pwc-archive/papers-with-abstracts huggingface dataset:
DPST: De Novo Peptide Sequencing with Amino-Acid-Aware Transformers
Authors: Yan Yang, Zakir Hossain, Khandaker Asif, Liyuan Pan, Shafin Rahman, Eric Stone
Date: 2022-03-23 00:00:00
Tasks: Decoder, de novo peptide sequencing

De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to over-trimming on receptive fields of MS data and restricts MS evidence associated with following undecoded amino acids. Our approach, DPST, circumvents these limitations with two key components: (1) A confidence value aggregation encoder to sketch spectrum representations according to amino-acid-based connectivity among MS; (2) A global-local fusion decoder to progressively assimilate contextualized spectrum representations with a predefined preconception of localized MS evidence and amino acid priors. Our components originate from a closed-form solution and selectively attend to informative amino-acid-aware MS representations. Through extensive empirical studies, we demonstrate the superiority of DPST, showing that it outperforms state-of-the-art approaches by a margin of 12% - 19% peptide accuracy.
Graph Neural Networks in Particle Physics: Implementations, Innovations, and Challenges
Authors: Savannah Thais, Paolo Calafiura, Grigorios Chachamis, Gage DeZoort, Javier Duarte, Sanmay Ganguly, Michael Kagan, Daniel Murnane, Mark S. Neubauer, Kazuhiro Terao
Date: 2022-03-23 00:00:00

Many physical systems can be best understood as sets of discrete data with associated relationships. Where previously these sets of data have been formulated as series or image data to match the available machine learning architectures, with the advent of graph neural networks (GNNs), these systems can be learned natively as graphs. This allows a wide variety of high- and low-level physical features to be attached to measurements and, by the same token, a wide variety of HEP tasks to be accomplished by the same GNN architectures. GNNs have found powerful use-cases in reconstruction, tagging, generation and end-to-end analysis. With the wide-spread adoption of GNNs in industry, the HEP community is well-placed to benefit from rapid improvements in GNN latency and memory usage. However, industry use-cases are not perfectly aligned with HEP and much work needs to be done to best match unique GNN capabilities to unique HEP obstacles. We present here a range of these capabilities, predictions of which are currently being well-adopted in HEP communities, and which are still immature. We hope to capture the landscape of graph techniques in machine learning as well as point out the most significant gaps that are inhibiting potentially large leaps in research.
Constrained Parameter Inference as a Principle for Learning
Authors: Nasir Ahmad, Ellen Schrader, Marcel van Gerven
Date: 2022-03-22 00:00:00

Learning in neural networks is often framed as a problem in which targeted error signals are directly propagated to parameters and used to produce updates that induce more optimal network behaviour. Backpropagation of error (BP) is an example of such an approach and has proven to be a highly successful application of stochastic gradient descent to deep neural networks. We propose constrained parameter inference (COPI) as a new principle for learning. The COPI approach assumes that learning can be set up in a manner where parameters infer their own values based upon observations of their local neuron activities. We find that this estimation of network parameters is possible under the constraints of decorrelated neural inputs and top-down perturbations of neural states for credit assignment. We show that the decorrelation required for COPI allows learning at extremely high learning rates, competitive with that of adaptive optimizers, as used by BP. We further demonstrate that COPI affords a new approach to feature analysis and network compression. Finally, we argue that COPI may shed new light on learning in biological networks given the evidence for decorrelation in the brain.
Pseudo Label Is Better Than Human Label
Authors: Dongseong Hwang, Khe Chai Sim, Zhouyuan Huo, Trevor Strohman
Date: 2022-03-22 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), Pseudo Label, speech-recognition, Speech Recognition

