Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Inductive logic programming”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

12 recordsLinked to original sources
PubMed1992

Drug design by machine learning: the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase.

The machine learning program GOLEM from the field of inductive logic programming was applied to the drug design problem of modeling structure-activity relationships. The training data for the program were 44 trimethoprim analogues and their observed inhibition of Escherichia coli dihydrofolate reductase. A further 11 compounds were used as unseen test data. GOLEM obtained rules that were statistically more accurate on the training data and also better on the test data than a Hansch linear regression model. Importantly machine learning yields understandable rules that characterized the chemistry of favored inhibitors in terms of polarity, flexibility, and hydrogen-bonding character. These rules agree with the stereochemistry of the interaction observed crystallographically.

Artificial Intelligence↗
PubMed1992

Protein secondary structure prediction using logic-based machine learning.

Many attempts have been made to solve the problem of predicting protein secondary structure from the primary sequence but the best performance results are still disappointing. In this paper, the use of a machine learning algorithm which allows relational descriptions is shown to lead to improved performance. The Inductive Logic Programming computer program, Golem, was applied to learning secondary structure prediction rules for alpha/alpha domain type proteins. The input to the program consisted of 12 non-homologous proteins (1612 residues) of known structure, together with a background knowledge describing the chemical and physical properties of the residues. Golem learned a small set of rules that predict which residues are part of the alpha-helices--based on their positional relationships and chemical and physical properties. The rules were tested on four independent non-homologous proteins (416 residues) giving an accuracy of 81% (+/- 2%). This is an improvement, on identical data, over the previously reported result of 73% by King and Sternberg (1990, J. Mol. Biol., 216, 441-457) using the machine learning program PROMIS, and of 72% using the standard Garnier-Osguthorpe-Robson method. The best previously reported result in the literature for the alpha/alpha domain type is 76%, achieved using a neural net approach. Machine learning also has the advantage over neural network and statistical methods in producing more understandable results.

Amino Acid Sequence↗
PubMed2025

Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models.

Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation. Genome-scale metabolic network models (GEMs) - comprehensive representations of metabolic genes and reactions - are widely used to evaluate genetic engineering of biological systems. However, GEMs often fail to accurately predict the behaviour of genetically engineered cells, primarily due to incomplete annotations of gene interactions. The task of learning the intricate genetic interactions within GEMs presents computational and empirical challenges. To efficiently predict using GEM, we describe a novel approach called Boolean Matrix Logic Programming (BMLP) by leveraging Boolean matrices to evaluate large logic programs. We developed a new system, [Formula: see text], which guides cost-effective experimentation and uses interpretable logic programs to encode a state-of-the-art GEM of a model bacterial organism. Notably, [Formula: see text] successfully learned the interaction between a gene pair with fewer training examples than random experimentation, overcoming the increase in experimental design space. [Formula: see text] enables rapid optimisation of metabolic models to reliably engineer biological systems for producing useful compounds. It offers a realistic approach to creating a self-driving lab for biological discovery, which would then facilitate microbial engineering for practical applications.

Active learning↗
PubMed1985

A program for machine learning of counting criteria: empirical induction of logic-based classification rules.

A program has been developed which derives classification rules from empirical observations and expresses these rules in a knowledge representation format called 'counting criteria'. Decision rules derived in this format are often more comprehensible than rules derived by existing machine learning programs such as AQ11. Use of the program is illustrated by the inference of discrimination criteria for certain types of bacteria based upon their biochemical characteristics. The program may be useful for the conceptual analysis of data and for the automatic generation of prototype knowledge bases for expert systems.

Artificial Intelligence↗
PubMedDate not supplied

Application of expert systems analysis to interpretation of fatal cases involving amitriptyline.

Part I. Expert 4: The object of this study was to investigate the applicability of commercially available expert system shells to interpretation in forensic toxicology. Amitriptyline toxicology was selected as a pilot trial. Blood and tissue concentrations of amitriptyline and nortriptyline in fatal and nonfatal amitriptyline cases from the literature and from the Registry of Human Toxicology databank were entered into the expert system shell Expert 4 (Rivers, Elsevier). The statistical evaluation routines of the shell were used to search for patterns in the data. Successive changes in the data base were made to test for the influence of the data base on the conclusions. Finally the data base was refined, based on the evaluations, to strengthen the probabilities of the conclusions. The refined database was coupled with the Expert 4 inference engine to infer unknown parameters in the cases. The results of the expert system analysis were compared to known values and published expert opinions. The ratio of amitriptyline/nortriptyline and tissue levels of nortriptyline were found to be the most significant measures for interpretation of effect and time since ingestion. Part II. Computer Induction of Rules: Blood and tissue concentrations of amitriptyline and nortriptyline in fatal and nonfatal amitriptyline cases from the literature and from the Registry of Human Toxicology databank were entered into the expert system shell BEAGLE, (Forsyth, Machine Learning Research, Ltd.). The automatic rule induction routines of the shell were used to search for patterns in the data. The program expressed these patterns as numerical predictions or Boolean logic rules. The results were compared to those obtained with the Expert 4 (Rivers, Elsevier) using the same case knowledge base.(ABSTRACT TRUNCATED AT 250 WORDS)

