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Michael Cochez

Publications and source records attributed to Michael Cochez.

At least 37 records · Page 2Linked to original sources

Adapting Neural Link Predictors for Data-Efficient Complex Query Answering

Answering complex queries on incomplete knowledge graphs is a challenging task where a model needs to answer complex logical queries in the presence of missing knowledge. Prior work in the literature has proposed to address this problem by designing architectures trained end-to-end for the complex query answering task with a reasoning process that is hard to interpret while requiring data and resource-intensive training. Other lines of research have proposed re-using simple neural link predictors to answer complex queries, reducing the amount of training data by orders of magnitude while providing interpretable answers. The neural link predictor used in such approaches is not explicitly optimised for the complex query answering task, implying that its scores are not calibrated to interact together. We propose to address these problems via CQD$^{\mathcal{A}}$, a parameter-efficient score \emph{adaptation} model optimised to re-calibrate neural link prediction scores for the complex query answering task. While the neural link predictor is frozen, the adaptation component -- which only increases the number of model parameters by $0.03\%$ -- is trained on the downstream complex query answering task. Furthermore, the calibration component enables us to support reasoning over queries that include atomic negations, which was previously impossible with link predictors. In our experiments, CQD$^{\mathcal{A}}$ produces significantly more accurate results than current state-of-the-art methods, improving from $34.4$ to $35.1$ Mean Reciprocal Rank values averaged across all datasets and query types while using $\leq 30\%$ of the available training query types. We further show that CQD$^{\mathcal{A}}$ is data-efficient, achieving competitive results with only $1\%$ of the training complex queries, and robust in out-of-domain evaluations.

cs.LG↗

Prompting as Probing: Using Language Models for Knowledge Base Construction

Language Models (LMs) have proven to be useful in various downstream applications, such as summarisation, translation, question answering and text classification. LMs are becoming increasingly important tools in Artificial Intelligence, because of the vast quantity of information they can store. In this work, we present ProP (Prompting as Probing), which utilizes GPT-3, a large Language Model originally proposed by OpenAI in 2020, to perform the task of Knowledge Base Construction (KBC). ProP implements a multi-step approach that combines a variety of prompting techniques to achieve this. Our results show that manual prompt curation is essential, that the LM must be encouraged to give answer sets of variable lengths, in particular including empty answer sets, that true/false questions are a useful device to increase precision on suggestions generated by the LM, that the size of the LM is a crucial factor, and that a dictionary of entity aliases improves the LM score. Our evaluation study indicates that these proposed techniques can substantially enhance the quality of the final predictions: ProP won track 2 of the LM-KBC competition, outperforming the baseline by 36.4 percentage points. Our implementation is available on https://github.com/HEmile/iswc-challenge.

cs.CL↗

BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphs

Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to predict new links in such graphs. Some methods ignore valuable attribute data associated with entities in biomedical KGs, such as protein sequences, or molecular graphs. Other works incorporate such data, but assume that entities can be represented with the same data modality. This is not always the case for biomedical KGs, where entities exhibit heterogeneous modalities that are central to their representation in the subject domain. We propose a modular framework for learning embeddings in KGs with entity attributes, that allows encoding attribute data of different modalities while also supporting entities with missing attributes. We additionally propose an efficient pretraining strategy for reducing the required training runtime. We train models using a biomedical KG containing approximately 2 million triples, and evaluate the performance of the resulting entity embeddings on the tasks of link prediction, and drug-protein interaction prediction, comparing against methods that do not take attribute data into account. In the standard link prediction evaluation, the proposed method results in competitive, yet lower performance than baselines that do not use attribute data. When evaluated in the task of drug-protein interaction prediction, the method compares favorably with the baselines. We find settings involving low degree entities, which make up for a substantial amount of the set of entities in the KG, where our method outperforms the baselines. Our proposed pretraining strategy yields significantly higher performance while reducing the required training runtime. Our implementation is available at https://github.com/elsevier-AI-Lab/BioBLP .

