arXiv subjects

Pasquale Minervini

Publications and source records attributed to Pasquale Minervini.

At least 91 records · Page 5Linked to original sources

arXiv2023

REFER: An End-to-end Rationale Extraction Framework for Explanation Regularization

Human-annotated textual explanations are becoming increasingly important in Explainable Natural Language Processing. Rationale extraction aims to provide faithful (i.e., reflective of the behavior of the model) and plausible (i.e., convincing to humans) explanations by highlighting the inputs that had the largest impact on the prediction without compromising the performance of the task model. In recent works, the focus of training rationale extractors was primarily on optimizing for plausibility using human highlights, while the task model was trained on jointly optimizing for task predictive accuracy and faithfulness. We propose REFER, a framework that employs a differentiable rationale extractor that allows to back-propagate through the rationale extraction process. We analyze the impact of using human highlights during training by jointly training the task model and the rationale extractor. In our experiments, REFER yields significantly better results in terms of faithfulness, plausibility, and downstream task accuracy on both in-distribution and out-of-distribution data. On both e-SNLI and CoS-E, our best setting produces better results in terms of composite normalized relative gain than the previous baselines by 11% and 3%, respectively.

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arXiv2023

Combining Inductive and Deductive Reasoning for Query Answering over Incomplete Knowledge Graphs

Current methods for embedding-based query answering over incomplete Knowledge Graphs (KGs) only focus on inductive reasoning, i.e., predicting answers by learning patterns from the data, and lack the complementary ability to do deductive reasoning, which requires the application of domain knowledge to infer further information. To address this shortcoming, we investigate the problem of incorporating ontologies into embedding-based query answering models by defining the task of embedding-based ontology-mediated query answering. We propose various integration strategies into prominent representatives of embedding models that involve (1) different ontology-driven data augmentation techniques and (2) adaptation of the loss function to enforce the ontology axioms. We design novel benchmarks for the considered task based on the LUBM and the NELL KGs and evaluate our methods on them. The achieved improvements in the setting that requires both inductive and deductive reasoning are from 20% to 55% in HITS@3.

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arXiv2023

Knowledge Graph Embeddings in the Biomedical Domain: Are They Useful? A Look at Link Prediction, Rule Learning, and Downstream Polypharmacy Tasks

Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.

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arXiv2023

Approximate Answering of Graph Queries

Knowledge graphs (KGs) are inherently incomplete because of incomplete world knowledge and bias in what is the input to the KG. Additionally, world knowledge constantly expands and evolves, making existing facts deprecated or introducing new ones. However, we would still want to be able to answer queries as if the graph were complete. In this chapter, we will give an overview of several methods which have been proposed to answer queries in such a setting. We will first provide an overview of the different query types which can be supported by these methods and datasets typically used for evaluation, as well as an insight into their limitations. Then, we give an overview of the different approaches and describe them in terms of expressiveness, supported graph types, and inference capabilities.

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arXiv2023

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.

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arXiv2023

XQA-DST: Multi-Domain and Multi-Lingual Dialogue State Tracking

Dialogue State Tracking (DST), a crucial component of task-oriented dialogue (ToD) systems, keeps track of all important information pertaining to dialogue history: filling slots with the most probable values throughout the conversation. Existing methods generally rely on a predefined set of values and struggle to generalise to previously unseen slots in new domains. To overcome these challenges, we propose a domain-agnostic extractive question answering (QA) approach with shared weights across domains. To disentangle the complex domain information in ToDs, we train our DST with a novel domain filtering strategy by excluding out-of-domain question samples. With an independent classifier that predicts the presence of multiple domains given the context, our model tackles DST by extracting spans in active domains. Empirical results demonstrate that our model can efficiently leverage domain-agnostic QA datasets by two-stage fine-tuning while being both domain-scalable and open-vocabulary in DST. It shows strong transferability by achieving zero-shot domain-adaptation results on MultiWOZ 2.1 with an average JGA of 36.7%. It further achieves cross-lingual transfer with state-of-the-art zero-shot results, 66.2% JGA from English to German and 75.7% JGA from English to Italian on WOZ 2.0.