Amitriptyline↗
PubMed1977

Logic as a tool for clinical training in social work.

The paper is an attempt to illustrate the usefulness of logic as a technique in the clinical training of mental health professionals. The specific concepts that are examined include the nature of deductive and inductive reasoning, hypothesis testing, necessary and sufficient conditions, "if-then" propositions, and the nature of clinical evidence. Knowledge and use of these concepts was tested in a tutorial program directed toward students who were beginning graduate studies in the field of social work. Some of the difficulties encountered by these students, especially in the clinical aspects of their training, were directly related to an inadequate understanding of these logical forms of reasoning. It is suggested that a portion of the clinical training in mental health fields be directed towards a deeper understanding and utilization of these basic concepts.

Curriculum↗
PubMed1988

Affect, affective resonance and a new theory for hypnosis.

New theory is most useful when it helps explain phenomena outside the observational realm within which it was derived. The growing body of evidence suggesting that adult human emotion is the result of neocortical modulation of phylogenetically earlier subcortical affect programs, and the logical system developed by Tomkins to explain the links between innate affect and adult behavior, has been reviewed in terms of newer work on infant observation. The study of interaffectivity and intersubjectivity leads to an understanding of the caregiver as an external modulator of infantile affect; the similarity between these processes of external modulation and the well known techniques of hypnotic induction suggests commonality. Save for a massive reorganization of our theories about affect and its relationship to the face, I do not think it can any longer be considered valid for an investigator to present data about hypnosis without meticulous attention to facial affect display.

Affect↗
PubMedDate not supplied

[Training in thinking for beginning students: a new approach to cognitive development].

Modern cognitive psychology uses training methods not only as research methods but also as means for cognitive fostering. This article deals with a new experimentally tested theory on inductive thinking and an training program based upon that theory. The program has been tried out several times. The results of four training experiments are reported. They show constantly high effect sizes lasting at last over several months. The program is applicable for normal children of age 5-7 as well as for older retardates or younger bright children.

Child↗
PubMed2024

A time-resolved single-cell roadmap of the logic driving anterior neural crest diversification from neural border to migration stages.

Neural crest cells exemplify cellular diversification from a multipotent progenitor population. However, the full sequence of early molecular choices orchestrating the emergence of neural crest heterogeneity from the embryonic ectoderm remains elusive. Gene-regulatory-networks (GRN) govern early development and cell specification toward definitive neural crest. Here, we combine ultradense single-cell transcriptomes with machine-learning and large-scale transcriptomic and epigenomic experimental validation of selected trajectories, to provide the general principles and highlight specific features of the GRN underlying neural crest fate diversification from induction to early migration stages using Xenopus frog embryos as a model. During gastrulation, a transient neural border zone state precedes the choice between neural crest and placodes which includes multiple converging gene programs. During neurulation, transcription factor connectome, and bifurcation analyses demonstrate the early emergence of neural crest fates at the neural plate stage, alongside an unbiased multipotent-like lineage persisting until epithelial-mesenchymal transition stage. We also decipher circuits driving cranial and vagal neural crest formation and provide a broadly applicable high-throughput validation strategy for investigating single-cell transcriptomes in vertebrate GRNs in development, evolution, and disease.

Animals↗
PubMed2026

Repurposing anti-phage defenses to differentially arrest the viral lifecycle reveals the regulatory logic of a parasitic satellite.

