scholarly journals LinkExplorer: Predicting, explaining and exploring links in large biomedical knowledge graphs

2022 ◽  
Author(s):  
Simon Ott ◽  
Adriano Barbosa-Silva ◽  
Matthias Samwald
Keyword(s):  
User Interfaces ◽  
Link Prediction ◽  
Black Box ◽  
Machine Learning Algorithms ◽  
Web Interface ◽  
Biomedical Knowledge ◽  
Software Suite ◽  
Black Boxes ◽  
Knowledge Graphs ◽  
Insight Into

Machine learning algorithms for link prediction can be valuable tools for hypothesis generation. However, many current algorithms are black boxes or lack good user interfaces that could facilitate insight into why predictions are made. We present LinkExplorer, a software suite for predicting, explaining and exploring links in large biomedical knowledge graphs. LinkExplorer integrates our novel, rule-based link prediction engine SAFRAN, which was recently shown to outcompete other explainable algorithms and established black box algorithms. Here, we demonstrate highly competitive evaluation results of our algorithm on multiple large biomedical knowledge graphs, and release a web interface that allows for interactive and intuitive exploration of predicted links and their explanations.

scholarly journals OpenBioLink: a benchmarking framework for large-scale biomedical link prediction

2020 ◽  
Vol 36 (13) ◽  
pp. 4097-4098 ◽  
Author(s):  
Anna Breit ◽  
Simon Ott ◽  
Asan Agibetov ◽  
Matthias Samwald
Keyword(s):  
Link Prediction ◽  
Large Scale ◽  
Source Code ◽  
Machine Learning Algorithms ◽  
Knowledge Networks ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Biomedical Knowledge ◽  
High Quality ◽  
Baseline Evaluation

Abstract Summary Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With OpenBioLink, we introduce a large-scale, high-quality and highly challenging biomedical link prediction benchmark to transparently and reproducibly evaluate such algorithms. Furthermore, we present preliminary baseline evaluation results. Availability and implementation Source code and data are openly available at https://github.com/OpenBioLink/OpenBioLink. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Analysis of Explainers of Black Box Deep Neural Networks for Computer Vision: A Survey

2021 ◽  
Vol 3 (4) ◽  
pp. 966-989
Author(s):  
Vanessa Buhrmester ◽  
David Münch ◽  
Michael Arens
Keyword(s):  
Neural Networks ◽  
Computer Vision ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Black Box ◽  
Complex Data ◽  
Comprehensive Overview ◽  
Nonlinear Structure ◽  
Black Boxes ◽  
Insight Into

Deep Learning is a state-of-the-art technique to make inference on extensive or complex data. As a black box model due to their multilayer nonlinear structure, Deep Neural Networks are often criticized as being non-transparent and their predictions not traceable by humans. Furthermore, the models learn from artificially generated datasets, which often do not reflect reality. By basing decision-making algorithms on Deep Neural Networks, prejudice and unfairness may be promoted unknowingly due to a lack of transparency. Hence, several so-called explanators, or explainers, have been developed. Explainers try to give insight into the inner structure of machine learning black boxes by analyzing the connection between the input and output. In this survey, we present the mechanisms and properties of explaining systems for Deep Neural Networks for Computer Vision tasks. We give a comprehensive overview about the taxonomy of related studies and compare several survey papers that deal with explainability in general. We work out the drawbacks and gaps and summarize further research ideas.

scholarly journals Reasoning on Knowledge Graphs with Debate Dynamics

2020 ◽  
Vol 34 (04) ◽  
pp. 4123-4131
Author(s):  
Marcel Hildebrandt ◽  
Jorge Andres Quintero Serna ◽  
Yunpu Ma ◽  
Martin Ringsquandl ◽  
Mitchell Joblin ◽  
...  
Keyword(s):  
Link Prediction ◽  
Predictive Accuracy ◽  
Main Idea ◽  
Black Box ◽  
Binary Classifier ◽  
Automatic Reasoning ◽  
Learning Agents ◽  
Benchmark Datasets ◽  
Novel Method ◽  
Knowledge Graphs

We propose a novel method for automatic reasoning on knowledge graphs based on debate dynamics. The main idea is to frame the task of triple classification as a debate game between two reinforcement learning agents which extract arguments – paths in the knowledge graph – with the goal to promote the fact being true (thesis) or the fact being false (antithesis), respectively. Based on these arguments, a binary classifier, called the judge, decides whether the fact is true or false. The two agents can be considered as sparse, adversarial feature generators that present interpretable evidence for either the thesis or the antithesis. In contrast to other black-box methods, the arguments allow users to get an understanding of the decision of the judge. Since the focus of this work is to create an explainable method that maintains a competitive predictive accuracy, we benchmark our method on the triple classification and link prediction task. Thereby, we find that our method outperforms several baselines on the benchmark datasets FB15k-237, WN18RR, and Hetionet. We also conduct a survey and find that the extracted arguments are informative for users.

scholarly journals Variable Selection and Parameter Tuning for BART Modeling in the Fragile Families Challenge

2019 ◽  
Vol 5 ◽  
pp. 237802311982588 ◽  
Author(s):  
Nicole Bohme Carnegie ◽  
James Wu
Keyword(s):  
Variable Selection ◽  
Missing Values ◽  
Linear Models ◽  
Parameter Tuning ◽  
Black Box ◽  
Machine Learning Algorithms ◽  
Outcome Variable ◽  
Fragile Families ◽  
Great Flexibility ◽  
Additive Regression

Our goal for the Fragile Families Challenge was to develop a hands-off approach that could be applied in many settings to identify relationships that theory-based models might miss. Data processing was our first and most time-consuming task, particularly handling missing values. Our second task was to reduce the number of variables for modeling, and we compared several techniques for variable selection: least absolute selection and shrinkage operator, regression with a horseshoe prior, Bayesian generalized linear models, and Bayesian additive regression trees (BART). We found minimal differences in final performance based on the choice of variable selection method. We proceeded with BART for modeling because it requires minimal assumptions and permits great flexibility in fitting surfaces and based on previous success using BART in black-box modeling competitions. In addition, BART allows for probabilistic statements about the predictions and other inferences, which is an advantage over most machine learning algorithms. A drawback to BART, however, is that it is often difficult to identify or characterize individual predictors that have strong influences on the outcome variable.

