Inductive inference of novel protein-molecule interactions using Heterogeneous Graph Transformer (HGT) AutoEncoder

Protein-molecule interactions are promoted by the physicochemical characteristics of the actors involved, but structural information alone does not capture expression patterns, localization and pharmacokinetics. In this work we propose an integrative strategy for protein-molecule interaction discovery that combines different layers of information through the use of convolutional operators on graph, and frame the problem as missing link prediction task on an heterogeneous graph constituted by three node types: 1) molecules 2) proteins 3) diseases. Physicochemical information of the actors are encoded using shallow embedding techniques (SeqVec, Mol2Vec, Doc2Vec respectively) and are supplied as feature vectors to a Graph AutoEncoer (GAE) that uses a Heterogeneous Graph Transformer (HGT) in the encoder module. We show in this work that HGT Autoencoder can be used to accurately recapitulate the protein-molecule interactions set and propose novel relationships in inductive settings that are grounded in biological and functional information extracted from the graph.

Scientific Variables

Despite their centrality to the scientific enterprise, both the nature of scientific variables and their relation to inductive inference remain obscure. I suggest that scientific variables should be viewed as equivalence classes of sets of physical states mapped to representations (often real numbers) in a structure preserving fashion, and argue that most scientific variables introduced to expand the degrees of freedom in terms of which we describe the world can be seen as products of an algorithmic inductive inference first identified by William W. Rozeboom. This inference algorithm depends upon a notion of natural kind previously left unexplicated. By appealing to dynamical kinds—equivalence classes of causal system characterized by the interventions which commute with their time evolution—to fill this gap, we attain a complete algorithm. I demonstrate the efficacy of this algorithm in a series of experiments involving the percolation of water through granular soils that result in the induction of three novel variables. Finally, I argue that variables obtained through this sort of inductive inference are guaranteed to satisfy a variety of norms that in turn suit them for use in further scientific inferences.

DEVELOPMENT OF A METHOD FOR CONSTRUCTING AND ASSESSING THE RELIABILITY OF HYPOTHESES ABOUT THE INTERRELATION OF A COMBINATION OF CYTOKINES AND OPHTHALMIC PREPARATIONS USING AN INTELLIGENT INFORMATION SYSTEM

В работе рассмотрено сравнение экспериментальных распределений количества клеток для определения цитологического и иммунологического эффекта, оказываемого одновременным воздействием офтальмологических препаратов Броксинак® и Офтальмоферон® на клетки с конъюнктивы больного человека, направленное на совершенствование методики оценки комбинаций офтальмологических лекарственных средств in vitro. Доклинические исследования дают возможность определить эффективность применения лекарственных средств, возможные противопоказания и побочные эффекты, чтобы в дальнейшем определиться с объемом клинических испытаний и самой возможностью их проведения. В последнее время в различных областях медицины применяют счетчики клеток. Счетчики определяют не только количество клеток в образце, но и их размеры и объем, что позволяет сделать предположение о виде клеточной структуры. Подобные приборы позволяют автоматизировать подсчет клеток, определение их размеров и объема, что исключает субъективный фактор и возможность получения ошибочных данных, а также упрощает процедуру и позволяет получить результаты в короткий срок. На основе использования методов индуктивного вывода предложена методика построения гипотез о взаимосвязи комбинации цитокинов с пролиферативной активностью клеток. Методика учитывает синергическое взаимодействие цитокинов и использует последовательное построение логических формул для отбора групп цитокинов, статистический анализ таблиц сопряженности и логическую интеграцию полученных оценок. Реализация предложенной методики в рамках ИС позволит существенно ускорить научные исследования в этой области. Приведена итоговая методика построения гипотез о взаимосвязи комбинации цитокинов с биологической активностью клеток The paper considers a comparison of experimental distributions of the number of cells to determine the cytological and immunological effect of the simultaneous action of ophthalmic drugs Broxinac® and Oftalmoferon® on cells from the conjunctiva of a sick person, aimed at improving the methodology for assessing combinations of ophthalmic drugs in vitro. Preclinical studies make it possible to determine the effectiveness of the use of drugs, possible contraindications and side effects, in order to further determine the volume of clinical trials and the very possibility of their conduct. Recently, cell counters have been used in various fields of medicine. Counters determine not only the number of cells in the sample, but also their size and volume, which allows us to make an assumption about the type of cell structure. Such devices allow automating the counting of cells, determining their size and volume, which eliminates the subjective factor and the possibility of obtaining erroneous data, and also simplifies the procedure and allows you to get results in a short time. Based on the use of inductive inference methods, a method is proposed for constructing hypotheses about the relationship between the combination of cytokines and the proliferative activity of cells. The method takes into account the synergistic interaction of cytokines and uses the sequential construction of logical formulas for the selection of groups of cytokines, statistical analysis of contingency tables and logical integration of the estimates obtained. The implementation of the proposed methodology within the Information System will significantly accelerate research in this area. The final technique for constructing hypotheses about the relationship of the combination of cytokines with the biological activity of cells is presented

Bilateral Trade By Products Between the V4 Countries and China in Years 2009–2019

