scholarly journals Products of weighted logic programs

2011 ◽  
Vol 11 (2-3) ◽  
pp. 263-296 ◽  
Author(s):  
SHAY B. COHEN ◽  
ROBERT J. SIMMONS ◽  
NOAH A. SMITH
Keyword(s):  
Machine Learning ◽  
Dynamic Programming ◽  
Logic Programming ◽  
Scoring Function ◽  
Logic Programs ◽  
Information Theoretic ◽  
Optimal Score ◽  
Leibler Divergence ◽  
Programming Algorithms ◽  
Output Space

AbstractWeighted logic programming, a generalization of bottom-up logic programming, is a well-suited framework for specifying dynamic programming algorithms. In this setting, proofs correspond to the algorithm's output space, such as a path through a graph or a grammatical derivation, and are given a real-valued score (often interpreted as a probability) that depends on the real weights of the base axioms used in the proof. The desired output is a function over all possible proofs, such as a sum of scores or an optimal score. We describe the product transformation, which can merge two weighted logic programs into a new one. The resulting program optimizes a product of proof scores from the original programs, constituting a scoring function known in machine learning as a “product of experts.” Through the addition of intuitive constraining side conditions, we show that several important dynamic programming algorithms can be derived by applying product to weighted logic programs corresponding to simpler weighted logic programs. In addition, we show how the computation of Kullback–Leibler divergence, an information-theoretic measure, can be interpreted using product.

scholarly journals Turning 30: New Ideas in Inductive Logic Programming

2020 ◽  
Author(s):  
Andrew Cropper ◽  
Sebastijan Dumančić ◽  
Stephen H. Muggleton
Keyword(s):  
Machine Learning ◽  
Logic Programming ◽  
Inductive Logic Programming ◽  
Inductive Logic ◽  
Background Knowledge ◽  
Training Data ◽  
Future Research ◽  
Logic Programs ◽  
Recursive Programs ◽  
New Ideas

Common criticisms of state-of-the-art machine learning include poor generalisation, a lack of interpretability, and a need for large amounts of training data. We survey recent work in inductive logic programming (ILP), a form of machine learning that induces logic programs from data, which has shown promise at addressing these limitations. We focus on new methods for learning recursive programs that generalise from few examples, a shift from using hand-crafted background knowledge to learning background knowledge, and the use of different technologies, notably answer set programming and neural networks. As ILP approaches 30, we also discuss directions for future research.

Large-sample confidence intervals of information-theoretic measures in linguistics

2020 ◽  
Vol 6 (1) ◽  
pp. 19-54
Author(s):  
Ryan Ka Yau Lai ◽  
Youngah Do
Keyword(s):  
Maximum Likelihood ◽  
Corpus Linguistics ◽  
Delta Method ◽  
Confidence Bounds ◽  
Likelihood Estimator ◽  
Information Theoretic ◽  
Leibler Divergence ◽  
Information Theoretic Measures ◽  
Data Points ◽  
Measure Of Uncertainty

This article explores a method of creating confidence bounds for information-theoretic measures in linguistics, such as entropy, Kullback-Leibler Divergence (KLD), and mutual information. We show that a useful measure of uncertainty can be derived from simple statistical principles, namely the asymptotic distribution of the maximum likelihood estimator (MLE) and the delta method. Three case studies from phonology and corpus linguistics are used to demonstrate how to apply it and examine its robustness against common violations of its assumptions in linguistics, such as insufficient sample size and non-independence of data points.

Random Forest Refinement of Pairwise Potentials for Protein-ligand Decoy Detection

2019 ◽  
Author(s):  
Jun Pei ◽  
Zheng Zheng ◽  
Hyunji Kim ◽  
Lin Song ◽  
Sarah Walworth ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Probability Function ◽  
Pair Potential ◽  
Scoring Function ◽  
Stable Structure ◽  
Scoring Functions ◽  
Atom Pair ◽  
Data Set ◽  
Atom Pairs

An accurate scoring function is expected to correctly select the most stable structure from a set of pose candidates. One can hypothesize that a scoring function’s ability to identify the most stable structure might be improved by emphasizing the most relevant atom pairwise interactions. However, it is hard to evaluate the relevant importance for each atom pair using traditional means. With the introduction of machine learning methods, it has become possible to determine the relative importance for each atom pair present in a scoring function. In this work, we use the Random Forest (RF) method to refine a pair potential developed by our laboratory (GARF6) by identifying relevant atom pairs that optimize the performance of the potential on our given task. Our goal is to construct a machine learning (ML) model that can accurately differentiate the native ligand binding pose from candidate poses using a potential refined by RF optimization. We successfully constructed RF models on an unbalanced data set with the ‘comparison’ concept and, the resultant RF models were tested on CASF-2013.5 In a comparison of the performance of our RF models against 29 scoring functions, we found our models outperformed the other scoring functions in predicting the native pose. In addition, we used two artificial designed potential models to address the importance of the GARF potential in the RF models: (1) a scrambled probability function set, which was obtained by mixing up atom pairs and probability functions in GARF, and (2) a uniform probability function set, which share the same peak positions with GARF but have fixed peak heights. The results of accuracy comparison from RF models based on the scrambled, uniform, and original GARF potential clearly showed that the peak positions in the GARF potential are important while the well depths are not. <br>

scholarly journals Semi-automated classification of colonial Microcystis by FlowCAM imaging flow cytometry in mesocosm experiment reveals high heterogeneity during seasonal bloom