Symptoms as Black Boxes: Time to Look Inside the Box

2021 ◽  
pp. 216770262198972
Author(s):  
Carolyn E. Wilshire ◽  
Tony Ward ◽  
Samuel Clack
Keyword(s):  
Black Box ◽  
Classification Systems ◽  
Subsequent Research ◽  
Black Boxes ◽  
Core Questions

In our original article (this issue, p. ♦♦♦), we argued that focusing research on individual symptoms of psychopathology might provide valuable information about their underlying nature and result in better classification systems, explanations, and treatment. To this end, we formulated five core questions that were intended to guide subsequent research and symptom conceptualizations in the psychopathology domain. In this article, we respond to two commentaries on our article. We conclude that it is time to open the black box of symptoms and to take seriously their status as complex constructs.

scholarly journals TransET: Knowledge Graph Embedding with Entity Types

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou
Keyword(s):  
Link Prediction ◽  
State Of The Art ◽  
Score Function ◽  
Graph Embedding ◽  
Vector Spaces ◽  
Knowledge Graph ◽  
Semantic Features ◽  
Knowledge Graphs ◽  
Real World Datasets ◽  
Low Dimensional

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.

scholarly journals Sampo-UI: A full stack JavaScript framework for developing semantic portal user interfaces

Semantic Web ◽  
2021 ◽  
pp. 1-16
Author(s):  
Esko Ikkala ◽  
Eero Hyvönen ◽  
Heikki Rantala ◽  
Mikko Koho
Keyword(s):  
User Interfaces ◽  
Linked Data ◽  
State Of The Art ◽  
Software Framework ◽  
End User ◽  
Faceted Search ◽  
Software Developer ◽  
Current State ◽  
Knowledge Graphs ◽  
User Friendly

This paper presents a new software framework, Sampo-UI, for developing user interfaces for semantic portals. The goal is to provide the end-user with multiple application perspectives to Linked Data knowledge graphs, and a two-step usage cycle based on faceted search combined with ready-to-use tooling for data analysis. For the software developer, the Sampo-UI framework makes it possible to create highly customizable, user-friendly, and responsive user interfaces using current state-of-the-art JavaScript libraries and data from SPARQL endpoints, while saving substantial coding effort. Sampo-UI is published on GitHub under the open MIT License and has been utilized in several internal and external projects. The framework has been used thus far in creating six published and five forth-coming portals, mostly related to the Cultural Heritage domain, that have had tens of thousands of end-users on the Web.

Rough Tolerance Equality and Tolerance Black Boxes

1988 ◽  
Vol 11 (3) ◽  
pp. 289-296
Author(s):  
Juhani Nieminen
Keyword(s):  
Black Box ◽  
Black Boxes

The rough equality concept of Z. Pawlak is modified and the rough top and the rough bottom tolerance equalities are given and characterized. The same tolerance idea is applied also to black box notion introduced by Novotný and Pawlak; the concept thus obtained is called tolerance black box. Tolerance black boxes are characterized and their properties are described.

scholarly journals Trans4E: Link Prediction on Scholarly Knowledge Graphs

2021 ◽  
Author(s):  
Mojtaba Nayyeri ◽  
Gokce Muge Cil ◽  
Sahar Vahdati ◽  
Francesco Osborne ◽  
Mahfuzur Rahman ◽  
...  
Keyword(s):  
Link Prediction ◽  
Knowledge Graphs

scholarly journals Mean Received Resources Meet Machine Learning Algorithms to Improve Link Prediction Methods

Information ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 35
Author(s):  
Jibouni Ayoub ◽  
Dounia Lotfi ◽  
Ahmed Hammouch
Keyword(s):  
Machine Learning ◽  
Link Prediction ◽  
Learning Algorithms ◽  
Area Under The Curve ◽  
Machine Learning Algorithms ◽  
Actual State ◽  
The Future ◽  
Auc Value ◽  
The Mean ◽  
Analysis Of Social Networks

The analysis of social networks has attracted a lot of attention during the last two decades. These networks are dynamic: new links appear and disappear. Link prediction is the problem of inferring links that will appear in the future from the actual state of the network. We use information from nodes and edges and calculate the similarity between users. The more users are similar, the higher the probability of their connection in the future will be. The similarity metrics play an important role in the link prediction field. Due to their simplicity and flexibility, many authors have proposed several metrics such as Jaccard, AA, and Katz and evaluated them using the area under the curve (AUC). In this paper, we propose a new parameterized method to enhance the AUC value of the link prediction metrics by combining them with the mean received resources (MRRs). Experiments show that the proposed method improves the performance of the state-of-the-art metrics. Moreover, we used machine learning algorithms to classify links and confirm the efficiency of the proposed combination.

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