cs.AI↗

Geometric Relational Embeddings: A Survey

Geometric relational embeddings map relational data as geometric objects that combine vector information suitable for machine learning and structured/relational information for structured/relational reasoning, typically in low dimensions. Their preservation of relational structures and their appealing properties and interpretability have led to their uptake for tasks such as knowledge graph completion, ontology and hierarchy reasoning, logical query answering, and hierarchical multi-label classification. We survey methods that underly geometric relational embeddings and categorize them based on (i) the embedding geometries that are used to represent the data; and (ii) the relational reasoning tasks that they aim to improve. We identify the desired properties (i.e., inductive biases) of each kind of embedding and discuss some potential future work.

cs.AI↗

Neural Graph Reasoning: Complex Logical Query Answering Meets Graph Databases

Complex logical query answering (CLQA) is a recently emerged task of graph machine learning that goes beyond simple one-hop link prediction and solves a far more complex task of multi-hop logical reasoning over massive, potentially incomplete graphs in a latent space. The task received a significant traction in the community; numerous works expanded the field along theoretical and practical axes to tackle different types of complex queries and graph modalities with efficient systems. In this paper, we provide a holistic survey of CLQA with a detailed taxonomy studying the field from multiple angles, including graph types (modality, reasoning domain, background semantics), modeling aspects (encoder, processor, decoder), supported queries (operators, patterns, projected variables), datasets, evaluation metrics, and applications. Refining the CLQA task, we introduce the concept of Neural Graph Databases (NGDBs). Extending the idea of graph databases (graph DBs), NGDB consists of a Neural Graph Storage and a Neural Graph Engine. Inside Neural Graph Storage, we design a graph store, a feature store, and further embed information in a latent embedding store using an encoder. Given a query, Neural Query Engine learns how to perform query planning and execution in order to efficiently retrieve the correct results by interacting with the Neural Graph Storage. Compared with traditional graph DBs, NGDBs allow for a flexible and unified modeling of features in diverse modalities using the embedding store. Moreover, when the graph is incomplete, they can provide robust retrieval of answers which a normal graph DB cannot recover. Finally, we point out promising directions, unsolved problems and applications of NGDB for future research.

cs.DB↗

Explainable AI for Bioinformatics: Methods, Tools, and Applications

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining.

q-bio.QM↗

Query Embedding on Hyper-relational Knowledge Graphs

Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational queries are often observed in real-world KG applications, and existing approaches for approximate query answering cannot make use of qualifier pairs. In this work, we bridge this gap and extend the multi-hop reasoning problem to hyper-relational KGs allowing to tackle this new type of complex queries. Building upon recent advancements in Graph Neural Networks and query embedding techniques, we study how to embed and answer hyper-relational conjunctive queries. Besides that, we propose a method to answer such queries and demonstrate in our experiments that qualifiers improve query answering on a diverse set of query patterns.

cs.AI↗

Scaling R-GCN Training with Graph Summarization

Training of Relational Graph Convolutional Networks (R-GCN) is a memory intense task. The amount of gradient information that needs to be stored during training for real-world graphs is often too large for the amount of memory available on most GPUs. In this work, we experiment with the use of graph summarization techniques to compress the graph and hence reduce the amount of memory needed. After training the R-GCN on the graph summary, we transfer the weights back to the original graph and attempt to perform inference on it. We obtain reasonable results on the AIFB, MUTAG and AM datasets. Our experiments show that training on the graph summary can yield a comparable or higher accuracy to training on the original graphs.Furthermore, if we take the time to compute the summary out of the equation, we observe that the smaller graph representations obtained with graph summarization methods reduces the computational overhead. However, further experiments are needed to evaluate additional graph summary models and whether our findings also holds true for very large graphs.

