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The protein design problem is to identify an amino acid sequence that folds to a desired structure. Given Anfinsen's thermodynamic hypothesis of folding, this can be recast as finding an amino acid sequence for which the desired structure is the lowest energy state. As this calculation involves not only all possible amino acid sequences but also, all possible structures, most current approaches focus instead on the more tractable problem of finding the lowest-energy amino acid sequence for the desired structure, often checking by protein structure prediction in a second step that the desired structure is indeed the lowest-energy conformation for the designed sequence, and typically discarding a large fraction of designed sequences for which this is not the case. Here, we show that by backpropagating gradients through the transform-restrained Rosetta (trRosetta) structure prediction network from the desired structure to the input amino acid sequence, we can directly optimize over all possible amino acid sequences and all possible structures in a single calculation. We find that trRosetta calculations, which consider the full conformational landscape, can be more effective than Rosetta single-point energy estimations in predicting folding and stability of de novo designed proteins. We compare sequence design by conformational landscape optimization with the standard energy-based sequence design methodology in Rosetta and show that the former can result in energy landscapes with fewer alternative energy minima. We show further that more funneled energy landscapes can be designed by combining the strengths of the two approaches: the low-resolution trRosetta model serves to disfavor alternative states, and the high-resolution Rosetta model serves to create a deep energy minimum at the design target structure. [ABSTRACT FROM AUTHOR]

Background: Screening programs use mammography as primary diagnostic tool for detecting breast cancer at an early stage. The diagnosis of some lesions, such as microcalcifications, is still difficult today for radiologists. In this paper, we proposed an automatic binary model for discriminating tissue in digital mammograms, as support tool for the radiologists. In particular, we compared the contribution of different methods on the feature selection process in terms of the learning performances and selected features. Results: For each ROI, we extracted textural features on Haar wavelet decompositions and also interest points and corners detected by using Speeded Up Robust Feature (SURF) and Minimum Eigenvalue Algorithm (MinEigenAlg). Then a Random Forest binary classifier is trained on a subset of a sub-set features selected by two different kinds of feature selection techniques, such as filter and embedded methods. We tested the proposed model on 260 ROIs extracted from digital mammograms of the BCDR public database. The best prediction performance for the normal/abnormal and benign/malignant problems reaches a median AUC value of 98.16% and 92.08%, and an accuracy of 97.31% and 88.46%, respectively. The experimental result was comparable with related work performance. Conclusions: The best performing result obtained with embedded method is more parsimonious than the filter one. The SURF and MinEigen algorithms provide a strong informative content useful for the characterization of microcalcification clusters. [ABSTRACT FROM AUTHOR]

First-Order Logic formulæ are a powerful representation formalism characterized by the use of relations, that cause serious computational problems due to the phenomenon of indeterminacy (various portions of one description are possibly mapped in different ways onto another description). Being able to identify the correct corresponding parts of two descriptions would help to tackle the problem: hence, the need for a framework for the comparison and similarity assessment. This could have many applications in Artificial Intelligence: guiding subsumption procedures and theory revision systems, implementing flexible matching, supporting instance-based learning and conceptual clustering. Unfortunately, few works on this subject are available in the literature. This paper focuses on Horn clauses, which are the basis for the Logic Programming paradigm, and proposes a novel similarity formula and evaluation criteria for identifying the descriptions components that are more similar and hence more likely to correspond to each other, based only on their syntactic structure. Experiments on real-world datasets prove the effectiveness of the proposal, and the efficiency of the corresponding implementation in the above tasks. [ABSTRACT FROM AUTHOR]

In real-life domains, learning systems often have to deal with various kinds of imperfections in data such as noise, incompleteness and inexactness. This problem seriously affects the knowledge discovery process, specifically in the case of traditional Machine Learning approaches that exploit simple or constrained knowledge representations and are based on single inference mechanisms. Indeed, this limits their capability of discovering fundamental knowledge in those situations. In order to broaden the investigation and the applicability of machine learning schemes in such particular situations, it is necessary to move on to more expressive representations which require more complex inference mechanisms. However, the applicability of such new and complex inference mechanisms, such as abductive reasoning, strongly relies on a deep background knowledge about the specific application domain. This work aims at automatically discovering the meta-knowledge needed to abduction inference strategy to complete the incoming information in order to handle cases of missing knowledge. [ABSTRACT FROM AUTHOR]

Exploring digital collections to find information relevant to a user's interests is a challenging task. Algorithms designed to solve this relevant information problem base their relevance computations on user profiles in which representations of the users' interests are maintained. This article presents a new method, based on the classic Rocchio algorithm for text categorization, able to discover user preferences from the analysis of textual descriptions of items in online catalog of e-commerce Web sites. Experiments have been carried out on several data sets, and results have been compared with those obtained using an inductive logic programming (ILP) approach and a probabilistic one. [ABSTRACT FROM AUTHOR]

Traditional Machine Learning approaches based on single inference mechanisms have reached their limits. This causes the need for a framework that integrates approaches based on abduction and abstraction capabilities in the inductive learning paradigm, in the light of Michalski's Inferential Theory of Learning (ITL). This work is intended as a survey of the most significant contributions that are present in the literature, concerning single reasoning strategies and practical ways for bringing them together and making them cooperate in order to improve the effectiveness and efficiency of the learning process. The elicited role of an abductive proof procedure is tackling the problem of incomplete relevance in the incoming examples. Moreover, the employment of abstraction operators based on (direct and inverse) resolution to reduce the complexity of the learning problem is discussed. Lastly, a case study that implements the combined framework into a real multistrategy learning system is briefly presented. [ABSTRACT FROM AUTHOR]