The Weighted First-Order Model Counting Problem (WFOMC) asks to compute the weighted sum of models of a given first-order logic sentence over a given domain. Conditioning WFOMC on evidence—fixing the truth values of a set of ground literals—has been shown impossible in time polynomial in the domain size (unless ♯P ⊆ FP) even for fragments of logic that are otherwise tractable for WFOMC without evidence. In this work, we address the barrier by restricting the binary evidence to the case where the underlying Gaifman graph has bounded treewidth. We present a polynomial-time algorithm in the domain size for computing WFOMC for the two-variable fragments ??² and ?² conditioned on such binary evidence. Furthermore, we show the applicability of our algorithm in combinatorial problems by solving the stable seating arrangement problem on bounded-treewidth graphs of bounded degree, which was an open problem. We also conducted experiments to show the scalability of our algorithm compared to the existing model counting solvers.

The Weighted First-Order Model Counting Problem (WFOMC) asks to compute the weighted sum of models of a given first-order logic sentence over a given domain. It can be solved in time polynomial in the domain size for sentences from the two-variable fragment with counting quantifiers, known as $C^2$. This polynomial-time complexity is known to be retained when extending $C^2$ by one of the following axioms: linear order axiom, tree axiom, forest axiom, directed acyclic graph axiom or connectedness axiom. An interesting question remains as to which other axioms can be added to the first-order sentences in this way. We provide a new perspective on this problem by associating WFOMC with graph polynomials. Using WFOMC, we define Weak Connectedness Polynomial and Strong Connectedness Polynomials for first-order logic sentences. It turns out that these polynomials have the following interesting properties. First, they can be computed in polynomial time in the domain size for sentences from $C^2$. Second, we can use them to solve WFOMC with all of the existing axioms known to be tractable as well as with new ones such as bipartiteness, strong connectedness, having $k$ connected components, etc. Third, the well-known Tutte polynomial can be recovered as a special case of the Weak Connectedness Polynomial, and the Strict and Non-Strict Directed Chromatic Polynomials can be recovered from the Strong Connectedness Polynomials.

Knowledge compilation transforms logical theories into circuit representations that support efficient reasoning. We study this problem for propositional groundings of FO², the two-variable fragment of first-order logic over finite domains. Given an FO² sentence and a domain of size n, its grounding yields a propositional theory over ground atoms. We ask whether such theories admit compact representations in DNNF-based and related knowledge compilation languages, and whether these can be constructed efficiently, both with respect to the domain size n for a fixed sentence. We show first that compact compilation is impossible in general: there exists an FO² sentence whose grounding over a domain of size n requires DNNF size 2^Ω(n). On the positive side, we develop a two-stage compiler that exploits the symmetries inherent in the propositional groundings of FO² sentences. It branches on unary and binary types rather than individual ground atoms, in a similar spirit to lifted inferences for probabilistic relational models. Moreover, it optimizes the compilation process by efficiently identifying and caching residual subproblems that are equivalent with respect to future extensions. Experiments show the practical efficiency of our approach, which often produces smaller circuits and compiles faster than straightforward grounding-based baselines.

We investigate lifted inference on ordered domains with predecessor relations, where the elements of the domain respect a total (cyclic) order, and every element has a distinct (clockwise) predecessor. Previous work has explored this problem through weighted first-order model counting (WFOMC), which computes the weighted sum of models for a given first-order logic sentence over a finite domain. In WFOMC, the order constraint is typically encoded by the linear order axiom introducing a binary predicate in the sentence to impose a linear ordering on the domain elements. The immediate and second predecessor relations are then encoded by the linear order predicate. Although WFOMC with the linear order axiom is theoretically tractable, existing algorithms struggle with practical applications, particularly when the predecessor relations are involved. In this paper, we treat predecessor relations as a native part of the axiom and devise a novel algorithm that inherently supports these relations. The proposed algorithm not only provides an exponential speedup for the immediate and second predecessor relations, which are known to be tractable, but also handles the general k-th predecessor relations. The extensive experiments on lifted inference tasks and combinatorics math problems demonstrate the efficiency of our algorithm, achieving speedups of a full order of magnitude.