State-of-the-art automatic speech recognition (ASR) systems are trained with tens of thousands of hours of labeled speech data. Human transcription is expensive and time consuming. Factors such as the quality and consistency of the transcription can greatly affect the performance of the ASR models trained with these data. In this paper, we show that we can train a strong teacher model to produce high quality pseudo labels by utilizing recent self-supervised and semi-supervised learning techniques. Specifically, we use JUST (Joint Unsupervised/Supervised Training) and iterative noisy student teacher training to train a 600 million parameter bi-directional teacher model. This model achieved 4.0% word error rate (WER) on a voice search task, 11.1% relatively better than a baseline. We further show that by using this strong teacher model to generate high-quality pseudo labels for training, we can achieve 13.6% relative WER reduction (5.9% to 5.1%) for a streaming model compared to using human labels.
SMARAGD: Learning SMatch for Accurate and Rapid Approximate Graph Distance
Authors: Juri Opitz, Philipp Meier, Anette Frank
Date: 2022-03-24 00:00:00
Tasks: Clustering, Data Augmentation, Graph Clustering, Graph Matching, Machine Translation, Semantic Similarity, Semantic Textual Similarity, Translation

The similarity of graph structures, such as Meaning Representations (MRs), is often assessed via structural matching algorithms, such as Smatch (Cai and Knight, 2013). However, Smatch involves a combinatorial problem that suffers from NP-completeness, making large-scale applications, e.g., graph clustering or search, infeasible. To alleviate this issue, we learn SMARAGD: Semantic Match for Accurate and Rapid Approximate Graph Distance. We show the potential of neural networks to approximate Smatch scores, i) in linear time using a machine translation framework to predict alignments, or ii) in constant time using a Siamese CNN to directly predict Smatch scores. We show that the approximation error can be substantially reduced through data augmentation and graph anonymization.
Direct parsing to sentiment graphs
Authors: David Samuel, Jeremy Barnes, Robin Kurtz, Stephan Oepen, Lilja Øvrelid, Erik Velldal
Date: 2022-03-24 00:00:00
Proceeding: ACL 2022 5
Tasks: Sentiment Analysis

This paper demonstrates how a graph-based semantic parser can be applied to the task of structured sentiment analysis, directly predicting sentiment graphs from text. We advance the state of the art on 4 out of 5 standard benchmark sets. We release the source code, models and predictions.
minicons: Enabling Flexible Behavioral and Representational Analyses of Transformer Language Models
Authors: Kanishka Misra
Date: 2022-03-24 00:00:00
Tasks: Benchmarking, Sentence

We present minicons, an open source library that provides a standard API for researchers interested in conducting behavioral and representational analyses of transformer-based language models (LMs). Specifically, minicons enables researchers to apply analysis methods at two levels: (1) at the prediction level -- by providing functions to efficiently extract word/sentence level probabilities; and (2) at the representational level -- by also facilitating efficient extraction of word/phrase level vectors from one or more layers. In this paper, we describe the library and apply it to two motivating case studies: One focusing on the learning dynamics of the BERT architecture on relative grammatical judgments, and the other on benchmarking 23 different LMs on zero-shot abductive reasoning. minicons is available at https://github.com/kanishkamisra/minicons
Ensembling and Knowledge Distilling of Large Sequence Taggers for Grammatical Error Correction
Authors: Maksym Tarnavskyi, Artem Chernodub, Kostiantyn Omelianchuk
Date: 2022-03-24 00:00:00
Proceeding: ACL 2022 5
Tasks: Grammatical Error Correction, Knowledge Distillation

In this paper, we investigate improvements to the GEC sequence tagging architecture with a focus on ensembling of recent cutting-edge Transformer-based encoders in Large configurations. We encourage ensembling models by majority votes on span-level edits because this approach is tolerant to the model architecture and vocabulary size. Our best ensemble achieves a new SOTA result with an $F_{0.5}$ score of 76.05 on BEA-2019 (test), even without pre-training on synthetic datasets. In addition, we perform knowledge distillation with a trained ensemble to generate new synthetic training datasets, "Troy-Blogs" and "Troy-1BW". Our best single sequence tagging model that is pretrained on the generated Troy-datasets in combination with the publicly available synthetic PIE dataset achieves a near-SOTA (To the best of our knowledge, our best single model gives way only to much heavier T5 model result with an $F_{0.5}$ score of 73.21 on BEA-2019 (test). The code, datasets, and trained models are publicly available).
Kratt: Developing an Automatic Subject Indexing Tool for The National Library of Estonia
Authors: Marit Asula, Jane Makke, Linda Freienthal, Hele-Andra Kuulmets, Raul Sirel
Date: 2022-03-24 00:00:00