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yersultan Mirasbekov ◽  
Adina Zhumakhanova ◽  
Almira Zhantuyakova ◽  
Kuanysh Sarkytbayev ◽  
Dmitry V. Malashenkov ◽  
...  
Keyword(s):  
Machine Learning ◽  
Flow Cytometry ◽  
Spatial Resolution ◽  
Mesocosm Experiment ◽  
Imaging Flow Cytometry ◽  
Leibler Divergence ◽  
Temporal And Spatial ◽  
High Level ◽  
Training Sets

AbstractA machine learning approach was employed to detect and quantify Microcystis colonial morphospecies using FlowCAM-based imaging flow cytometry. The system was trained and tested using samples from a long-term mesocosm experiment (LMWE, Central Jutland, Denmark). The statistical validation of the classification approaches was performed using Hellinger distances, Bray–Curtis dissimilarity, and Kullback–Leibler divergence. The semi-automatic classification based on well-balanced training sets from Microcystis seasonal bloom provided a high level of intergeneric accuracy (96–100%) but relatively low intrageneric accuracy (67–78%). Our results provide a proof-of-concept of how machine learning approaches can be applied to analyze the colonial microalgae. This approach allowed to evaluate Microcystis seasonal bloom in individual mesocosms with high level of temporal and spatial resolution. The observation that some Microcystis morphotypes completely disappeared and re-appeared along the mesocosm experiment timeline supports the hypothesis of the main transition pathways of colonial Microcystis morphoforms. We demonstrated that significant changes in the training sets with colonial images required for accurate classification of Microcystis spp. from time points differed by only two weeks due to Microcystis high phenotypic heterogeneity during the bloom. We conclude that automatic methods not only allow a performance level of human taxonomist, and thus be a valuable time-saving tool in the routine-like identification of colonial phytoplankton taxa, but also can be applied to increase temporal and spatial resolution of the study.

scholarly journals Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1

Molecules ◽  
2019 ◽  
Vol 24 (15) ◽  
pp. 2747 ◽  
Author(s):  
Eliane Briand ◽  
Ragnar Thomsen ◽  
Kristian Linnet ◽  
Henrik Berg Rasmussen ◽  
Søren Brunak ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Interactions ◽  
Scoring Function ◽  
Docking Study ◽  
Inhibitory Effect ◽  
Therapeutic Agents ◽  
Learning Approaches ◽  
Ensemble Docking ◽  
Ic50 Values

The human carboxylesterase 1 (CES1), responsible for the biotransformation of many diverse therapeutic agents, may contribute to the occurrence of adverse drug reactions and therapeutic failure through drug interactions. The present study is designed to address the issue of potential drug interactions resulting from the inhibition of CES1. Based on an ensemble of 10 crystal structures complexed with different ligands and a set of 294 known CES1 ligands, we used docking (Autodock Vina) and machine learning methodologies (LDA, QDA and multilayer perceptron), considering the different energy terms from the scoring function to assess the best combination to enable the identification of CES1 inhibitors. The protocol was then applied on a library of 1114 FDA-approved drugs and eight drugs were selected for in vitro CES1 inhibition. An inhibition effect was observed for diltiazem (IC50 = 13.9 µM). Three others drugs (benztropine, iloprost and treprostinil), exhibited a weak CES1 inhibitory effects with IC50 values of 298.2 µM, 366.8 µM and 391.6 µM respectively. In conclusion, the binding site of CES1 is relatively flexible and can adapt its conformation to different types of ligands. Combining ensemble docking and machine learning approaches improves the prediction of CES1 inhibitors compared to a docking study using only one crystal structure.

Efficient Execution of Dynamic Programming Algorithms on Apache Spark

2020 ◽  
Author(s):  
Mohammad Mahdi Javanmard ◽  
Zafar Ahmad ◽  
Jaroslaw Zola ◽  
Louis-Noel Pouchet ◽  
Rezaul Chowdhury ◽  
...  
Keyword(s):  
Dynamic Programming ◽  
Apache Spark ◽  
Programming Algorithms ◽  
Efficient Execution

A Modal Semantics of Negation in Logic Programming

1992 ◽  
Vol 16 (3-4) ◽  
pp. 231-262
Author(s):  
Philippe Balbiani
Keyword(s):  
Modal Logic ◽  
Logic Programming ◽  
Modal Logics ◽  
Kripke Models ◽  
Logic Programs ◽  
Modal Semantics ◽  
Soundness And Completeness ◽  
Modal Completion ◽  
Well Foundedness

The beauty of modal logics and their interest lie in their ability to represent such different intensional concepts as knowledge, time, obligation, provability in arithmetic, … according to the properties satisfied by the accessibility relations of their Kripke models (transitivity, reflexivity, symmetry, well-foundedness, …). The purpose of this paper is to study the ability of modal logics to represent the concepts of provability and unprovability in logic programming. The use of modal logic to study the semantics of logic programming with negation is defended with the help of a modal completion formula. This formula is a modal translation of Clack’s formula. It gives soundness and completeness proofs for the negation as failure rule. It offers a formal characterization of unprovability in logic programs. It characterizes as well its stratified semantics.

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