We study the model enumeration problem of the function-free, finite domain fragment of first-order logic with two variables (FO2). Specifically, given an FO2sentence Γ and a positive integer n, how can one enumerate all the models of Γ over a domain of size n? In this paper, we devise a novel algorithm to address this problem. The delay complexity, the time required between producing two consecutive models, of our algorithm is quadratic in the given domain size n (up to logarithmic factors) when the sentence is fixed. This complexity is almost optimal since the interpretation of binary predicates in any model requires at least Ω(n2) bits to represent.

We consider the task of weighted first-order model counting (WFOMC), a fundamental problem of probabilistic inference in statistical relational learning. The goal of WFOMC is to compute the weighted sum of models of a given first-order logic sentence over a finite domain, where each model is assigned a weight by a pair of weighting functions. Past work has shown that WFOMC can be solved in polynomial time in the domain size if the sentence is in the two-variable fragment of first-order logic (FO2). This result is later extended to the case where the sentence is in FO2with the linear order axiom, which requires a binary predicate in the sentence to introduce a linear ordering of the domain elements. However, despite its polynomial theoretical complexity, the existing domain-liftable algorithm for WFOMC with the linear order often suffers from inefficiencies when applied to real-world problems. This paper introduces a novel domain-lifted algorithm for WFOMC with the linear order axiom. Compared to the existing approach, our proposed algorithm exploits the inherent symmetries within first-order logic sentences and weighting functions to minimize redundant computations. Experimental results verify the efficiency of our approach, demonstrating a significant speedup over the existing approach.

We study the time complexity of weighted first-order model counting (WFOMC) over the logical language with two variables and counting quantifiers. The problem is known to be solvable in time polynomial in the domain size. However, the degree of the polynomial, which turns out to be relatively high for most practical applications, has never been properly addressed. First, we formulate a time complexity bound for the existing techniques for solving WFOMC with counting quantifiers. The bound is already known to be a polynomial with its degree depending on the number of cells of the input formula. We observe that the number of cells depends, in turn, exponentially on the parameters of the counting quantifiers appearing in the formula. Second, we propose a new approach to dealing with counting quantifiers, reducing the exponential dependency to a quadratic one, therefore obtaining a tighter upper bound. It remains an open question whether the dependency of the polynomial degree on the counting quantifiers can be reduced further, thus making our new bound a bound to beat.

Tree ensembles are one of the most widely used model classes. However, these models are susceptible to adversarial examples, i.e., slightly perturbed examples that elicit a misprediction. There has been significant research on designing approaches to construct such examples for tree ensembles. But this is a computationally challenging problem that often must be solved a large number of times (e.g., for all examples in a training set). This is compounded by the fact that current approaches attempt to find such examples from scratch. In contrast, we exploit the fact that multiple similar problems are being solved. Specifically, our approach exploits the insight that adversarial examples for tree ensembles tend to perturb a consistent but relatively small set of features. We show that we can quickly identify this set of features and use this knowledge to speedup constructing adversarial examples.

We consider the task of weighted first-order model counting (WFOMC) used for probabilistic inference in the area of statistical relational learning. Given a formula φ, domain size n and a pair of weight functions, what is the weighted sum of all models of φ over a domain of size n? It was shown that computing WFOMC of any logical sentence with at most two logical variables can be done in time polynomial in n. However, it was also shown that the task is #P1-complete once we add the third variable, which inspired the search for extensions of the two-variable fragment that would still permit a running time polynomial in n. One of such extension is the two-variable fragment with counting quantifiers. In this paper, we prove that adding a linear order axiom (which forces one of the predicates in φ to introduce a linear ordering of the domain elements in each model of φ) on top of the counting quantifiers still permits a computation time polynomial in the domain size. We present a new dynamic programming-based algorithm which can compute WFOMC with linear order in time polynomial in n, thus proving our primary claim.

First-order model counting (FOMC) is the task of counting models of a first-order logic sentence over a given set of domain elements. Its weighted variant, WFOMC, generalizes FOMC by assigning weights to the models and has many applications in statistical relational learning. More than ten years of research by various authors has led to identification of non-trivial classes of WFOMC problems that can be solved in time polynomial in the number of domain elements. In this paper, we describe recent works on WFOMC and the related problem of weighted first-order model sampling (WFOMS). We also discuss possible applications of WFOMC and WFOMS within statistical relational learning and beyond, e.g., automated solving of problems from enumerative combinatorics and elementary probability theory. Finally, we mention research problems that still need to be tackled in order to make applications of these methods really practical more broadly.

