Within this paper, we show that the evaluation protocol currently used for inductive link prediction is heavily flawed as it relies on ranking the true entity in a small set of randomly sampled negative entities. Due to the limited size of the set of negatives, a simple rule-based baseline can achieve state-of-the-art results, which simply ranks entities higher based on the validity of their type. As a consequence of these insights, we reevaluate current approaches for inductive link prediction on several benchmarks using the link prediction protocol usually applied to the transductive setting. As some inductive methods suffer from scalability issues when evaluated in this setting, we propose and apply additionally an improved sampling protocol, which does not suffer from the problem mentioned above. The results of our evaluation differ drastically from the results reported in so far.

The task of inductive knowledge graph completion requires models to learn inference patterns from a training graph, which can then be used to make predictions on a disjoint test graph. Rule-based methods seem like a natural fit for this task, but in practice they significantly underperform state-of-the-art methods based on Graph Neural Networks (GNNs), such as NBFNet. We hypothesise that the underperformance of rule-based methods is due to two factors: (i) implausible entities are not ranked at all and (ii) only the most informative path is taken into account when determining the confidence in a given link prediction answer. To analyse the impact of these factors, we study a number of variants of a rule-based approach, which are specifically aimed at addressing the aforementioned issues. We find that the resulting models can achieve a performance which is close to that of NBFNet. Crucially, the considered variants only use a small fraction of the evidence that NBFNet relies on, which means that they largely keep the interpretability advantage of rule-based methods. Moreover, we show that a further variant, which does look at the full KG, consistently outperforms NBFNet.

For Artificial Intelligence to have a greater impact in biology and medicine, it is crucial that recommendations are both accurate and transparent. In other domains, a neurosymbolic approach of multi-hop reasoning on knowledge graphs has been shown to produce transparent explanations. However, there is a lack of research applying it to complex biomedical datasets and problems. In this paper, the approach is explored for drug discovery to draw solid conclusions on its applicability. For the first time, we systematically apply it to multiple biomedical datasets and recommendation tasks with fair benchmark comparisons. The approach is found to outperform the best baselines by 21.7% on average whilst producing novel, biologically relevant explanations.

Neural embedding-based machine learning models have shown promise for predicting novel links in knowledge graphs. Unfortunately, their practical utility is diminished by their lack of interpretability. Recently, the fully interpretable, rule-based algorithm AnyBURL yielded highly competitive results on many general-purpose link prediction benchmarks. However, current approaches for aggregating predictions made by multiple rules are affected by redundancies. We improve upon AnyBURL by introducing the SAFRAN rule application framework, which uses a novel aggregation approach called Non-redundant Noisy-OR that detects and clusters redundant rules prior to aggregation. SAFRAN yields new state-of-the-art results for fully interpretable link prediction on the established general-purpose benchmarks FB15K-237, WN18RR and YAGO3-10. Furthermore, it exceeds the results of multiple established embedding-based algorithms on FB15K-237 and WN18RR and narrows the gap between rule-based and embedding-based algorithms on YAGO3-10.

Multi-hop reasoning has been widely studied in recent years to obtain more interpretable link prediction. However, we find in experiments that many paths given by these models are actually unreasonable, while little works have been done on interpretability evaluation for them. In this paper, we propose a unified framework to quantitatively evaluate the interpretability of multi-hop reasoning models so as to advance their development. In specific, we define three metrics including path recall, local interpretability, and global interpretability for evaluation, and design an approximate strategy to calculate them using the interpretability scores of rules. Furthermore, we manually annotate all possible rules and establish a Benchmark to detect the Interpretability of Multi-hop Reasoning (BIMR). In experiments, we run nine baselines on our benchmark. The experimental results show that the interpretability of current multi-hop reasoning models is less satisfactory and is still far from the upper bound given by our benchmark. Moreover, the rule-based models outperform the multi-hop reasoning models in terms of performance and interpretability, which points to a direction for future research, i.e., we should investigate how to better incorporate rule information into the multi-hop reasoning model. Our codes and datasets can be obtained from https://github.com/THU-KEG/BIMR.

Neural embedding-based machine learning models have shown promise for predicting novel links in biomedical knowledge graphs. Unfortunately, their practical utility is diminished by their lack of interpretability. Recently, the fully interpretable, rule-based algorithm AnyBURL yielded highly competitive results on many general-purpose link prediction benchmarks. However, its applicability to large-scale prediction tasks on complex biomedical knowledge bases is limited by long inference times and difficulties with aggregating predictions made by multiple rules. We improve upon AnyBURL by introducing the SAFRAN rule application framework which aggregates rules through a scalable clustering algorithm. SAFRAN yields new state-of-the-art results for fully interpretable link prediction on the established general-purpose benchmark FB15K-237 and the large-scale biomedical benchmark OpenBioLink. Furthermore, it exceeds the results of multiple established embedding-based algorithms on FB15K-237 and narrows the gap between rule-based and embedding-based algorithms on OpenBioLink. We also show that SAFRAN increases inference speeds by up to two orders of magnitude.

Most of todays work on knowledge graph completion is concerned with sub-symbolic approaches that focus on the concept of embedding a given graph in a low dimensional vector space. Against this trend, we propose an approach called AnyBURL that is rooted in the symbolic space. Its core algorithm is based on sampling paths, which are generalized into Horn rules. Previously published results show that the prediction quality of AnyBURL is on the same level as current state of the art with the additional benefit of offering an explanation for the predicted fact. In this paper, we are concerned with two extensions of AnyBURL. Firstly, we change AnyBURLs interpretation of rules from $\Theta$-subsumption into $\Theta$-subsumption under Object Identity. Secondly, we introduce reinforcement learning to better guide the sampling process. We found out that reinforcement learning helps finding more valuable rules earlier in the search process. We measure the impact of both extensions and compare the resulting approach with current state of the art approaches. Our results show that AnyBURL outperforms most sub-symbolic methods.