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Published biomedical information has and continues to rapidly increase. The recent advancements in Natural Language Processing (NLP), have generated considerable interest in automating the extraction, normalization, and representation of biomedical knowledge about entities such as genes and diseases. Our study analyzes germline abstracts in the construction of knowledge graphs of the of the immense work that has been done in this area for genes and diseases. This paper presents SimpleGermKG, an automatic knowledge graph construction approach that connects germline genes and diseases. For the extraction of genes and diseases, we employ BioBERT, a pre-trained BERT model on biomedical corpora. We propose an ontology-based and rule-based algorithm to standardize and disambiguate medical terms. For semantic relationships between articles, genes, and diseases, we implemented a part-whole relation approach to connect each entity with its data source and visualize them in a graph-based knowledge representation. Lastly, we discuss the knowledge graph applications, limitations, and challenges to inspire the future research of germline corpora. Our knowledge graph contains 297 genes, 130 diseases, and 46,747 triples. Graph-based visualizations are used to show the results.

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In this paper, we investigate the performances of tunable quantum neural networks in the Quantum Probably Approximately Correct (QPAC) learning framework. Tunable neural networks are quantum circuits made of multi-controlled X gates. By tuning the set of controls these circuits are able to approximate any Boolean functions. This architecture is particularly suited to be used in the QPAC-learning framework as it can handle the superposition produced by the oracle. In order to tune the network so that it can approximate a target concept, we have devised and implemented an algorithm based on amplitude amplification. The numerical results show that this approach can efficiently learn concepts from a simple class.

Machine Translation (MT) continues to improve in quality and adoption, yet the inadvertent perpetuation of gender bias remains a significant concern. Despite numerous studies into gender bias in translations from gender-neutral languages such as Turkish into more strongly gendered languages like English, there are no benchmarks for evaluating this phenomenon or for assessing mitigation strategies. To address this gap, we introduce GATE X-E, an extension to the GATE (Rarrick et al., 2023) corpus, that consists of human translations from Turkish, Hungarian, Finnish, and Persian into English. Each translation is accompanied by feminine, masculine, and neutral variants for each possible gender interpretation. The dataset, which contains between 1250 and 1850 instances for each of the four language pairs, features natural sentences with a wide range of sentence lengths and domains, challenging translation rewriters on various linguistic phenomena. Additionally, we present an English gender rewriting solution built on GPT-3.5 Turbo and use GATE X-E to evaluate it. We open source our contributions to encourage further research on gender debiasing.

Individuals and organizations cope with an always-growing data amount, heterogeneous in contents and formats. A prerequisite to get value out this data and minimise inherent risks related to multiple usages is an adequate data management process yielding data quality and control over its lifecycle. Common data governance frameworks relying on people, policies and processes falls short of the overwhelming data complexity. Yet, harnessing this complexity is necessary to achieve high quality standards. The later will condition the outcome of any downstream data usage, including generative artificial intelligence trained on this data. In this paper, we report our concrete experience establishing a simple, cost-efficient framework, that enables metadata-driven, agile and (semi-)automated data governance (i.e. Data Governance 4.0). We explain how we implement and use this framework to integrate 25 years of clinical study data at enterprise scale, in a fully productive environment. The framework encompasses both methodologies and technologies leveraging semantic web principles. We built a knowledge graph describing avatars of data assets in their business context including governance principles. Multiple ontologies articulated by an enterprise upper ontology enable key governance actions such as FAIRification, lifecycle management, definition of roles and responsibilities, lineage across transformations and provenance from source systems. This metadata model is the keystone to data governance 4.0: a semi-automatized data management process, taking in account the business context in an agile manner to adapt governance constraints to each use case and dynamically tune it based on business changes.

We evaluate how well LLMs understand African American Language (AAL) in comparison to their performance on White Mainstream English (WME), the encouraged "standard" form of English taught in American classrooms. We measure LLM performance using automatic metrics and human judgments for two tasks: a counterpart generation task, where a model generates AAL (or WME) given WME (or AAL), and a masked span prediction (MSP) task, where models predict a phrase that was removed from their input. Our contributions include: (1) evaluation of six pre-trained, large language models on the two language generation tasks; (2) a novel dataset of AAL text from multiple contexts (social media, hip-hop lyrics, focus groups, and linguistic interviews) with human-annotated counterparts in WME; and (3) documentation of model performance gaps that suggest bias and identification of trends in lack of understanding of AAL features.

Recently, Zhang et al. have proposed the Diffusion Exponential Integrator Sampler (DEIS) for fast generation of samples from Diffusion Models. It leverages the semi-linear nature of the probability flow ordinary differential equation (ODE) in order to greatly reduce integration error and improve generation quality at low numbers of function evaluations (NFEs). Key to this approach is the score function reparameterisation, which reduces the integration error incurred from using a fixed score function estimate over each integration step. The original authors use the default parameterisation used by models trained for noise prediction -- multiply the score by the standard deviation of the conditional forward noising distribution. We find that although the mean absolute value of this score parameterisation is close to constant for a large portion of the reverse sampling process, it changes rapidly at the end of sampling. As a simple fix, we propose to instead reparameterise the score (at inference) by dividing it by the average absolute value of previous score estimates at that time step collected from offline high NFE generations. We find that our score normalisation (DEIS-SN) consistently improves FID compared to vanilla DEIS, showing an improvement at 10 NFEs from 6.44 to 5.57 on CIFAR-10 and from 5.9 to 4.95 on LSUN-Church 64x64. Our code is available at //github.com/mtkresearch/Diffusion-DEIS-SN