We study the problem of generating interesting integer sequences with a combinatorial interpretation. For this we introduce a two-step approach. In the first step, we generate first-order logic sentences which define some combinatorial objects, e.g., undirected graphs, permutations, matchings etc. In the second step, we use algorithms for lifted first-order model counting to generate integer sequences that count the objects encoded by the first-order logic formulas generated in the first step. For instance, if the first-order sentence defines permutations then the generated integer sequence is the sequence of factorial numbers n!. We demonstrate that our approach is able to generate interesting new sequences by showing that a non-negligible fraction of the automatically generated sequences can actually be found in the Online Encyclopaedia of Integer Sequences (OEIS) while generating many other similar sequences which are not present in OEIS and which are potentially interesting. A key technical contribution of our work is the method for generation of first-order logic sentences which is able to drastically prune the space of sentences by discarding large fraction of sentences which would lead to redundant integer sequences.

In this paper, we study the sampling problem for first-order logic proposed recently by Wang et al.—how to efficiently sample a model of a given first-order sentence on a finite domain? We extend their result for the universally-quantified subfragment of two-variable logic FO2(UFO2) to the entire fragment of FO2. Specifically, we prove the domain-liftability under sampling of FO2, meaning that there exists a sampling algorithm for FO2that runs in time polynomial in the domain size. We then further show that this result continues to hold even in the presence of counting constraints, such as ∀x∃=ky : φ(x, y) and ∃=kx∀y : φ(x, y), for some quantifier-free formula φ(x, y). Our proposed method is constructive, and the resulting sampling algorithms have potential applications in various areas, including the uniform generation of combinatorial structures and sampling in statistical-relational models such as Markov logic networks and probabilistic logic programs.

Statistical relational AI and probabilistic logic programming have so far mostly focused on discrete probabilistic models. The reasons for this is that one needs to provide constructs to succinctly model the independencies in such models, and also provide efficient inference. Three types of independencies are important to represent and exploit for scalable inference in hybrid models: conditional independencies elegantly modeled in Bayesian networks, context-specific independencies naturally represented by logical rules, and independencies amongst attributes of related objects in relational models succinctly expressed by combining rules. This paper introduces a hybrid probabilistic logic programming language, DC#, which integrates distributional clauses' syntax and semantics principles of Bayesian logic programs. It represents the three types of independencies qualitatively. More importantly, we also introduce the scalable inference algorithm FO-CS-LW for DC#. FO-CS-LW is a first-order extension of the context-specific likelihood weighting algorithm (CS-LW), a novel sampling method that exploits conditional independencies and context-specific independencies in ground models. The FO-CS-LW algorithm upgrades CS-LW with unification and combining rules to the first-order case.

Given a first-order sentence ? and a domain size n, how can one sample a model of ? on the domain {1, . . . , n} efficiently as n scales? We consider two variants of this problem: the uniform sampling regime, in which the goal is to sample a model uniformly at random, and the symmetric weighted sampling regime, in which models are weighted according to the number of groundings of each predicate appearing in them. Solutions to this problem have applications to the scalable generation of combinatorial structures, as well as sampling in several statistical-relational models such as Markov logic networks and probabilistic logic programs. In this paper, we identify certain classes of sentences that are domain-liftable under sampling, in the sense that they admit a sampling algorithm that runs in time polynomial in n. In particular, we prove that every sentence of the form ∀x∀y: ?(x, y) for some quantifier-free formula ?(x,y) is domain-liftable under sampling. We then further show that this result continues to hold in the presence of one or more cardinality constraints as well as a single tree axiom constraint.

Abstract Relational autocompletion is the problem of automatically filling out some missing values in multi-relational data. We tackle this problem within the probabilistic logic programming framework ofDistributional Clauses(DCs), which supports both discrete and continuous probability distributions. Within this framework, we introduceDiceML– an approach to learn both the structure and the parameters of DC programs from relational data (with possibly missing data). To realize this,DiceMLintegrates statistical modeling and DCs with rule learning. The distinguishing features ofDiceMLare that it (1) tackles autocompletion in relational data, (2) learns DCs extended with statistical models, (3) deals with both discrete and continuous distributions, (4) can exploit background knowledge, and (5) uses an expectation–maximization-based (EM) algorithm to cope with missing data. The empirical results show the promise of the approach, even when there is missing data.

