pwc-archive/papers-with-abstracts huggingface dataset:
TripHLApan: predicting HLA molecules binding peptides based on triple coding matrix and transfer learning
Authors: Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li
Date: 2022-08-06 00:00:00
Tasks: Prediction, Transfer Learning

Human leukocyte antigen (HLA) is an important molecule family in the field of human immunity, which recognizes foreign threats and triggers immune responses by presenting peptides to T cells. In recent years, the synthesis of tumor vaccines to induce specific immune responses has become the forefront of cancer treatment. Computationally modeling the binding patterns between peptide and HLA can greatly accelerate the development of tumor vaccines. However, most of the prediction methods performance is very limited and they cannot fully take advantage of the analysis of existing biological knowledge as the basis of modeling. In this paper, we propose TripHLApan, a novel pan-specific prediction model, for HLA molecular peptide binding prediction. TripHLApan exhibits powerful prediction ability by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. The comprehensive evaluations demonstrate the effectiveness of TripHLApan in predicting HLA-I and HLA-II peptide binding in different test environments. The predictive power of HLA-I is further demonstrated in the latest data set. In addition, we show that TripHLApan has strong binding reconstitution ability in the samples of a melanoma patient. In conclusion, TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines.
NRBdMF: A recommendation algorithm for predicting drug effects considering directionality
Authors: Iori Azuma, Tadahaya Mizuno, Hiroyuki Kusuhara
Date: 2022-08-05 00:00:00
Tasks: Recommendation Systems

Predicting the novel effects of drugs based on information about approved drugs can be regarded as a recommendation system. Matrix factorization is one of the most used recommendation systems and various algorithms have been devised for it. A literature survey and summary of existing algorithms for predicting drug effects demonstrated that most such methods, including neighborhood regularized logistic matrix factorization, which was the best performer in benchmark tests, used a binary matrix that considers only the presence or absence of interactions. However, drug effects are known to have two opposite aspects, such as side effects and therapeutic effects. In the present study, we proposed using neighborhood regularized bidirectional matrix factorization (NRBdMF) to predict drug effects by incorporating bidirectionality, which is a characteristic property of drug effects. We used this proposed method for predicting side effects using a matrix that considered the bidirectionality of drug effects, in which known side effects were assigned a positive label (plus 1) and known treatment effects were assigned a negative (minus 1) label. The NRBdMF model, which utilizes drug bidirectional information, achieved enrichment of side effects at the top and indications at the bottom of the prediction list. This first attempt to consider the bidirectional nature of drug effects using NRBdMF showed that it reduced false positives and produced a highly interpretable output.
Compositional Evaluation on Japanese Textual Entailment and Similarity
Authors: Hitomi Yanaka, Koji Mineshima
Date: 2022-08-09 00:00:00
Tasks: Natural Language Inference, Semantic Textual Similarity, STS

Natural Language Inference (NLI) and Semantic Textual Similarity (STS) are widely used benchmark tasks for compositional evaluation of pre-trained language models. Despite growing interest in linguistic universals, most NLI/STS studies have focused almost exclusively on English. In particular, there are no available multilingual NLI/STS datasets in Japanese, which is typologically different from English and can shed light on the currently controversial behavior of language models in matters such as sensitivity to word order and case particles. Against this background, we introduce JSICK, a Japanese NLI/STS dataset that was manually translated from the English dataset SICK. We also present a stress-test dataset for compositional inference, created by transforming syntactic structures of sentences in JSICK to investigate whether language models are sensitive to word order and case particles. We conduct baseline experiments on different pre-trained language models and compare the performance of multilingual models when applied to Japanese and other languages. The results of the stress-test experiments suggest that the current pre-trained language models are insensitive to word order and case marking.
Thai Wav2Vec2.0 with CommonVoice V8
Authors: Wannaphong Phatthiyaphaibun, Chompakorn Chaksangchaichot, Peerat Limkonchotiwat, Ekapol Chuangsuwanich, Sarana Nutanong
Date: 2022-08-09 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), Language Modeling, Language Modelling, Speech Recognition

Recently, Automatic Speech Recognition (ASR), a system that converts audio into text, has caught a lot of attention in the machine learning community. Thus, a lot of publicly available models were released in HuggingFace. However, most of these ASR models are available in English; only a minority of the models are available in Thai. Additionally, most of the Thai ASR models are closed-sourced, and the performance of existing open-sourced models lacks robustness. To address this problem, we train a new ASR model on a pre-trained XLSR-Wav2Vec model with the Thai CommonVoice corpus V8 and train a trigram language model to boost the performance of our ASR model. We hope that our models will be beneficial to individuals and the ASR community in Thailand.
Where's the Learning in Representation Learning for Compositional Semantics and the Case of Thematic Fit
Authors: Mughilan Muthupari, Samrat Halder, Asad Sayeed, Yuval Marton
Date: 2022-08-09 00:00:00
Tasks: Multi-Task Learning, Relation, Representation Learning, Word Embeddings