Manual subject indexing in libraries is a time-consuming and costly process and the quality of the assigned subjects is affected by the cataloguer's knowledge on the specific topics contained in the book. Trying to solve these issues, we exploited the opportunities arising from artificial intelligence to develop Kratt: a prototype of an automatic subject indexing tool. Kratt is able to subject index a book independent of its extent and genre with a set of keywords present in the Estonian Subject Thesaurus. It takes Kratt approximately 1 minute to subject index a book, outperforming humans 10-15 times. Although the resulting keywords were not considered satisfactory by the cataloguers, the ratings of a small sample of regular library users showed more promise. We also argue that the results can be enhanced by including a bigger corpus for training the model and applying more careful preprocessing techniques.
Generating Scientific Claims for Zero-Shot Scientific Fact Checking
Authors: Dustin Wright, David Wadden, Kyle Lo, Bailey Kuehl, Arman Cohan, Isabelle Augenstein, Lucy Lu Wang
Date: 2022-03-24 00:00:00
Proceeding: ACL 2022 5
Tasks: Fact Checking, Negation

Automated scientific fact checking is difficult due to the complexity of scientific language and a lack of significant amounts of training data, as annotation requires domain expertise. To address this challenge, we propose scientific claim generation, the task of generating one or more atomic and verifiable claims from scientific sentences, and demonstrate its usefulness in zero-shot fact checking for biomedical claims. We propose CLAIMGEN-BART, a new supervised method for generating claims supported by the literature, as well as KBIN, a novel method for generating claim negations. Additionally, we adapt an existing unsupervised entity-centric method of claim generation to biomedical claims, which we call CLAIMGEN-ENTITY. Experiments on zero-shot fact checking demonstrate that both CLAIMGEN-ENTITY and CLAIMGEN-BART, coupled with KBIN, achieve up to 90% performance of fully supervised models trained on manually annotated claims and evidence. A rigorous evaluation study demonstrates significant improvement in generated claim and negation quality over existing baselines
Probing for Labeled Dependency Trees
Authors: Max Müller-Eberstein, Rob van der Goot, Barbara Plank
Date: 2022-03-24 00:00:00
Proceeding: ACL 2022 5
Tasks: Dependency Parsing, Informativeness

Probing has become an important tool for analyzing representations in Natural Language Processing (NLP). For graphical NLP tasks such as dependency parsing, linear probes are currently limited to extracting undirected or unlabeled parse trees which do not capture the full task. This work introduces DepProbe, a linear probe which can extract labeled and directed dependency parse trees from embeddings while using fewer parameters and compute than prior methods. Leveraging its full task coverage and lightweight parametrization, we investigate its predictive power for selecting the best transfer language for training a full biaffine attention parser. Across 13 languages, our proposed method identifies the best source treebank 94% of the time, outperforming competitive baselines and prior work. Finally, we analyze the informativeness of task-specific subspaces in contextual embeddings as well as which benefits a full parser's non-linear parametrization provides.
Multitasking Framework for Unsupervised Simple Definition Generation
Authors: Cunliang Kong, Yun Chen, Hengyuan Zhang, Liner Yang, Erhong Yang
Date: 2022-03-24 00:00:00
Proceeding: ACL 2022 5

