pwc-archive/papers-with-abstracts huggingface dataset:
Predicting pathways for old and new metabolites through clustering
Authors: Thiru Siddharth, Nathan Lewis
Date: 2022-11-28 00:00:00
Tasks: Clustering

The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new metabolites and pathways continues, the prediction of pathways for new metabolites can be challenging. It can take vast amounts of time to elucidate pathways for new metabolites; thus, according to HMDB only 60% of metabolites get assigned to pathways. Here, we present an approach to identify pathways based on metabolite structure. We extracted 201 features from SMILES annotations, and identified new metabolites from PubMed abstracts and HMDB. After applying clustering algorithms to both groups of features, we quantified correlations between metabolites, and found the clusters accurately linked 92% of known metabolites to their respective pathways. Thus, this approach could be valuable for predicting metabolic pathways for new metabolites.
Neural networks: solving the chemistry of the interstellar medium
Authors: Lorenzo Branca, Andrea Pallottini
Date: 2022-11-28 00:00:00

Non-equilibrium chemistry is a key process in the study of the InterStellar Medium (ISM), in particular the formation of molecular clouds and thus stars. However, computationally it is among the most difficult tasks to include in astrophysical simulations, because of the typically high (>40) number of reactions, the short evolutionary timescales (about $10^4$ times less than the ISM dynamical time) and the characteristic non-linearity and stiffness of the associated Ordinary Differential Equations system (ODEs). In this proof of concept work, we show that Physics Informed Neural Networks (PINN) are a viable alternative to traditional ODE time integrators for stiff thermo-chemical systems, i.e. up to molecular hydrogen formation (9 species and 46 reactions). Testing different chemical networks in a wide range of densities ($-2< \log n/{\rm cm}^{-3}< 3$) and temperatures ($1 < \log T/{\rm K}< 5$), we find that a basic architecture can give a comfortable convergence only for simplified chemical systems: to properly capture the sudden chemical and thermal variations a Deep Galerkin Method is needed. Once trained ($\sim 10^3$ GPUhr), the PINN well reproduces the strong non-linear nature of the solutions (errors $\lesssim 10\%$) and can give speed-ups up to a factor of $\sim 200$ with respect to traditional ODE solvers. Further, the latter have completion times that vary by about $\sim 30\%$ for different initial $n$ and $T$, while the PINN method gives negligible variations. Both the speed-up and the potential improvement in load balancing imply that PINN-powered simulations are a very palatable way to solve complex chemical calculation in astrophysical and cosmological problems.
PyTorch Adapt
Authors: Kevin Musgrave, Serge Belongie, Ser-Nam Lim
Date: 2022-11-28 00:00:00
Tasks: Domain Adaptation

PyTorch Adapt is a library for domain adaptation, a type of machine learning algorithm that re-purposes existing models to work in new domains. It is a fully-featured toolkit, allowing users to create a complete train/test pipeline in a few lines of code. It is also modular, so users can import just the parts they need, and not worry about being locked into a framework. One defining feature of this library is its customizability. In particular, complex training algorithms can be easily modified and combined, thanks to a system of composable, lazily-evaluated hooks. In this technical report, we explain in detail these features and the overall design of the library. Code is available at https://www.github.com/KevinMusgrave/pytorch-adapt
Physics Informed Neural Network for Dynamic Stress Prediction
Authors: Hamed Bolandi, Gautam Sreekumar, Xuyang Li, Nizar Lajnef, Vishnu Naresh Boddeti
Date: 2022-11-28 00:00:00
Tasks: Prediction

Structural failures are often caused by catastrophic events such as earthquakes and winds. As a result, it is crucial to predict dynamic stress distributions during highly disruptive events in real time. Currently available high-fidelity methods, such as Finite Element Models (FEMs), suffer from their inherent high complexity. Therefore, to reduce computational cost while maintaining accuracy, a Physics Informed Neural Network (PINN), PINN-Stress model, is proposed to predict the entire sequence of stress distribution based on Finite Element simulations using a partial differential equation (PDE) solver. Using automatic differentiation, we embed a PDE into a deep neural network's loss function to incorporate information from measurements and PDEs. The PINN-Stress model can predict the sequence of stress distribution in almost real-time and can generalize better than the model without PINN.
Découvrir de nouvelles classes dans des données tabulaires
Authors: Colin Troisemaine, Joachim Flocon-Cholet, Stéphane Gosselin, Sandrine Vaton, Alexandre Reiffers-Masson, Vincent Lemaire
Date: 2022-11-28 00:00:00
Tasks: Multi-Task Learning, Novel Class Discovery