Sampling is a popular method for approximate inference when exact inference is impractical. Generally, sampling algorithms do not exploit context-specific independence (CSI) properties of probability distributions. We introduce context-specific likelihood weighting (CS-LW), a new sampling methodology, which besides exploiting the classical conditional independence properties, also exploits CSI properties. Unlike the standard likelihood weighting, CS-LW is based on partial assignments of random variables and requires fewer samples for convergence due to the sampling variance reduction. Furthermore, the speed of generating samples increases. Our novel notion of contextual assignments theoretically justifies CS-LW. We empirically show that CS-LW is competitive with state-of-the-art algorithms for approximate inference in the presence of a significant amount of CSIs.

We study the problem of constructing the relational marginal polytope (RMP) of a given set of first-order formulas. Past work has shown that the RMP construction problem can be reduced to weighted first-order model counting (WFOMC). However, existing reductions in the literature are intractable in practice, since they typically require an infeasibly large number of calls to a WFOMC oracle. In this paper, we propose an algorithm to construct RMPs using fewer oracle calls. As an application, we also show how to apply this new algorithm to improve an existing approximation scheme for WFOMC. We demonstrate the efficiency of the proposed approaches experimentally, and find that our method provides speed-ups over the baseline for RMP construction of a full order of magnitude.

We consider the problem of weighted first-order model counting (WFOMC): given a first-order sentence ϕ and domain size n ∈ ℕ, determine the weighted sum of models of ϕ over the domain {1, ..., n}. Past work has shown that any sentence using at most two logical variables admits an algorithm for WFOMC that runs in time polynomial in the given domain size (Van den Broeck 2011; Van den Broeck, Meert, and Darwiche 2014). In this paper, we extend this result to any two-variable sentence ϕ with the addition of a tree axiom, stating that some distinguished binary relation in ϕ forms a tree in the graph-theoretic sense.

We consider the weighted first-order model counting (WFOMC) task, a problem with important applications to inference and learning in structured graphical models. Bringing together earlier work [Van den Broeck et al., 2011, 2014], a formal proof was given by Beame et al. [2015] showing that the two-variable fragment of first-order logic, FO^2, is domain-liftable, meaning it admits an algorithm for WFOMC whose runtime is polynomial in the given domain size. However, applying this theoretical upper bound is often impractical for real-world problem instances. We show how to adapt their proof into a fast algorithm for lifted inference in FO^2, using only off-the-shelf tools for knowledge compilation, and several careful optimizations involving the cell graph of the input sentence, a novel construct we define that encodes the interactions between the cells of the sentence. Experimental results show that, despite our approach being largely orthogonal to that of Forclift [Van den Broeck et al., 2011], our algorithm often outperforms it, scaling to larger domain sizes on more complex input sentences.

We introduce neural Markov logic networks (NMLNs), a statistical relational learning system that borrows ideas from Markov logic. Like Markov logic networks (MLNs), NMLNs are an exponential-family model for modelling distributions over possible worlds, but unlike MLNs, they do not rely on explicitly specified first-order logic rules. Instead, NMLNs learn an implicit representation of such rules as a neural network that acts as a potential function on fragments of the relational structure. Similarly to many neural symbolic methods, NMLNs can exploit embeddings of constants but, unlike them, NMLNs work well also in their absence. This is extremely important for predicting in settings other than the transductive one. We showcase the potential of NMLNs on knowledge-base completion, triple classification and on generation of molecular (graph) data.

It is known due to the work of Van den Broeck, Meert and Darwiche that weighted first-order model counting (WFOMC) in the two-variable fragment of first-order logic can be solved in time polynomial in the number of domain elements. In this paper we extend this result to the two-variable fragment with counting quantifiers.

We study computational aspects of "relational marginal polytopes" which are statistical relational learning counterparts of marginal polytopes, well-known from probabilistic graphical models. Here, given some first-order logic formula, we can define its relational marginal statistic to be the fraction of groundings that make this formula true in a given possible world. For a list of first-order logic formulas, the relational marginal polytope is the set of all points that correspond to expected values of the relational marginal statistics that are realizable. In this paper we study the following two problems: (i) Do domain-liftability results for the partition functions of Markov logic networks (MLNs)carry over to the problem of relational marginal polytope construction? (ii) Is the relational marginal polytope containment problem hard under some plausible complexity-theoretic assumptions? Our positive results have consequences for lifted weight learning of MLNs. In particular, we show that weight learning of MLNs is domain-liftable whenever the computation of the partition function of the respective MLNs is domain-liftable (this result has not been rigorously proven before).