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arXiv2023

Adaptive Perturbation-Based Gradient Estimation for Discrete Latent Variable Models

The integration of discrete algorithmic components in deep learning architectures has numerous applications. Recently, Implicit Maximum Likelihood Estimation (IMLE, Niepert, Minervini, and Franceschi 2021), a class of gradient estimators for discrete exponential family distributions, was proposed by combining implicit differentiation through perturbation with the path-wise gradient estimator. However, due to the finite difference approximation of the gradients, it is especially sensitive to the choice of the finite difference step size, which needs to be specified by the user. In this work, we present Adaptive IMLE (AIMLE), the first adaptive gradient estimator for complex discrete distributions: it adaptively identifies the target distribution for IMLE by trading off the density of gradient information with the degree of bias in the gradient estimates. We empirically evaluate our estimator on synthetic examples, as well as on Learning to Explain, Discrete Variational Auto-Encoders, and Neural Relational Inference tasks. In our experiments, we show that our adaptive gradient estimator can produce faithful estimates while requiring orders of magnitude fewer samples than other gradient estimators.

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arXiv2022

Machine Learning-Assisted Recurrence Prediction for Early-Stage Non-Small-Cell Lung Cancer Patients

Background: Stratifying cancer patients according to risk of relapse can personalize their care. In this work, we provide an answer to the following research question: How to utilize machine learning to estimate probability of relapse in early-stage non-small-cell lung cancer patients? Methods: For predicting relapse in 1,387 early-stage (I-II), non-small-cell lung cancer (NSCLC) patients from the Spanish Lung Cancer Group data (65.7 average age, 24.8% females, 75.2% males) we train tabular and graph machine learning models. We generate automatic explanations for the predictions of such models. For models trained on tabular data, we adopt SHAP local explanations to gauge how each patient feature contributes to the predicted outcome. We explain graph machine learning predictions with an example-based method that highlights influential past patients. Results: Machine learning models trained on tabular data exhibit a 76% accuracy for the Random Forest model at predicting relapse evaluated with a 10-fold cross-validation (model was trained 10 times with different independent sets of patients in test, train and validation sets, the reported metrics are averaged over these 10 test sets). Graph machine learning reaches 68% accuracy over a 200-patient, held-out test set, calibrated on a held-out set of 100 patients. Conclusions: Our results show that machine learning models trained on tabular and graph data can enable objective, personalised and reproducible prediction of relapse and therefore, disease outcome in patients with early-stage NSCLC. With further prospective and multisite validation, and additional radiological and molecular data, this prognostic model could potentially serve as a predictive decision support tool for deciding the use of adjuvant treatments in early-stage lung cancer. Keywords: Non-Small-Cell Lung Cancer, Tumor Recurrence Prediction, Machine Learning

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arXiv2022

An Efficient Memory-Augmented Transformer for Knowledge-Intensive NLP Tasks

Access to external knowledge is essential for many natural language processing tasks, such as question answering and dialogue. Existing methods often rely on a parametric model that stores knowledge in its parameters, or use a retrieval-augmented model that has access to an external knowledge source. Parametric and retrieval-augmented models have complementary strengths in terms of computational efficiency and predictive accuracy. To combine the strength of both approaches, we propose the Efficient Memory-Augmented Transformer (EMAT) -- it encodes external knowledge into a key-value memory and exploits the fast maximum inner product search for memory querying. We also introduce pre-training tasks that allow EMAT to encode informative key-value representations, and to learn an implicit strategy to integrate multiple memory slots into the transformer. Experiments on various knowledge-intensive tasks such as question answering and dialogue datasets show that, simply augmenting parametric models (T5-base) using our method produces more accurate results (e.g., 25.8 -> 44.3 EM on NQ) while retaining a high throughput (e.g., 1000 queries/s on NQ). Compared to retrieval-augmented models, EMAT runs substantially faster across the board and produces more accurate results on WoW and ELI5. Our code and datasets are available at https://github. com/uclnlp/EMAT.