cs.LG↗

Updating Embeddings for Dynamic Knowledge Graphs

Data in Knowledge Graphs often represents part of the current state of the real world. Thus, to stay up-to-date the graph data needs to be updated frequently. To utilize information from Knowledge Graphs, many state-of-the-art machine learning approaches use embedding techniques. These techniques typically compute an embedding, i.e., vector representations of the nodes as input for the main machine learning algorithm. If a graph update occurs later on -- specifically when nodes are added or removed -- the training has to be done all over again. This is undesirable, because of the time it takes and also because downstream models which were trained with these embeddings have to be retrained if they change significantly. In this paper, we investigate embedding updates that do not require full retraining and evaluate them in combination with various embedding models on real dynamic Knowledge Graphs covering multiple use cases. We study approaches that place newly appearing nodes optimally according to local information, but notice that this does not work well. However, we find that if we continue the training of the old embedding, interleaved with epochs during which we only optimize for the added and removed parts, we obtain good results in terms of typical metrics used in link prediction. This performance is obtained much faster than with a complete retraining and hence makes it possible to maintain embeddings for dynamic Knowledge Graphs.

cs.LG↗

Knowledge Graphs

In this paper we provide a comprehensive introduction to knowledge graphs, which have recently garnered significant attention from both industry and academia in scenarios that require exploiting diverse, dynamic, large-scale collections of data. After some opening remarks, we motivate and contrast various graph-based data models and query languages that are used for knowledge graphs. We discuss the roles of schema, identity, and context in knowledge graphs. We explain how knowledge can be represented and extracted using a combination of deductive and inductive techniques. We summarise methods for the creation, enrichment, quality assessment, refinement, and publication of knowledge graphs. We provide an overview of prominent open knowledge graphs and enterprise knowledge graphs, their applications, and how they use the aforementioned techniques. We conclude with high-level future research directions for knowledge graphs.

cs.AI↗

Complex Query Answering with Neural Link Predictors

Neural link predictors are immensely useful for identifying missing edges in large scale Knowledge Graphs. However, it is still not clear how to use these models for answering more complex queries that arise in a number of domains, such as queries using logical conjunctions ($\land$), disjunctions ($\lor$) and existential quantifiers ($\exists$), while accounting for missing edges. In this work, we propose a framework for efficiently answering complex queries on incomplete Knowledge Graphs. We translate each query into an end-to-end differentiable objective, where the truth value of each atom is computed by a pre-trained neural link predictor. We then analyse two solutions to the optimisation problem, including gradient-based and combinatorial search. In our experiments, the proposed approach produces more accurate results than state-of-the-art methods -- black-box neural models trained on millions of generated queries -- without the need of training on a large and diverse set of complex queries. Using orders of magnitude less training data, we obtain relative improvements ranging from 8% up to 40% in Hits@3 across different knowledge graphs containing factual information. Finally, we demonstrate that it is possible to explain the outcome of our model in terms of the intermediate solutions identified for each of the complex query atoms. All our source code and datasets are available online, at https://github.com/uclnlp/cqd.

cs.LG↗

Secure Evaluation of Knowledge Graph Merging Gain

Finding out the differences and commonalities between the knowledge of two parties is an important task. Such a comparison becomes necessary, when one party wants to determine how much it is worth to acquire the knowledge of the second party, or similarly when two parties try to determine, whether a collaboration could be beneficial. When these two parties cannot trust each other (for example, due to them being competitors) performing such a comparison is challenging as neither of them would be willing to share any of their assets. This paper addresses this problem for knowledge graphs, without a need for non-disclosure agreements nor a third party during the protocol. During the protocol, the intersection between the two knowledge graphs is determined in a privacy preserving fashion. This is followed by the computation of various metrics, which give an indication of the potential gain from obtaining the other parties knowledge graph, while still keeping the actual knowledge graph contents secret. The protocol makes use of blind signatures and (counting) Bloom filters to reduce the amount of leaked information. Finally, the party who wants to obtain the other's knowledge graph can get a part of such in a way that neither party is able to know beforehand which parts of the graph are obtained (i.e., they cannot choose to only get or share the good parts). After inspection of the quality of this part, the Buyer can decide to proceed with the transaction. The analysis of the protocol indicates that the developed protocol is secure against malicious participants. Further experimental analysis shows that the resource consumption scales linear with the number of statements in the knowledge graph.