Relational learning for knowledge base completion has been receiving considerable attention. Intuitively, rule-based strategies are clearly appealing, given their transparency and their ability to capture complex relational dependencies. In practice, however, pure rule-based strategies are currently not competitive with state-of-the-art methods, which is a reflection of the fact that (i) learning high-quality rules is challenging, and (ii) classical entailment is too brittle to cope with the noisy nature of the learned rules and the given knowledge base. In this paper, we introduce STRiKE, a new approach for relational learning in knowledge bases which addresses these concerns. Our contribution is three-fold. First, we introduce a new method for learning stratified rule bases from relational data. Second, to use these rules in a noise-tolerant way, we propose a strategy which extends k-entailment, a recently introduced cautious entailment relation, to stratified rule bases. Finally, we introduce an efficient algorithm for reasoning based on k-entailment.

We study the symmetric weighted first-order model counting task and present ApproxWFOMC, a novel anytime method for efficiently bounding the weighted first-order model count of a sentence given an unweighted first-order model counting oracle. The algorithm has applications to inference in a variety of first-order probabilistic representations, such as Markov logic networks and probabilistic logic programs. Crucially for many applications, no assumptions are made on the form of the input sentence. Instead, the algorithm makes use of the symmetry inherent in the problem by imposing cardinality constraints on the number of possible true groundings of a sentence's literals. Realising the first-order model counting oracle in practice using the approximate hashing-based model counter ApproxMC3, we show how our algorithm is competitive with existing approximate and exact techniques for inference in first-order probabilistic models. We additionally provide PAC guarantees on the accuracy of the bounds generated.

We study expressivity of Markov logic networks (MLNs). We introduce complex MLNs, which use complex-valued weights, and show that, unlike standard MLNs with real-valued weights, complex MLNs are"fully expressive". We then observe that discrete Fourier transform can be computed using weighted first order model counting (WFOMC) with complex weights and use this observation to design an algorithm for computing "relational marginal polytopes" which needs substantially less calls to a WFOMC oracle than an existing recent algorithm.

We study lifted weight learning of Markov logic networks. We show that there is an algorithm for maximum-likelihood learning of 2-variable Markov logic networks which runs in time polynomial in the domain size. Our results are based on existing lifted-inference algorithms and recent algorithmic results on computing maximum entropy distributions.

In the propositional setting, the marginal problem is to find a (maximum-entropy) distribution that has some given marginals. We study this problem in a relational setting and make the following contributions. First, we compare two different notions of relational marginals. Second, we show a duality between the resulting relational marginal problems and the maximum likelihood estimation of the parameters of relational models, which generalizes a well-known duality from the propositional setting. Third, by exploiting the relational marginal formulation, we present a statistically sound method to learn the parameters of relational models that will be applied in settings where the number of constants differs between the training and test data. Furthermore, based on a relational generalization of marginal polytopes, we characterize cases where the standard estimators based on feature's number of true groundings needs to be adjusted and we quantitatively characterize the consequences of these adjustments. Fourth, we prove bounds on expected errors of the estimated parameters, which allows us to lower-bound, among other things, the effective sample size of relational training data.

In this paper we consider semantic spaces consisting of objects from some particular domain (e.g.IMDB movie reviews).Various authors have observed that such semantic spaces often model salient features (e.g.how scary a movie is) as directions.These feature directions allow us to rank objects according to how much they have the corresponding feature, and can thus play an important role in interpretable classifiers, recommendation systems, or entity-oriented search engines, among others.Methods for learning semantic spaces, however, are mostly aimed at modelling similarity.In this paper, we argue that there is an inherent trade-off between capturing similarity and faithfully modelling features as directions.Following this observation, we propose a simple method to fine-tune existing semantic spaces, with the aim of improving the quality of their feature directions.Crucially, our method is fully unsupervised, requiring only a bag-of-words representation of the objects as input.