Observing that for certain NLP tasks, such as semantic role prediction or thematic fit estimation, random embeddings perform as well as pretrained embeddings, we explore what settings allow for this and examine where most of the learning is encoded: the word embeddings, the semantic role embeddings, or ``the network''. We find nuanced answers, depending on the task and its relation to the training objective. We examine these representation learning aspects in multi-task learning, where role prediction and role-filling are supervised tasks, while several thematic fit tasks are outside the models' direct supervision. We observe a non-monotonous relation between some tasks' quality score and the training data size. In order to better understand this observation, we analyze these results using easier, per-verb versions of these tasks.
ASR Error Correction with Constrained Decoding on Operation Prediction
Authors: Jingyuan Yang, Rongjun Li, Wei Peng
Date: 2022-08-09 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), Decoder, Prediction, speech-recognition, Speech Recognition

Error correction techniques remain effective to refine outputs from automatic speech recognition (ASR) models. Existing end-to-end error correction methods based on an encoder-decoder architecture process all tokens in the decoding phase, creating undesirable latency. In this paper, we propose an ASR error correction method utilizing the predictions of correction operations. More specifically, we construct a predictor between the encoder and the decoder to learn if a token should be kept ("K"), deleted ("D"), or changed ("C") to restrict decoding to only part of the input sequence embeddings (the "C" tokens) for fast inference. Experiments on three public datasets demonstrate the effectiveness of the proposed approach in reducing the latency of the decoding process in ASR correction. It enhances the inference speed by at least three times (3.4 and 5.7 times) while maintaining the same level of accuracy (with WER reductions of 0.53% and 1.69% respectively) for our two proposed models compared to a solid encoder-decoder baseline. In the meantime, we produce and release a benchmark dataset contributing to the ASR error correction community to foster research along this line.
Positively transitioned sentiment dialogue corpus for developing emotion-affective open-domain chatbots
Authors: Weixuan Wang, Wei Peng, Chong Hsuan Huang, Haoran Wang
Date: 2022-08-09 00:00:00
Tasks: Chatbot

In this paper, we describe a data enhancement method for developing Emily, an emotion-affective open-domain chatbot. The proposed method is based on explicitly modeling positively transitioned (PT) sentiment data from multi-turn dialogues. We construct a dialogue corpus with PT sentiment data and will release it for public use. By fine-tuning a pretrained dialogue model using the produced PT-enhanced dialogues, we are able to develop an emotion-affective open-domain chatbot exhibiting close-to-human performance in various emotion-affective metrics. We evaluate Emily against a few state-of-the-art (SOTA) open-domain chatbots and show the effectiveness of the proposed approach. The corpus is made publicly available.
Emotion Detection From Tweets Using a BERT and SVM Ensemble Model
Authors: Ionuţ-Alexandru Albu, Stelian Spînu
Date: 2022-08-09 00:00:00
Tasks: Emotion Recognition

Automatic identification of emotions expressed in Twitter data has a wide range of applications. We create a well-balanced dataset by adding a neutral class to a benchmark dataset consisting of four emotions: fear, sadness, joy, and anger. On this extended dataset, we investigate the use of Support Vector Machine (SVM) and Bidirectional Encoder Representations from Transformers (BERT) for emotion recognition. We propose a novel ensemble model by combining the two BERT and SVM models. Experiments show that the proposed model achieves a state-of-the-art accuracy of 0.91 on emotion recognition in tweets.
An Embarrassingly Easy but Strong Baseline for Nested Named Entity Recognition
Authors: Hang Yan, Yu Sun, Xiaonan Li, Xipeng Qiu
Date: 2022-08-09 00:00:00
Tasks: named-entity-recognition, Named Entity Recognition, Named Entity Recognition (NER), NER, Nested Named Entity Recognition, Sentence

Named entity recognition (NER) is the task to detect and classify the entity spans in the text. When entity spans overlap between each other, this problem is named as nested NER. Span-based methods have been widely used to tackle the nested NER. Most of these methods will get a score $n \times n$ matrix, where $n$ means the length of sentence, and each entry corresponds to a span. However, previous work ignores spatial relations in the score matrix. In this paper, we propose using Convolutional Neural Network (CNN) to model these spatial relations in the score matrix. Despite being simple, experiments in three commonly used nested NER datasets show that our model surpasses several recently proposed methods with the same pre-trained encoders. Further analysis shows that using CNN can help the model find more nested entities. Besides, we found that different papers used different sentence tokenizations for the three nested NER datasets, which will influence the comparison. Thus, we release a pre-processing script to facilitate future comparison.
Exploring Hate Speech Detection with HateXplain and BERT
Authors: Arvind Subramaniam, Aryan Mehra, Sayani Kundu
Date: 2022-08-09 00:00:00
Tasks: Hate Speech Detection