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arXiv2022

Learning Discrete Directed Acyclic Graphs via Backpropagation

Recently continuous relaxations have been proposed in order to learn Directed Acyclic Graphs (DAGs) from data by backpropagation, instead of using combinatorial optimization. However, a number of techniques for fully discrete backpropagation could instead be applied. In this paper, we explore that direction and propose DAG-DB, a framework for learning DAGs by Discrete Backpropagation. Based on the architecture of Implicit Maximum Likelihood Estimation [I-MLE, arXiv:2106.01798], DAG-DB adopts a probabilistic approach to the problem, sampling binary adjacency matrices from an implicit probability distribution. DAG-DB learns a parameter for the distribution from the loss incurred by each sample, performing competitively using either of two fully discrete backpropagation techniques, namely I-MLE and Straight-Through Estimation.

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arXiv2022

Logical Reasoning with Span-Level Predictions for Interpretable and Robust NLI Models

Current Natural Language Inference (NLI) models achieve impressive results, sometimes outperforming humans when evaluating on in-distribution test sets. However, as these models are known to learn from annotation artefacts and dataset biases, it is unclear to what extent the models are learning the task of NLI instead of learning from shallow heuristics in their training data. We address this issue by introducing a logical reasoning framework for NLI, creating highly transparent model decisions that are based on logical rules. Unlike prior work, we show that improved interpretability can be achieved without decreasing the predictive accuracy. We almost fully retain performance on SNLI, while also identifying the exact hypothesis spans that are responsible for each model prediction. Using the e-SNLI human explanations, we verify that our model makes sensible decisions at a span level, despite not using any span labels during training. We can further improve model performance and span-level decisions by using the e-SNLI explanations during training. Finally, our model is more robust in a reduced data setting. When training with only 1,000 examples, out-of-distribution performance improves on the MNLI matched and mismatched validation sets by 13% and 16% relative to the baseline. Training with fewer observations yields further improvements, both in-distribution and out-of-distribution.

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arXiv2022

MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction

Relation extraction in the biomedical domain is challenging due to the lack of labeled data and high annotation costs, needing domain experts. Distant supervision is commonly used to tackle the scarcity of annotated data by automatically pairing knowledge graph relationships with raw texts. Such a pipeline is prone to noise and has added challenges to scale for covering a large number of biomedical concepts. We investigated existing broad-coverage distantly supervised biomedical relation extraction benchmarks and found a significant overlap between training and test relationships ranging from 26% to 86%. Furthermore, we noticed several inconsistencies in the data construction process of these benchmarks, and where there is no train-test leakage, the focus is on interactions between narrower entity types. This work presents a more accurate benchmark MedDistant19 for broad-coverage distantly supervised biomedical relation extraction that addresses these shortcomings and is obtained by aligning the MEDLINE abstracts with the widely used SNOMED Clinical Terms knowledge base. Lacking thorough evaluation with domain-specific language models, we also conduct experiments validating general domain relation extraction findings to biomedical relation extraction.

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arXiv2022

Differentiable Reasoning over Long Stories -- Assessing Systematic Generalisation in Neural Models

Contemporary neural networks have achieved a series of developments and successes in many aspects; however, when exposed to data outside the training distribution, they may fail to predict correct answers. In this work, we were concerned about this generalisation issue and thus analysed a broad set of models systematically and robustly over long stories. Related experiments were conducted based on the CLUTRR, which is a diagnostic benchmark suite that can analyse generalisation of natural language understanding (NLU) systems by training over small story graphs and testing on larger ones. In order to handle the multi-relational story graph, we consider two classes of neural models: "E-GNN", the graph-based models that can process graph-structured data and consider the edge attributes simultaneously; and "L-Graph", the sequence-based models which can process linearized version of the graphs. We performed an extensive empirical evaluation, and we found that the modified recurrent neural network yield surprisingly accurate results across every systematic generalisation tasks which outperform the modified graph neural network, while the latter produced more robust models.