We propose a method to combine the interpretability and expressive power of firstorder logic with the effectiveness of neural network learning. In particular, we introduce a lifted framework in which first-order rules are used to describe the structure of a given problem setting. These rules are then used as a template for constructing a number of neural networks, one for each training and testing example. As the different networks corresponding to different examples share their weights, these weights can be efficiently learned using stochastic gradient descent. Our framework provides a flexible way for implementing and combining a wide variety of modelling constructs. In particular, the use of first-order logic allows for a declarative specification of latent relational structures, which can then be efficiently discovered in a given data set using neural network learning. Experiments on 78 relational learning benchmarks clearly demonstrate the effectiveness of the framework.

The field of statistical relational learning (SRL) is concerned with learning probabilistic models from relational data. Learned SRL models are typically represented using some kind of weighted logical formulas, which makes them considerably more interpretable than those obtained by e.g. neural networks. In practice, however, these models are often still difficult to interpret correctly, as they can contain many formulas that interact in non-trivial ways and weights do not always have an intuitive meaning. To address this, we propose a new SRL method which uses possibilistic logic to encode relational models. Learned models are then essentially stratified classical theories, which explicitly encode what can be derived with a given level of certainty. Compared to Markov Logic Networks (MLNs), our method is faster and produces considerably more interpretable models.

Probability density estimation from data is a widely studied problem. Often, the primary goal is to faithfully mimic the underlying empirical density. Having an interpretable model that allows insight into why certain predictions were made is often of secondary importance. Using logic-based formalisms, such as Markov logic, can help with interpretability, but even in Markov logic it can be difficult to gain insight into a model's behavior due to interactions between the logical formulas used to specific the model. This paper explores an alternative approach to representing densities that makes use of possibilistic logic. Concretely, we propose a novel way to transform a learned density tree into a possibilistic logic theory. An advantage of our transformation is that it permits performing both MAP and, surprisingly, marginal inference, with the converted possibilistic logic theory. At the same time, we still retain the benefits conferred by using possibilistic logic, such as the ability to compact the theory and the interpretability of the model.

BACKGROUND: Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. METHODS: We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. RESULTS: The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. CONCLUSION: Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.

We introduce a novel method for prediction of DNA-binding propensity of proteins which extends our recently introduced ball-histogram method (Szabóova et al. 2012). Unlike the original ball-histogram method, it allows handling of continuous properties of protein regions. In experiments on four datasets of proteins, we show that the method improves upon the original ball-histogram method as well as other existing methods in terms of predictive accuracy.

We describe a conceptually simple framework for transformation-based learning in hybrid relational domains. The proposed approach is related to hybrid Markov logic and to Gaussian logic framework. We evaluate the approach in three domains and show that it can achieve state-of-the-art performance while using only limited amount of information.

We contribute a novel, ball-histogram approach to DNA-binding propensity prediction of proteins. Unlike state-of-the-art methods based on constructing an ad-hoc set of features describing physicochemical properties of the proteins, the ball-histogram technique enables a systematic, Monte-Carlo exploration of the spatial distribution of amino acids complying with automatically selected properties. This exploration yields a model for the prediction of DNA binding propensity. We validate our method in prediction experiments, improving on state-of-the-art accuracies. Moreover, our method also provides interpretable features involving spatial distributions of selected amino acids.

We describe an algorithm for constructing a set of acyclic conjunctive relational features by combining smaller conjunctive blocks. Unlike traditional level-wise approaches which preserve the monotonicity of frequency, our block-wise approach preserves a form of monotonicity of the irreducibility and relevancy feature properties, which are important in propositionalization employed in the context of classification learning. With pruning based on these properties, our block-wise approach efficiently scales to features including tens of first-order literals, far beyond the reach of state-of-the art propositionalization or inductive logic programming systems.

In inductive logic programming, θ-subsumption is a widely used coverage test. Unfortunately, testing θ-subsumption is NP-complete, which represents a crucial efficiency bottleneck for many relational learners. In this paper, we present a probabilistic estimator of clause coverage, based on a randomized restarted search strategy. Under a distribution assumption, our algorithm can estimate clause coverage without having to decide subsumption for all examples. We implement this algorithm in program ReCovEr. On generated graph data and real-world datasets, we show that ReCovEr provides reasonably accurate estimates while achieving dramatic runtimes improvements compared to a state-of-the-art algorithm.