The definition generation task can help language learners by providing explanations for unfamiliar words. This task has attracted much attention in recent years. We propose a novel task of Simple Definition Generation (SDG) to help language learners and low literacy readers. A significant challenge of this task is the lack of learner's dictionaries in many languages, and therefore the lack of data for supervised training. We explore this task and propose a multitasking framework SimpDefiner that only requires a standard dictionary with complex definitions and a corpus containing arbitrary simple texts. We disentangle the complexity factors from the text by carefully designing a parameter sharing scheme between two decoders. By jointly training these components, the framework can generate both complex and simple definitions simultaneously. We demonstrate that the framework can generate relevant, simple definitions for the target words through automatic and manual evaluations on English and Chinese datasets. Our method outperforms the baseline model by a 1.77 SARI score on the English dataset, and raises the proportion of the low level (HSK level 1-3) words in Chinese definitions by 3.87%.
Lahjoita puhetta -- a large-scale corpus of spoken Finnish with some benchmarks
Authors: Anssi Moisio, Dejan Porjazovski, Aku Rouhe, Yaroslav Getman, Anja Virkkunen, Tamás Grósz, Krister Lindén, Mikko Kurimo
Date: 2022-03-24 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), speech-recognition, Speech Recognition

The Donate Speech campaign has so far succeeded in gathering approximately 3600 hours of ordinary, colloquial Finnish speech into the Lahjoita puhetta (Donate Speech) corpus. The corpus includes over twenty thousand speakers from all the regions of Finland and from all age brackets. The primary goals of the collection were to create a representative, large-scale resource to study spontaneous spoken Finnish and to accelerate the development of language technology and speech-based services. In this paper, we present the collection process and the collected corpus, and showcase its versatility through multiple use cases. The evaluated use cases include: automatic speech recognition of spontaneous speech, detection of age, gender, dialect and topic and metadata analysis. We provide benchmarks for the use cases, as well down loadable, trained baseline systems with open-source code for reproducibility. One further use case is to verify the metadata and transcripts given in this corpus itself, and to suggest artificial metadata and transcripts for the part of the corpus where it is missing.
Automatic Speech Recognition for Speech Assessment of Persian Preschool Children
Authors: Amirhossein Abaskohi, Fatemeh Mortazavi, Hadi Moradi
Date: 2022-03-24 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), speech-recognition, Speech Recognition

Preschool evaluation is crucial because it gives teachers and parents influential knowledge about children's growth and development. The COVID-19 pandemic has highlighted the necessity of online assessment for preschool children. One of the areas that should be tested is their ability to speak. Employing an Automatic Speech Recognition (ASR) system would not help since they are pre-trained on voices that differ from children's in terms of frequency and amplitude. Because most of these are pre-trained with data in a specific range of amplitude, their objectives do not make them ready for voices in different amplitudes. To overcome this issue, we added a new objective to the masking objective of the Wav2Vec 2.0 model called Random Frequency Pitch (RFP). In addition, we used our newly introduced dataset to fine-tune our model for Meaningless Words (MW) and Rapid Automatic Naming (RAN) tests. Using masking in concatenation with RFP outperforms the masking objective of Wav2Vec 2.0 by reaching a Word Error Rate (WER) of 1.35. Our new approach reaches a WER of 6.45 on the Persian section of the CommonVoice dataset. Furthermore, our novel methodology produces positive outcomes in zero- and few-shot scenarios.
Revisiting the Effects of Leakage on Dependency Parsing
Authors: Nathaniel Krasner, Miriam Wanner, Antonios Anastasopoulos
Date: 2022-03-24 00:00:00
Proceeding: Findings (ACL) 2022 5
Tasks: Dependency Parsing

Recent work by S{\o}gaard (2020) showed that, treebank size aside, overlap between training and test graphs (termed leakage) explains more of the observed variation in dependency parsing performance than other explanations. In this work we revisit this claim, testing it on more models and languages. We find that it only holds for zero-shot cross-lingual settings. We then propose a more fine-grained measure of such leakage which, unlike the original measure, not only explains but also correlates with observed performance variation. Code and data are available here: https://github.com/miriamwanner/reu-nlp-project
Disentangleing Content and Fine-grained Prosody Information via Hybrid ASR Bottleneck Features for Voice Conversion
Authors: Xintao Zhao, Feng Liu, Changhe Song, Zhiyong Wu, Shiyin Kang, Deyi Tuo, Helen Meng
Date: 2022-03-24 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), Decoder, speech-recognition, Speech Recognition, Voice Conversion