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arXiv2021

Implicit MLE: Backpropagating Through Discrete Exponential Family Distributions

Combining discrete probability distributions and combinatorial optimization problems with neural network components has numerous applications but poses several challenges. We propose Implicit Maximum Likelihood Estimation (I-MLE), a framework for end-to-end learning of models combining discrete exponential family distributions and differentiable neural components. I-MLE is widely applicable as it only requires the ability to compute the most probable states and does not rely on smooth relaxations. The framework encompasses several approaches such as perturbation-based implicit differentiation and recent methods to differentiate through black-box combinatorial solvers. We introduce a novel class of noise distributions for approximating marginals via perturb-and-MAP. Moreover, we show that I-MLE simplifies to maximum likelihood estimation when used in some recently studied learning settings that involve combinatorial solvers. Experiments on several datasets suggest that I-MLE is competitive with and often outperforms existing approaches which rely on problem-specific relaxations.

cs.LG↗

arXiv2021

A Probabilistic Framework for Knowledge Graph Data Augmentation

We present NNMFAug, a probabilistic framework to perform data augmentation for the task of knowledge graph completion to counter the problem of data scarcity, which can enhance the learning process of neural link predictors. Our method can generate potentially diverse triples with the advantage of being efficient and scalable as well as agnostic to the choice of the link prediction model and dataset used. Experiments and analysis done on popular models and benchmarks show that NNMFAug can bring notable improvements over the baselines.

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arXiv2021

Relation Prediction as an Auxiliary Training Objective for Improving Multi-Relational Graph Representations

Learning good representations on multi-relational graphs is essential to knowledge base completion (KBC). In this paper, we propose a new self-supervised training objective for multi-relational graph representation learning, via simply incorporating relation prediction into the commonly used 1vsAll objective. The new training objective contains not only terms for predicting the subject and object of a given triple, but also a term for predicting the relation type. We analyse how this new objective impacts multi-relational learning in KBC: experiments on a variety of datasets and models show that relation prediction can significantly improve entity ranking, the most widely used evaluation task for KBC, yielding a 6.1% increase in MRR and 9.9% increase in Hits@1 on FB15k-237 as well as a 3.1% increase in MRR and 3.4% in Hits@1 on Aristo-v4. Moreover, we observe that the proposed objective is especially effective on highly multi-relational datasets, i.e. datasets with a large number of predicates, and generates better representations when larger embedding sizes are used.

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arXiv2021

NeurIPS 2020 EfficientQA Competition: Systems, Analyses and Lessons Learned

We review the EfficientQA competition from NeurIPS 2020. The competition focused on open-domain question answering (QA), where systems take natural language questions as input and return natural language answers. The aim of the competition was to build systems that can predict correct answers while also satisfying strict on-disk memory budgets. These memory budgets were designed to encourage contestants to explore the trade-off between storing retrieval corpora or the parameters of learned models. In this report, we describe the motivation and organization of the competition, review the best submissions, and analyze system predictions to inform a discussion of evaluation for open-domain QA.

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arXiv2021

Training Adaptive Computation for Open-Domain Question Answering with Computational Constraints

Adaptive Computation (AC) has been shown to be effective in improving the efficiency of Open-Domain Question Answering (ODQA) systems. However, current AC approaches require tuning of all model parameters, and training state-of-the-art ODQA models requires significant computational resources that may not be available for most researchers. We propose Adaptive Passage Encoder, an AC method that can be applied to an existing ODQA model and can be trained efficiently on a single GPU. It keeps the parameters of the base ODQA model fixed, but it overrides the default layer-by-layer computation of the encoder with an AC policy that is trained to optimise the computational efficiency of the model. Our experimental results show that our method improves upon a state-of-the-art model on two datasets, and is also more accurate than previous AC methods due to the stronger base ODQA model. All source code and datasets are available at https://github.com/uclnlp/APE.

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