Hate Speech takes many forms to target communities with derogatory comments, and takes humanity a step back in societal progress. HateXplain is a recently published and first dataset to use annotated spans in the form of rationales, along with speech classification categories and targeted communities to make the classification more humanlike, explainable, accurate and less biased. We tune BERT to perform this task in the form of rationales and class prediction, and compare our performance on different metrics spanning across accuracy, explainability and bias. Our novelty is threefold. Firstly, we experiment with the amalgamated rationale class loss with different importance values. Secondly, we experiment extensively with the ground truth attention values for the rationales. With the introduction of conservative and lenient attentions, we compare performance of the model on HateXplain and test our hypothesis. Thirdly, in order to improve the unintended bias in our models, we use masking of the target community words and note the improvement in bias and explainability metrics. Overall, we are successful in achieving model explanability, bias removal and several incremental improvements on the original BERT implementation.
The Analysis of Synonymy and Antonymy in Discourse Relations: An interpretable Modeling Approach
Authors: A. Reig-Alamillo, D. Torres-Moreno, E. Morales-González, M. Toledo-Acosta, A. Taroni, J. Hermosillo-Valadez
Date: 2022-08-09 00:00:00
Tasks: Explainable Models

The idea that discourse relations are construed through explicit content and shared, or implicit, knowledge between producer and interpreter is ubiquitous in discourse research and linguistics. However, the actual contribution of the lexical semantics of arguments is unclear. We propose a computational approach to the analysis of contrast and concession relations in the PDTB corpus. Our work sheds light on the extent to which lexical semantics contributes to signaling explicit and implicit discourse relations and clarifies the contribution of different parts of speech in both. This study contributes to bridging the gap between corpus linguistics and computational linguistics by proposing transparent and explainable models of discourse relations based on the synonymy and antonymy of their arguments.
A Systematic Evaluation of Response Selection for Open Domain Dialogue
Authors: Behnam Hedayatnia, Di Jin, Yang Liu, Dilek Hakkani-Tur
Date: 2022-08-08 00:00:00
Proceeding: SIGDIAL (ACL) 2022 9

Recent progress on neural approaches for language processing has triggered a resurgence of interest on building intelligent open-domain chatbots. However, even the state-of-the-art neural chatbots cannot produce satisfying responses for every turn in a dialog. A practical solution is to generate multiple response candidates for the same context, and then perform response ranking/selection to determine which candidate is the best. Previous work in response selection typically trains response rankers using synthetic data that is formed from existing dialogs by using a ground truth response as the single appropriate response and constructing inappropriate responses via random selection or using adversarial methods. In this work, we curated a dataset where responses from multiple response generators produced for the same dialog context are manually annotated as appropriate (positive) and inappropriate (negative). We argue that such training data better matches the actual use case examples, enabling the models to learn to rank responses effectively. With this new dataset, we conduct a systematic evaluation of state-of-the-art methods for response selection, and demonstrate that both strategies of using multiple positive candidates and using manually verified hard negative candidates can bring in significant performance improvement in comparison to using the adversarial training data, e.g., increase of 3% and 13% in Recall@1 score, respectively.
Investigating Efficiently Extending Transformers for Long Input Summarization
Authors: Jason Phang, Yao Zhao, Peter J. Liu
Date: 2022-08-08 00:00:00
Tasks: 16k, Long-range modeling, Text Summarization

While large pretrained Transformer models have proven highly capable at tackling natural language tasks, handling long sequence inputs continues to be a significant challenge. One such task is long input summarization, where inputs are longer than the maximum input context of most pretrained models. Through an extensive set of experiments, we investigate what model architectural changes and pretraining paradigms can most efficiently adapt a pretrained Transformer for long input summarization. We find that a staggered, block-local Transformer with global encoder tokens strikes a good balance of performance and efficiency, and that an additional pretraining phase on long sequences meaningfully improves downstream summarization performance. Based on our findings, we introduce PEGASUS-X, an extension of the PEGASUS model with additional long input pretraining to handle inputs of up to 16K tokens. PEGASUS-X achieves strong performance on long input summarization tasks comparable with much larger models while adding few additional parameters and not requiring model parallelism to train.
Boosting with copula-based components
Authors: Simon Boge Brant, Ingrid Hobæk Haff
Date: 2022-08-09 00:00:00
Tasks: Additive models, Model Selection, regression

