoning to evolving multi-agent systems.

Value-based Argumentation Frameworks as Neural-symbolic Learning Systems

While neural networks have been successfully used in a number of machine learning applications, logical languages have been the standard for the representation of argumentative reasoning. In this paper, we establish a relationship between neural networks and argumentation networks, combining reasoning and learning in the same argumentation framework. We do so by presenting a new neural argumentation algorithm, responsible for translating argumentation networks into standard neural networks. We then show a correspondence between the two networks. The algorithm works not only for acyclic argumentation networks, but also for circular networks, and it enables the accrual of arguments through learning as well as the parallel computation of arguments.

A connectionist inductive learning system for modal logic programming

Neural-Symbolic integration has become a very active research area in the last decade. In this paper, we present a new massively parallel model for modal logic. We do so by extending the language of Modal Prolog to allow modal operators in the head of the clauses. We then use an ensemble of C-IL/sup 2/p neural networks to encode the extended modal theory (and its relations), and show that the ensemble computes a fixpoint semantics of the extended theory. An immediate result of our approach is the ability to perform learning from examples efficiently using each network of the ensemble. Therefore, one can adapt the extended C-IL/sup 2/P system by training possible world representations.

Using UML as front-end for heterogeneous software code generation strategies

In this paper we propose an embedded software design flow, which starts from an UML model and provides automatic mapping to other models like Simulink or finite-state machines (FSM). An automatic synthesis of an executable and synthesizable Simulink model is also proposed, enabling the use of UML as front-end for a multi-model design strategy that includes a Simulink-based MPSoC target design flow. In addition, the proposed synthesis tool automatically handles processor allocation, mapping of threads to processors, and insertion of required Simulink temporal barriers, ports, and dataflow connections. Following this approach, the UML model is mapped to the more appropriated model and specialized code generators are used. Therefore, this approach allows designers to employ UML to model the whole system and reuse this model to generate code using different strategies and targeting different platforms.

Towards understanding the role of learning models in the dynamics of the minority game

We report experiments in a boundedly rational evolutionary game, namely the minority game, where agents apply a very simple learning algorithm to discard bad strategies and create new ones. The results show that even such simplified learning model presents qualitative differences from the behavior of the traditional game, where strategies are fixed and cannot be modified or discarded. We show that this result is qualitatively similar to other, more complex, learning approaches. Also, we study how the learning parameters of our model affect the dynamics of the game and we provide experimental evidence of a high dependence between the behavior of the system and the way fitness is attributed as new strategies enter the game.

A connectionist computational model for epistemic and temporal reasoning

The importance of the efforts to bridge the gap between the connectionist and symbolic paradigms of artificial intelligence has been widely recognized. The merging of theory (background knowledge) and data learning (learning from examples) into neural-symbolic systems has indicated that such a learning system is more effective than purely symbolic or purely connectionist systems. Until recently, however, neural-symbolic systems were not able to fully represent, reason, and learn expressive languages other than classical propositional and fragments of first-order logic. In this article, we show that nonclassical logics, in particular propositional temporal logic and combinations of temporal and epistemic (modal) reasoning, can be effectively computed by artificial neural networks. We present the language of a connectionist temporal logic of knowledge (CTLK). We then present a temporal algorithm that translates CTLK theories into ensembles of neural networks and prove that the translation is correct. Finally, we apply CTLK to the muddy children puzzle, which has been widely used as a testbed for distributed knowledge representation. We provide a complete solution to the puzzle with the use of simple neural networks, capable of reasoning about knowledge evolution in time and of knowledge acquisition through learning.

APPLYING CONNECTIONIST MODAL LOGICS TO DISTRIBUTED KNOWLEDGE REPRESENTATION PROBLEMS

Neural-Symbolic Systems concern the integration of the symbolic and connectionist paradigms of Artificial Intelligence. Distributed knowledge representation is traditionally seen under a symbolic perspective. In this paper, we show how neural networks can represent distributed symbolic knowledge, acting as multi-agent systems with learning capability (a key feature of neural networks). We apply the framework of Connectionist Modal Logics to well-known testbeds for distributed knowledge representation formalisms, namely the muddy children and the wise men puzzles. Finally, we sketch a full solution to these problems by extending our approach to deal with knowledge evolution over time.

A neural-symbolic cognitive agent for online learning and reasoning

In real-world applications, the effective integration of learning and reasoning in a cognitive agent model is a difficult task. However, such integration may lead to a better understanding, use and construction of more realistic models. Unfortunately, existing models are either oversimplified or require much processing time, which is unsuitable for online learning and reasoning. Currently, controlled environments like training simulators do not effectively integrate learning and reasoning. In particular, higher-order concepts and cognitive abilities have many unknown temporal relations with the data, making it impossible to represent such relationships by hand. We introduce a novel cognitive agent model and architecture for online learning and reasoning that seeks to effectively represent, learn and reason in complex training environments. The agent architecture of the model combines neural learning with symbolic knowledge representation. It is capable of learning new hypotheses from observed data, and infer new beliefs based on these hypotheses. Furthermore, it deals with uncertainty and errors in the data using a Bayesian inference model. The validation of the model on real-time simulations and the results presented here indicate the promise of the approach when performing online learning and reasoning in real-world scenarios, with possible applications in a range of areas.

Formalizing traceability relations for product lines

Traceability is considered an important activity during the development of software systems. Despite the various classifications that have been proposed for different types of traceability relations, there is still a lack of standard semantic definitions for traceability relations. In this paper, we present an ontology-based formalism for semantic representation of various types of traceability relations for product line systems and associations between these various types of traceability relations.