Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network architectures with a fixed, and relatively short, input window of amino acids, centered at the prediction site. Although a fixed small window avoids overfitting problems, it does not permit to capture variable long-ranged information. Results: We introduce a family of novel architectures which can learn to make predictions based on variable ranges of dependencies. These architectures extend recurrent neural networks, introducing non-causal bidirectional dynamics to capture both upstream and downstream information. The prediction algorithm is completed by the use of mixtures of estimators that leverage evolutionary information, expressed in terms of multiple alignments, both at the input and output levels. While our system currently achieves an overall performance close to 76% correct prediction---at least comparable to the best existing systems---the main emphasis here is on the development of new algorithmic ideas. Availability: The executable program for predicting protein secondary structure is available from the authors free of charge. Contact: pfbaldi@ics.uci.edu, gpollast@ics.uci.edu, brunak@cbs.dtu.dk, paolo@dsi.unifi.it. 1

We are capable of drawing a variety of inferences effortlessly, spontaneously, and with remarkable efficiency — as though these inferences are a reflex response of our cognitive apparatus. This remarkable human ability poses a challenge for cognitive science and computational neuroscience: How can a network of slow neuron-like elements represent a large body of systematic knowledge and perform a wide range of inferences with such speed? The connectionist model Shruti attempts to address this challenge by demonstrating how a neurally plausible network can encode a large body of semantic and episodic facts, systematic rules, and knowledge about entities and types, and yet perform a wide range of explanatory and predictive inferences within a few hundred milliseconds. Relational structures (frames, schemas) are represented in Shruti by clusters of cells, and inference in Shruti corresponds to a transient propagation of rhythmic activity over such cell-clusters wherein dynamic bindings are represented by the synchronous firing of appropriate cells. Shruti encodes mappings across relational structures using high-efficacy links that enable the propagation of rhythmic activity, and it encodes items in long-term memory as coincidence and conincidence-error detector circuits that become active in response to the occurrence (or non-occurrence) of appropriate coincidences in the on going flux of rhythmic activity.

Motivation: Accurate prediction of protein contact maps is an important step in computational structural proteomics. Because contact maps provide a translation and rotation invariant topological representation of a protein, they can be used as a fundamental intermediary step in protein structure prediction.

The past few years have witnessed an significant interest in probabilistic logic learning, i.e. in research lying at the intersection of probabilistic reasoning, logical representations, and machine learning. A rich variety of di#erent formalisms and learning techniques have been developed. This paper provides an introductory survey and overview of the stateof -the-art in probabilistic logic learning through the identification of a number of important probabilistic, logical and learning concepts.

Motivation. We focus on the prediction of disulfide bridges in proteins starting from their amino acid sequence and from the knowledge of the disulfide bonding state of each cysteine. The location of disulfide bridges is a structural feature that conveys important information about the protein main chain conformation and can therefore help towards the solution of the folding problem. Existing approaches based on weighted graph matching algorithms do not take advantage of evolutionary information. Recursive neural networks (RNN), on the other hand, can handle in a natural way complex data structures such as graphs whose vertices are labeled by real vectors, allowing us to incorporate multiple alignment profiles in the graphical representation of disulfide connectivity patterns. Results. The core of the method is the use of machine learning tools to rank alternative disulfide connectivity patterns. We develop an ad-hoc RNN architecture for scoring labeled undirected graphs that represent connectivity patterns. In order to compare our algorithm with previous methods, we report experimental results on the SWISS-PROT 39 data set. We find that using multiple alignment profiles allows us to obtain significant prediction accuracy improvements, clearly demonstrating the important role played by evolutionary information. Availability. The Web interface of the predictor is available at

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We have recently shown that when initialized with "small" weights, recurrent neural networks (RNNs) with standard sigmoid-type activation functions are inherently biased towards Markov models, i.e. even prior to any training, RNN dynamics can be readily used to extract finite memory machines (Hammer & Tino, 2002; Tino, Cernansky & Benuskova, 2002; Tino, Cernansky & Benuskova, 2002a). Following Christiansen and Chater (1999), we refer to this phenomenon as the architectural bias of RNNs. In this paper we further extend our work on the architectural bias in RNNs by performing a rigorous fractal analysis of recurrent activation patterns. We assume the network is driven by sequences obtained by traversing an underlying finite-state transition diagram -- a scenario that has been frequently considered in the past e.g. when studying RNN-based learning and implementation of regular grammars and finite-state transducers. We obtain lower and upper bounds on various types of fractal dimensions, such as box-counting and Hausdor# dimensions. It turns out that not only can the recurrent activations inside RNNs with small initial weights be explored to build Markovian predictive models, but also the activations form fractal clusters the dimension of which can be bounded by the scaled entropy of the underlying driving source. The scaling factors are fixed and are given by the RNN parameters.

Classification is an important problem in image document processing and is often a preliminary step towards recognition, understanding, and information extraction. In this paper, the problem is formulated in the framework of concept learning and each category corresponds to the set of image documents with similar physical structure. We propose a solution based on two algorithmic ideas. First, we obtain a structured representation of images based on labeled XY-trees (this representation informs the learner about important relationships between image sub-constituents). Second, we propose a probabilistic architecture that extends hidden Markov models for learning probability distributions defined on spaces of labeled trees. Finally, a successful application of this method to the categorization of commercial invoices is presented.

This article explores the use of Simple Synchrony Networks (SSNs) for learning to parse English sentences drawn from a corpus of naturally occurring text. Parsing natural language sentences requires taking a sequence of words and outputting a hierarchical structure representing how those words fit together to form constituents. Feed-forward and Simple Recurrent Networks have had great difficulty with this task, in part because the number of relationships required to specify a structure is too large for the number of unit outputs they have available. SSNs have the representational power to output the necessary O(n 2 ) possible structural relationships, because SSNs extend the O(n) incremental outputs of Simple Recurrent Networks with the O(n) entity outputs provided by Temporal Synchrony Variable Binding. This article presents an incremental representation of constituent structures which allows SSNs to make effective use of both these dimensions. Experiments on learning to ...

... This paper is focused on the extraction and use of logical rules for data understanding. All aspects of rule generation, optimization, and application are described, including the problem of finding good symbolic descriptors for continuous data, tradeoffs between accuracy and simplicity at the rule-extraction stage, and tradeoffs between rejection and error level at the rule optimization stage. Stability of rule-based description, calculation of probabilities from rules, and other related issues are also discussed. Major approaches to extraction of logical rules based on neural networks, decision trees, machine learning, and statistical methods are introduced. Optimization and application issues for sets of logical rules are described. Applications of such methods to benchmark and real-life problems are reported and illustrated with simple logical rules for many datasets. Challenges and new directions for research are outlined.