The authors propose new additive models for binary outcomes, where the components are copula-based regression models (Noh et al, 2013), and designed such that the model may capture potentially complex interaction effects. The models do not require discretisation of continuous covariates, and are therefore suitable for problems with many such covariates. A fitting algorithm, and efficient procedures for model selection and evaluation of the components are described. Software is provided in the R-package copulaboost. Simulations and illustrations on data sets indicate that the method's predictive performance is either better than or comparable to the other methods.
Early Stage Sparse Retrieval with Entity Linking
Authors: Dahlia Shehata, Negar Arabzadeh, Charles L. A. Clarke
Date: 2022-08-09 00:00:00
Tasks: Entity Linking, Information Retrieval, Retrieval

Despite the advantages of their low-resource settings, traditional sparse retrievers depend on exact matching approaches between high-dimensional bag-of-words (BoW) representations of both the queries and the collection. As a result, retrieval performance is restricted by semantic discrepancies and vocabulary gaps. On the other hand, transformer-based dense retrievers introduce significant improvements in information retrieval tasks by exploiting low-dimensional contextualized representations of the corpus. While dense retrievers are known for their relative effectiveness, they suffer from lower efficiency and lack of generalization issues, when compared to sparse retrievers. For a lightweight retrieval task, high computational resources and time consumption are major barriers encouraging the renunciation of dense models despite potential gains. In this work, we propose boosting the performance of sparse retrievers by expanding both the queries and the documents with linked entities in two formats for the entity names: 1) explicit and 2) hashed. We employ a zero-shot end-to-end dense entity linking system for entity recognition and disambiguation to augment the corpus. By leveraging the advanced entity linking methods, we believe that the effectiveness gap between sparse and dense retrievers can be narrowed. We conduct our experiments on the MS MARCO passage dataset. Since we are concerned with the early stage retrieval in cascaded ranking architectures of large information retrieval systems, we evaluate our results using recall@1000. Our approach is also capable of retrieving documents for query subsets judged to be particularly difficult in prior work. We further demonstrate that the non-expanded and the expanded runs with both explicit and hashed entities retrieve complementary results. Consequently, we adopt a run fusion approach to maximize the benefits of entity linking.
Unsupervised Question Clarity Prediction Through Retrieved Item Coherency
Authors: Negar Arabzadeh, Mahsa Seifikar, Charles L. A. Clarke
Date: 2022-08-09 00:00:00
Tasks: Conversational Question Answering, Prediction, Question Answering, Retrieval

Despite recent progress on conversational systems, they still do not perform smoothly and coherently when faced with ambiguous requests. When questions are unclear, conversational systems should have the ability to ask clarifying questions, rather than assuming a particular interpretation or simply responding that they do not understand. Previous studies have shown that users are more satisfied when asked a clarifying question, rather than receiving an unrelated response. While the research community has paid substantial attention to the problem of predicting query ambiguity in traditional search contexts, researchers have paid relatively little attention to predicting when this ambiguity is sufficient to warrant clarification in the context of conversational systems. In this paper, we propose an unsupervised method for predicting the need for clarification. This method is based on the measured coherency of results from an initial answer retrieval step, under the assumption that a less ambiguous query is more likely to retrieve more coherent results when compared to an ambiguous query. We build a graph from retrieved items based on their context similarity, treating measures of graph connectivity as indicators of ambiguity. We evaluate our approach on two recently released open-domain conversational question answering datasets, ClariQ and AmbigNQ, comparing it with neural and non-neural baselines. Our unsupervised approach performs as well as supervised approaches while providing better generalization.
Time Lag Aware Sequential Recommendation
Authors: Lihua Chen, Ning Yang, Philip S Yu
Date: 2022-08-09 00:00:00
Tasks: Sequential Recommendation

Although a variety of methods have been proposed for sequential recommendation, it is still far from being well solved partly due to two challenges. First, the existing methods often lack the simultaneous consideration of the global stability and local fluctuation of user preference, which might degrade the learning of a user's current preference. Second, the existing methods often use a scalar based weighting schema to fuse the long-term and short-term preferences, which is too coarse to learn an expressive embedding of current preference. To address the two challenges, we propose a novel model called Time Lag aware Sequential Recommendation (TLSRec), which integrates a hierarchical modeling of user preference and a time lag sensitive fine-grained fusion of the long-term and short-term preferences. TLSRec employs a hierarchical self-attention network to learn users' preference at both global and local time scales, and a neural time gate to adaptively regulate the contributions of the long-term and short-term preferences for the learning of a user's current preference at the aspect level and based on the lag between the current time and the time of the last behavior of a user. The extensive experiments conducted on real datasets verify the effectiveness of TLSRec.