cs.CR↗

Approximate Knowledge Graph Query Answering: From Ranking to Binary Classification

Large, heterogeneous datasets are characterized by missing or even erroneous information. This is more evident when they are the product of community effort or automatic fact extraction methods from external sources, such as text. A special case of the aforementioned phenomenon can be seen in knowledge graphs, where this mostly appears in the form of missing or incorrect edges and nodes. Structured querying on such incomplete graphs will result in incomplete sets of answers, even if the correct entities exist in the graph, since one or more edges needed to match the pattern are missing. To overcome this problem, several algorithms for approximate structured query answering have been proposed. Inspired by modern Information Retrieval metrics, these algorithms produce a ranking of all entities in the graph, and their performance is further evaluated based on how high in this ranking the correct answers appear. In this work we take a critical look at this way of evaluation. We argue that performing a ranking-based evaluation is not sufficient to assess methods for complex query answering. To solve this, we introduce Message Passing Query Boxes (MPQB), which takes binary classification metrics back into use and shows the effect this has on the recently proposed query embedding method MPQE.

cs.DB↗

Message Passing Query Embedding

Recent works on representation learning for Knowledge Graphs have moved beyond the problem of link prediction, to answering queries of an arbitrary structure. Existing methods are based on ad-hoc mechanisms that require training with a diverse set of query structures. We propose a more general architecture that employs a graph neural network to encode a graph representation of the query, where nodes correspond to entities and variables. The generality of our method allows it to encode a more diverse set of query types in comparison to previous work. Our method shows competitive performance against previous models for complex queries, and in contrast with these models, it can answer complex queries when trained for link prediction only. We show that the model learns entity embeddings that capture the notion of entity type without explicit supervision.

cs.AI↗

DeepCOVIDExplainer: Explainable COVID-19 Diagnosis Based on Chest X-ray Images

Amid the coronavirus disease(COVID-19) pandemic, humanity experiences a rapid increase in infection numbers across the world. Challenge hospitals are faced with, in the fight against the virus, is the effective screening of incoming patients. One methodology is the assessment of chest radiography(CXR) images, which usually requires expert radiologist's knowledge. In this paper, we propose an explainable deep neural networks(DNN)-based method for automatic detection of COVID-19 symptoms from CXR images, which we call DeepCOVIDExplainer. We used 15,959 CXR images of 15,854 patients, covering normal, pneumonia, and COVID-19 cases. CXR images are first comprehensively preprocessed, before being augmented and classified with a neural ensemble method, followed by highlighting class-discriminating regions using gradient-guided class activation maps(Grad-CAM++) and layer-wise relevance propagation(LRP). Further, we provide human-interpretable explanations of the predictions. Evaluation results based on hold-out data show that our approach can identify COVID-19 confidently with a positive predictive value(PPV) of 91.6%, 92.45%, and 96.12%; precision, recall, and F1 score of 94.6%, 94.3%, and 94.6%, respectively for normal, pneumonia, and COVID-19 cases, respectively, making it comparable or improved results over recent approaches. We hope that our findings will be a useful contribution to the fight against COVID-19 and, in more general, towards an increasing acceptance and adoption of AI-assisted applications in the clinical practice.

eess.IV↗

Convolutional Embedded Networks for Population Scale Clustering and Bio-ancestry Inferencing