Subject and purpose: Using annual data for the periods 2009–2019, this paper examines trade flows between China and the Visegrad Group countries. The aim of this article is to assess real changes taking place in international trade in the Visegrad Group countries (V4) over the last eleven years. The starting point for the analysis was 2009 – the time after the 2008 economic crisis, and it was compared especially to 2018 – a year marked by a significant improvement in the economy. The purpose is to discuss concerns related to the differences in bilateral trade between China and Poland, Czech Republic, Hungary, and Slovak Republic. The main aim of this research is to distinguish the characteristics of bilateral trade by products between V4 and China in years 2009–2019. The purpose of this article is also to systematize and discuss points of view, rationalizing further empirical research. Two research hypotheses, resulting from the research purpose, were formulated: H1: in the V4 countries import exceeds export, and this trend seems to be growing, H2: Chinese goods imported to the V4 are much more sophisticated than those exported. Design/Methodology/Approach: To assess the initial and current situation on international trade between the V4 and China, the author uses variables obtained from WTO and OEC resources, diagnosing the situation in Poland, Czech Republic, Hungary, and Slovak Republic. The collected empirical data were processed using theoretical methods such as analysis, synthesis, and comparison to formulate conclusions using deductive and inductive inference methods. Practical Implications: The results can be used in scientific and expert work on diagnostic and forecast trends in bilateral trade by products between the V4 and China. Originality/Value: It concerns the indication of the importance of the V4 trade with China compared to the share of the V4 countries in world trade. It was also possible to identify the top export and import products of the V4. The findings also confirm the significant change in China’s trading structure.

Algorithms of Adaptation in Inductive Inference

We investigate the idea that human concept inference utilizes local incremental search within a compositional mental theory space. To explore this, we study judgments in a challenging task, where participants actively gather evidence about a symbolic rule governing the behavior of a simulated environment. Participants construct mini-experiments before making generalizations and explicit guesses about the hidden rule. They then collect additional evidence themselves (Experiment 1) or observe evidence gathered by someone else (Experiment 2) before revising their own generalizations and guesses. In each case, we focus on the relationship between participants’ initial and revised guesses about the hidden rule concept. We find an order effect whereby revised guesses are anchored to idiosyncratic elements of the earlier guesses. To explain this pattern, we develop a family of process accounts that combine program induction ideas with local (MCMC-like) adaptation mechanisms. A particularly local variant of this adaptive account captures participants’ revisions better than a range of alternatives. We take this as suggestive that people deal with the inherent complexity of concept inference partly through use of local adaptive search in a latent compositional theory space.

Pictorial Statistics

This essay discusses Francis Galton’s method of inductive inference where the data are photographs of human faces. His aim of induction was to determine the typical characteristics of the natural class to which the individuals belong by composing the relevant photographs in a specific photographic way. The three populations studied by Galton were people suffering tuberculosis, Jews, and criminals. This essay argues that despite the fact that Galton aimed at mechanical objectivity, subjective judgements nevertheless appear to be a necessary part of this kind of inductive inference. At first sight, this seems very much in the line of Lorraine Daston and Peter Galison’s account of objectivity. They argue that in the twentieth century the awareness arose that mechanical-objective pictures still could contain errors that should be erased by trained judgement. Galton’s case of inductive reasoning, however, departs from this account by showing that the correct composites were achieved by a combination of mechanical procedures and untrained judgements. To arrive at the typical characterizations one first has to familiarize oneself with the data, but the familiarization should be done by someone who is not an expert on the cases under study.

Naturalizing Logic: How Knowledge of Mechanisms Enhances Inductive Inference

This paper naturalizes inductive inference by showing how scientific knowledge of real mechanisms provides large benefits to it. I show how knowledge about mechanisms contributes to generalization, inference to the best explanation, causal inference, and reasoning with probabilities. Generalization from some A are B to all A are B is more plausible when a mechanism connects A to B. Inference to the best explanation is strengthened when the explanations are mechanistic and when explanatory hypotheses are themselves mechanistically explained. Causal inference in medical explanation, counterfactual reasoning, and analogy also benefit from mechanistic connections. Mechanisms also help with problems concerning the interpretation, availability, and computation of probabilities.

Renewable Energy Producers’ Strategies in the Visegrád Group Countries

Companies that belong to the energy sector can use Sustainable Development Goals (SDGs) for their strategies and diversify electrical energy production with reverence to the natural environment. This article aims to analyze sustainability strategy types among the Visegrád Group (V4) countries’ energy producers, who decided to generate electrical energy from the renewable resources. This research uses an inductive inference approach supported by a literature study and deductive reasoning supported by a statistical reference method. The main finding is that the energy producers from the V4 group have a common direction of evolution in their strategies. This change is based on a growing share of renewable energy sources to achieve environmental excellence strategies. The lack of renewable energy sector organizations’ strategies translates into disappointment with the goals pursued by these organizations. The significance of this study lies in an explanation of how sustainability strategies compare at a firm and country-level in a proposed classification. The analysis can open future research areas to examine development of strategies in the renewable energy sector.

What do our sampling assumptions affect: how we encode data or how we reason from it?

In describing how people generalize from observed samples of data to novel cases, theories of inductive inference have emphasized the learner's reliance on the contents of the sample. More recently, a growing body of literature suggests that different assumptions about how a data sample was generated can lead the learner to draw qualitatively different inferences on the basis of the same evidence. Yet relatively little is known about how and when these two sources of evidence are combined. For instance, do sampling assumptions affect how the sample contents are encoded, or is any influence exerted only at the point of retrieval when a decision is to be made? We report two experiments aimed at exploring this issue. By systematically varying both the sampling cover story and whether it is given before or after the training stimuli we are able to determine whether encoding or retrieval issues drive the impact of sampling assumptions. Across two experiments we find that the sampling cover story affects generalization when it is presented before the training stimuli, but not after, which we interpret in favor of an encoding account.