Mobile genetic elements frequently encode defense mechanisms to protect their bacterial hosts from viral attack. In Vibrio cholerae, these defensive elements include phage-inducible chromosomal island-like elements (PLEs), which are phage satellites that act as highly specialized parasites of the lytic phage ICP1. While PLE transcriptional activation upon ICP1 infection is known to be temporally regulated, the underlying regulatory logic and dependencies on the progression of the phage's developmental program required for activation remain unclear. In this study, we took a novel approach to define these dependencies by introducing independent anti-phage defense systems, BREX and DarTG, as molecular roadblocks to impede the ICP1 lifecycle. We discovered that, for both ICP1 and PLE, late-stage gene expression is fundamentally uncoupled from genome replication, representing a striking departure from the standard paradigm for double-stranded DNA phages. While BREX restricts ICP1 to an immediate-early transcriptional state that stalls PLE activation, DarTG allows the phage to execute its full transcriptional cascade despite the total block in DNA replication. This permissive environment provides the necessary cues for complete PLE induction, revealing that the extent of ICP1 transcriptional progression is a key determinant of PLE transcriptional activation. Unlike other phage satellites that rely on a single cue for activation, our results demonstrate that PLE uses a progressive licensing strategy that relies on multiple cues tied to milestones in the phage's developmental program. This regulatory architecture ensures robust PLE activation resilient to phage escape.

Journal Article↗
PubMed2026

Repurposing anti-phage defenses to differentially arrest the viral lifecycle reveals the regulatory logic of a parasitic satellite.

Mobile genetic elements frequently encode defense mechanisms to protect their bacterial hosts from viral attack. In Vibrio cholerae, these defensive elements include phage-inducible chromosomal island-like elements (PLEs), which are phage satellites that act as highly specialized parasites of the lytic phage ICP1. While PLE transcriptional activation upon ICP1 infection is known to be temporally regulated, the underlying regulatory logic and dependencies on the progression of the phage's developmental program required for activation remain unclear. In this study, we took a novel approach to define these dependencies by introducing independent anti-phage defense systems, BREX and DarTG, as molecular roadblocks to impede the ICP1 lifecycle. We discovered that, for both ICP1 and PLE, late-stage gene expression is fundamentally uncoupled from genome replication, representing a striking departure from the standard paradigm for double-stranded DNA phages. While BREX restricts ICP1 to an immediate-early transcriptional state that stalls PLE activation, DarTG allows the phage to execute its full transcriptional cascade despite the total block in DNA replication. This permissive environment provides the necessary cue(s) for complete PLE induction, revealing that robust PLE activation is profoundly dependent on the transcriptional progression of its helper phage.IMPORTANCEBacteria and their viruses (phages) are locked in perpetual evolutionary conflict. Some bacteria harbor phage satellites, specialized parasites that are activated to hijack the phage's components to spread all the while inhibiting viral production. While some satellites respond to a single viral trigger, the regulation of many satellites, including clinically relevant phage-inducible chromosomal island-like elements (PLEs) in Vibrio cholerae, remains poorly understood. Here, we used bacterial defense systems as molecular roadblocks to probe how PLE activation depends on its helper phage. We found that severe disruptions to viral transcription stall PLE activation. Unexpectedly, both the virus and the satellite can execute their full transcriptional programs even when DNA replication is completely blocked, challenging a fundamental paradigm in virology. These insights reveal a sophisticated level of phage-satellite coordination, illustrating how satellite activation is tightly linked to the transcriptional state of its helper phage, a dependency that ultimately drives the dissemination of mobile genetic elements.

Vibrio cholerae↗
PubMed1988

Reflections on the epistemology of psychiatry.

A re-examination of the theoretical basis of our practice of psychiatry (that is, its epistemology) reveals the insufficiency of the empirical, inductive approach which we have come to regard, too myopically, as the sine qua non of our science. Traditionally in psychiatry, the discipline of philosophy, of which epistemology is one of its major fields of endeavour, has generally come to be regarded as irrelevant or unreliable as a source of true knowledge. But an objective look at our variegated practice of psychiatry--roughly divided into two groups--the biological on the one side and the psychosocial on the other--reveals a glaring lack of integration, cohesion, or synthesis in basic theory. While analysis is the prime modus operandi of science, synthesis is the main objective of philosophy. While we subscribe to various operational theories to explain how our various procedures work, we lack an overarching, unified, general theory to subsume them. Hence we lack a truly holistic concept of the person who is our patient. In this we are much in need of the discipline of philosophy, which promotes clarity of thought, breadth of comprehension, and systematic (logical) reasoning. Psychiatrists acquire more of this philosophic expertise through collaboration with professional philosophers (epistemologists in particular) and through the introduction into our graduate psychiatric training programs of some specific course content from the literature of philosophy. As a preliminary suggestion for this, an "Annotated Reading List" is appended.

Canada↗