Knowledge Graph Embedding (KGE) aims to learn representations for entities and relations. Most KGE models have gained great success, especially on extrapolation scenarios. Specifically, given an unseen triple (h, r, t), a trained model can still correctly predict t from (h, r, ?), or h from (?, r, t), such extrapolation ability is impressive. However, most existing KGE works focus on the design of delicate triple modeling function, which mainly tells us how to measure the plausibility of observed triples, but offers limited explanation of why the methods can extrapolate to unseen data, and what are the important factors to help KGE extrapolate. Therefore in this work, we attempt to study the KGE extrapolation of two problems: 1. How does KGE extrapolate to unseen data? 2. How to design the KGE model with better extrapolation ability? For the problem 1, we first discuss the impact factors for extrapolation and from relation, entity and triple level respectively, propose three Semantic Evidences (SEs), which can be observed from train set and provide important semantic information for extrapolation. Then we verify the effectiveness of SEs through extensive experiments on several typical KGE methods. For the problem 2, to make better use of the three levels of SE, we propose a novel GNN-based KGE model, called Semantic Evidence aware Graph Neural Network (SE-GNN). In SE-GNN, each level of SE is modeled explicitly by the corresponding neighbor pattern, and merged sufficiently by the multi-layer aggregation, which contributes to obtaining more extrapolative knowledge representation. Finally, through extensive experiments on FB15k-237 and WN18RR datasets, we show that SE-GNN achieves state-of-the-art performance on Knowledge Graph Completion task and performs a better extrapolation ability.

Reasoning with knowledge expressed in natural language and Knowledge Bases (KBs) is a major challenge for Artificial Intelligence, with applications in machine reading, dialogue, and question answering. General neural architectures that jointly learn representations and transformations of text are very data-inefficient, and it is hard to analyse their reasoning process. These issues are addressed by end-to-end differentiable reasoning systems such as Neural Theorem Provers (NTPs), although they can only be used with small-scale symbolic KBs. In this paper we first propose Greedy NTPs (GNTPs), an extension to NTPs addressing their complexity and scalability limitations, thus making them applicable to real-world datasets. This result is achieved by dynamically constructing the computation graph of NTPs and including only the most promising proof paths during inference, thus obtaining orders of magnitude more efficient models. Then, we propose a novel approach for jointly reasoning over KBs and textual mentions, by embedding logic facts and natural language sentences in a shared embedding space. We show that GNTPs perform on par with NTPs at a fraction of their cost while achieving competitive link prediction results on large datasets, providing explanations for predictions, and inducing interpretable models. Source code, datasets, and supplementary material are available online at //github.com/uclnlp/gntp.

Deep convolutional neural networks (CNNs) have recently achieved great success in many visual recognition tasks. However, existing deep neural network models are computationally expensive and memory intensive, hindering their deployment in devices with low memory resources or in applications with strict latency requirements. Therefore, a natural thought is to perform model compression and acceleration in deep networks without significantly decreasing the model performance. During the past few years, tremendous progress has been made in this area. In this paper, we survey the recent advanced techniques for compacting and accelerating CNNs model developed. These techniques are roughly categorized into four schemes: parameter pruning and sharing, low-rank factorization, transferred/compact convolutional filters, and knowledge distillation. Methods of parameter pruning and sharing will be described at the beginning, after that the other techniques will be introduced. For each scheme, we provide insightful analysis regarding the performance, related applications, advantages, and drawbacks etc. Then we will go through a few very recent additional successful methods, for example, dynamic capacity networks and stochastic depths networks. After that, we survey the evaluation matrix, the main datasets used for evaluating the model performance and recent benchmarking efforts. Finally, we conclude this paper, discuss remaining challenges and possible directions on this topic.

Bidirectional Encoder Representations from Transformers (BERT) has shown marvelous improvements across various NLP tasks. Recently, an upgraded version of BERT has been released with Whole Word Masking (WWM), which mitigate the drawbacks of masking partial WordPiece tokens in pre-training BERT. In this technical report, we adapt whole word masking in Chinese text, that masking the whole word instead of masking Chinese characters, which could bring another challenge in Masked Language Model (MLM) pre-training task. The model was trained on the latest Chinese Wikipedia dump. We aim to provide easy extensibility and better performance for Chinese BERT without changing any neural architecture or even hyper-parameters. The model is verified on various NLP tasks, across sentence-level to document-level, including sentiment classification (ChnSentiCorp, Sina Weibo), named entity recognition (People Daily, MSRA-NER), natural language inference (XNLI), sentence pair matching (LCQMC, BQ Corpus), and machine reading comprehension (CMRC 2018, DRCD, CAIL RC). Experimental results on these datasets show that the whole word masking could bring another significant gain. Moreover, we also examine the effectiveness of Chinese pre-trained models: BERT, ERNIE, BERT-wwm. We release the pre-trained model (both TensorFlow and PyTorch) on GitHub: //github.com/ymcui/Chinese-BERT-wwm

Visual Question Answering (VQA) models have struggled with counting objects in natural images so far. We identify a fundamental problem due to soft attention in these models as a cause. To circumvent this problem, we propose a neural network component that allows robust counting from object proposals. Experiments on a toy task show the effectiveness of this component and we obtain state-of-the-art accuracy on the number category of the VQA v2 dataset without negatively affecting other categories, even outperforming ensemble models with our single model. On a difficult balanced pair metric, the component gives a substantial improvement in counting over a strong baseline by 6.6%.

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