In Novel Class Discovery (NCD), the goal is to find new classes in an unlabeled set given a labeled set of known but different classes. While NCD has recently gained attention from the community, no framework has yet been proposed for heterogeneous tabular data, despite being a very common representation of data. In this paper, we propose TabularNCD, a new method for discovering novel classes in tabular data. We show a way to extract knowledge from already known classes to guide the discovery process of novel classes in the context of tabular data which contains heterogeneous variables. A part of this process is done by a new method for defining pseudo labels, and we follow recent findings in Multi-Task Learning to optimize a joint objective function. Our method demonstrates that NCD is not only applicable to images but also to heterogeneous tabular data.
Deep Semi-supervised Learning with Double-Contrast of Features and Semantics
Authors: Quan Feng, Jiayu Yao, Zhison Pan, Guojun Zhou
Date: 2022-11-28 00:00:00
Tasks: Representation Learning

In recent years, the field of intelligent transportation systems (ITS) has achieved remarkable success, which is mainly due to the large amount of available annotation data. However, obtaining these annotated data has to afford expensive costs in reality. Therefore, a more realistic strategy is to leverage semi-supervised learning (SSL) with a small amount of labeled data and a large amount of unlabeled data. Typically, semantic consistency regularization and the two-stage learning methods of decoupling feature extraction and classification have been proven effective. Nevertheless, representation learning only limited to semantic consistency regularization may not guarantee the separation or discriminability of representations of samples with different semantics; due to the inherent limitations of the two-stage learning methods, the extracted features may not match the specific downstream tasks. In order to deal with the above drawbacks, this paper proposes an end-to-end deep semi-supervised learning double contrast of semantic and feature, which extracts effective tasks specific discriminative features by contrasting the semantics/features of positive and negative augmented samples pairs. Moreover, we leverage information theory to explain the rationality of double contrast of semantics and features and slack mutual information to contrastive loss in a simpler way. Finally, the effectiveness of our method is verified in benchmark datasets.
Latent Graph Inference using Product Manifolds
Authors: Haitz Sáez de Ocáriz Borde, Anees Kazi, Federico Barbero, Pietro Liò
Date: 2022-11-26 00:00:00
Tasks: Graph Learning

Graph Neural Networks usually rely on the assumption that the graph topology is available to the network as well as optimal for the downstream task. Latent graph inference allows models to dynamically learn the intrinsic graph structure of problems where the connectivity patterns of data may not be directly accessible. In this work, we generalize the discrete Differentiable Graph Module (dDGM) for latent graph learning. The original dDGM architecture used the Euclidean plane to encode latent features based on which the latent graphs were generated. By incorporating Riemannian geometry into the model and generating more complex embedding spaces, we can improve the performance of the latent graph inference system. In particular, we propose a computationally tractable approach to produce product manifolds of constant curvature model spaces that can encode latent features of varying structure. The latent representations mapped onto the inferred product manifold are used to compute richer similarity measures that are leveraged by the latent graph learning model to obtain optimized latent graphs. Moreover, the curvature of the product manifold is learned during training alongside the rest of the network parameters and based on the downstream task, rather than it being a static embedding space. Our novel approach is tested on a wide range of datasets, and outperforms the original dDGM model.
A locally time-invariant metric for climate model ensemble predictions of extreme risk
Authors: Mala Virdee, Markus Kaiser, Emily Shuckburgh, Carl Henrik Ek, Ieva Kazlauskaite
Date: 2022-11-26 00:00:00

Adaptation-relevant predictions of climate change are often derived by combining climate model simulations in a multi-model ensemble. Model evaluation methods used in performance-based ensemble weighting schemes have limitations in the context of high-impact extreme events. We introduce a locally time-invariant method for evaluating climate model simulations with a focus on assessing the simulation of extremes. We explore the behaviour of the proposed method in predicting extreme heat days in Nairobi and provide comparative results for eight additional cities.
TyDiP: A Dataset for Politeness Classification in Nine Typologically Diverse Languages
Authors: Anirudh Srinivasan, Eunsol Choi
Date: 2022-11-29 00:00:00

We study politeness phenomena in nine typologically diverse languages. Politeness is an important facet of communication and is sometimes argued to be cultural-specific, yet existing computational linguistic study is limited to English. We create TyDiP, a dataset containing three-way politeness annotations for 500 examples in each language, totaling 4.5K examples. We evaluate how well multilingual models can identify politeness levels -- they show a fairly robust zero-shot transfer ability, yet fall short of estimated human accuracy significantly. We further study mapping the English politeness strategy lexicon into nine languages via automatic translation and lexicon induction, analyzing whether each strategy's impact stays consistent across languages. Lastly, we empirically study the complicated relationship between formality and politeness through transfer experiments. We hope our dataset will support various research questions and applications, from evaluating multilingual models to constructing polite multilingual agents.
Neural Transducer Training: Reduced Memory Consumption with Sample-wise Computation
Authors: Stefan Braun, Erik McDermott, Roger Hsiao
Date: 2022-11-29 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), speech-recognition, Speech Recognition