Non-parallel data voice conversion (VC) have achieved considerable breakthroughs recently through introducing bottleneck features (BNFs) extracted by the automatic speech recognition(ASR) model. However, selection of BNFs have a significant impact on VC result. For example, when extracting BNFs from ASR trained with Cross Entropy loss (CE-BNFs) and feeding into neural network to train a VC system, the timbre similarity of converted speech is significantly degraded. If BNFs are extracted from ASR trained using Connectionist Temporal Classification loss (CTC-BNFs), the naturalness of the converted speech may decrease. This phenomenon is caused by the difference of information contained in BNFs. In this paper, we proposed an any-to-one VC method using hybrid bottleneck features extracted from CTC-BNFs and CE-BNFs to complement each other advantages. Gradient reversal layer and instance normalization were used to extract prosody information from CE-BNFs and content information from CTC-BNFs. Auto-regressive decoder and Hifi-GAN vocoder were used to generate high-quality waveform. Experimental results show that our proposed method achieves higher similarity, naturalness, quality than baseline method and reveals the differences between the information contained in CE-BNFs and CTC-BNFs as well as the influence they have on the converted speech.
Evaluating Distributional Distortion in Neural Language Modeling
Authors: Benjamin LeBrun, Alessandro Sordoni, Timothy J. O'Donnell
Date: 2022-03-24 00:00:00
Proceeding: ICLR 2022 4
Tasks: Language Modeling, Language Modelling

A fundamental characteristic of natural language is the high rate at which speakers produce novel expressions. Because of this novelty, a heavy-tail of rare events accounts for a significant amount of the total probability mass of distributions in language (Baayen, 2001). Standard language modeling metrics such as perplexity quantify the performance of language models (LM) in aggregate. As a result, we have relatively little understanding of whether neural LMs accurately estimate the probability of sequences in this heavy-tail of rare events. To address this gap, we develop a controlled evaluation scheme which uses generative models trained on natural data as artificial languages from which we can exactly compute sequence probabilities. Training LMs on generations from these artificial languages, we compare the sequence-level probability estimates given by LMs to the true probabilities in the target language. Our experiments reveal that LSTM and Transformer language models (i) systematically underestimate the probability of sequences drawn from the target language, and (ii) do so more severely for less-probable sequences. Investigating where this probability mass went, (iii) we find that LMs tend to overestimate the probability of ill formed (perturbed) sequences. In addition, we find that this underestimation behaviour (iv) is weakened, but not eliminated by greater amounts of training data, and (v) is exacerbated for target distributions with lower entropy.
Classifying Cyber-Risky Clinical Notes by Employing Natural Language Processing
Authors: Suzanna Schmeelk, Martins Samuel Dogo, Yifan Peng, Braja Gopal Patra
Date: 2022-03-24 00:00:00
Proceeding: 55th Hawaii International Conference on System Sciences 2022 1
Tasks: Classification, De-identification, Sentence

Clinical notes, which can be embedded into electronic medical records, document patient care delivery and summarize interactions between healthcare providers and patients. These clinical notes directly inform patient care and can also indirectly inform research and quality/safety metrics, among other indirect metrics. Recently, some states within the United States of America require patients to have open access to their clinical notes to improve the exchange of patient information for patient care. Thus, developing methods to assess the cyber risks of clinical notes before sharing and exchanging data is critical. While existing natural language processing techniques are geared to de-identify clinical notes, to the best of our knowledge, few have focused on classifying sensitive-information risk, which is a fundamental step toward developing effective, widespread protection of patient health information. To bridge this gap, this research investigates methods for identifying security/privacy risks within clinical notes. The classification either can be used upstream to identify areas within notes that likely contain sensitive information or downstream to improve the identification of clinical notes that have not been entirely de-identified. We develop several models using unigram and word2vec features with different classifiers to categorize sentence risk. Experiments on i2b2 de-identification dataset show that the SVM classifier using word2vec features obtained a maximum F1-score of 0.792. Future research involves articulation and differentiation of risk in terms of different global regulatory requirements.