The study of genetic variants can help find correlating population groups to identify cohorts that are predisposed to common diseases and explain differences in disease susceptibility and how patients react to drugs. Machine learning algorithms are increasingly being applied to identify interacting GVs to understand their complex phenotypic traits. Since the performance of a learning algorithm not only depends on the size and nature of the data but also on the quality of underlying representation, deep neural networks can learn non-linear mappings that allow transforming GVs data into more clustering and classification friendly representations than manual feature selection. In this paper, we proposed convolutional embedded networks in which we combine two DNN architectures called convolutional embedded clustering and convolutional autoencoder classifier for clustering individuals and predicting geographic ethnicity based on GVs, respectively. We employed CAE-based representation learning on 95 million GVs from the 1000 genomes and Simons genome diversity projects. Quantitative and qualitative analyses with a focus on accuracy and scalability show that our approach outperforms state-of-the-art approaches such as VariantSpark and ADMIXTURE. In particular, CEC can cluster targeted population groups in 22 hours with an adjusted rand index of 0.915, the normalized mutual information of 0.92, and the clustering accuracy of 89%. Contrarily, the CAE classifier can predict the geographic ethnicity of unknown samples with an F1 and Mathews correlation coefficient(MCC) score of 0.9004 and 0.8245, respectively. To provide interpretations of the predictions, we identify significant biomarkers using gradient boosted trees(GBT) and SHAP. Overall, our approach is transparent and faster than the baseline methods, and scalable for 5% to 100% of the full human genome.

cs.LG↗

Classification Benchmarks for Under-resourced Bengali Language based on Multichannel Convolutional-LSTM Network

Exponential growths of social media and micro-blogging sites not only provide platforms for empowering freedom of expressions and individual voices but also enables people to express anti-social behaviour like online harassment, cyberbullying, and hate speech. Numerous works have been proposed to utilize these data for social and anti-social behaviours analysis, document characterization, and sentiment analysis by predicting the contexts mostly for highly resourced languages such as English. However, there are languages that are under-resources, e.g., South Asian languages like Bengali, Tamil, Assamese, Telugu that lack of computational resources for the NLP tasks. In this paper, we provide several classification benchmarks for Bengali, an under-resourced language. We prepared three datasets of expressing hate, commonly used topics, and opinions for hate speech detection, document classification, and sentiment analysis, respectively. We built the largest Bengali word embedding models to date based on 250 million articles, which we call BengFastText. We perform three different experiments, covering document classification, sentiment analysis, and hate speech detection. We incorporate word embeddings into a Multichannel Convolutional-LSTM (MConv-LSTM) network for predicting different types of hate speech, document classification, and sentiment analysis. Experiments demonstrate that BengFastText can capture the semantics of words from respective contexts correctly. Evaluations against several baseline embedding models, e.g., Word2Vec and GloVe yield up to 92.30%, 82.25%, and 90.45% F1-scores in case of document classification, sentiment analysis, and hate speech detection, respectively during 5-fold cross-validation tests.

cs.CL↗

Privacy Attacks on Network Embeddings

Data ownership and data protection are increasingly important topics with ethical and legal implications, e.g., with the right to erasure established in the European General Data Protection Regulation (GDPR). In this light, we investigate network embeddings, i.e., the representation of network nodes as low-dimensional vectors. We consider a typical social network scenario with nodes representing users and edges relationships between them. We assume that a network embedding of the nodes has been trained. After that, a user demands the removal of his data, requiring the full deletion of the corresponding network information, in particular the corresponding node and incident edges. In that setting, we analyze whether after the removal of the node from the network and the deletion of the vector representation of the respective node in the embedding significant information about the link structure of the removed node is still encoded in the embedding vectors of the remaining nodes. This would require a (potentially computationally expensive) retraining of the embedding. For that purpose, we deploy an attack that leverages information from the remaining network and embedding to recover information about the neighbors of the removed node. The attack is based on (i) measuring distance changes in network embeddings and (ii) a machine learning classifier that is trained on networks that are constructed by removing additional nodes. Our experiments demonstrate that substantial information about the edges of a removed node/user can be retrieved across many different datasets. This implies that to fully protect the privacy of users, node deletion requires complete retraining - or at least a significant modification - of original network embeddings. Our results suggest that deleting the corresponding vector representation from network embeddings alone is not sufficient from a privacy perspective.

cs.LG↗