The neural transducer is an end-to-end model for automatic speech recognition (ASR). While the model is well-suited for streaming ASR, the training process remains challenging. During training, the memory requirements may quickly exceed the capacity of state-of-the-art GPUs, limiting batch size and sequence lengths. In this work, we analyze the time and space complexity of a typical transducer training setup. We propose a memory-efficient training method that computes the transducer loss and gradients sample by sample. We present optimizations to increase the efficiency and parallelism of the sample-wise method. In a set of thorough benchmarks, we show that our sample-wise method significantly reduces memory usage, and performs at competitive speed when compared to the default batched computation. As a highlight, we manage to compute the transducer loss and gradients for a batch size of 1024, and audio length of 40 seconds, using only 6 GB of memory.
Measuring the Measuring Tools: An Automatic Evaluation of Semantic Metrics for Text Corpora
Authors: George Kour, Samuel Ackerman, Orna Raz, Eitan Farchi, Boaz Carmeli, Ateret Anaby-Tavor
Date: 2022-11-29 00:00:00
Tasks: Semantic Similarity, Semantic Textual Similarity

The ability to compare the semantic similarity between text corpora is important in a variety of natural language processing applications. However, standard methods for evaluating these metrics have yet to be established. We propose a set of automatic and interpretable measures for assessing the characteristics of corpus-level semantic similarity metrics, allowing sensible comparison of their behavior. We demonstrate the effectiveness of our evaluation measures in capturing fundamental characteristics by evaluating them on a collection of classical and state-of-the-art metrics. Our measures revealed that recently-developed metrics are becoming better in identifying semantic distributional mismatch while classical metrics are more sensitive to perturbations in the surface text levels.
Which Shortcut Solution Do Question Answering Models Prefer to Learn?
Authors: Kazutoshi Shinoda, Saku Sugawara, Akiko Aizawa
Date: 2022-11-29 00:00:00
Tasks: Multiple-choice, Question Answering, Reading Comprehension

Question answering (QA) models for reading comprehension tend to learn shortcut solutions rather than the solutions intended by QA datasets. QA models that have learned shortcut solutions can achieve human-level performance in shortcut examples where shortcuts are valid, but these same behaviors degrade generalization potential on anti-shortcut examples where shortcuts are invalid. Various methods have been proposed to mitigate this problem, but they do not fully take the characteristics of shortcuts themselves into account. We assume that the learnability of shortcuts, i.e., how easy it is to learn a shortcut, is useful to mitigate the problem. Thus, we first examine the learnability of the representative shortcuts on extractive and multiple-choice QA datasets. Behavioral tests using biased training sets reveal that shortcuts that exploit answer positions and word-label correlations are preferentially learned for extractive and multiple-choice QA, respectively. We find that the more learnable a shortcut is, the flatter and deeper the loss landscape is around the shortcut solution in the parameter space. We also find that the availability of the preferred shortcuts tends to make the task easier to perform from an information-theoretic viewpoint. Lastly, we experimentally show that the learnability of shortcuts can be utilized to construct an effective QA training set; the more learnable a shortcut is, the smaller the proportion of anti-shortcut examples required to achieve comparable performance on shortcut and anti-shortcut examples. We claim that the learnability of shortcuts should be considered when designing mitigation methods.
CUNI Submission in WMT22 General Task
Authors: Josef Jon, Martin Popel, Ondřej Bojar
Date: 2022-11-29 00:00:00
Tasks: Translation

We present the CUNI-Bergamot submission for the WMT22 General translation task. We compete in English$\rightarrow$Czech direction. Our submission further explores block backtranslation techniques. Compared to the previous work, we measure performance in terms of COMET score and named entities translation accuracy. We evaluate performance of MBR decoding compared to traditional mixed backtranslation training and we show a possible synergy when using both of the techniques simultaneously. The results show that both approaches are effective means of improving translation quality and they yield even better results when combined.
Learnings from Technological Interventions in a Low Resource Language: Enhancing Information Access in Gondi
Authors: Devansh Mehta, Harshita Diddee, Ananya Saxena, Anurag Shukla, Sebastin Santy, Ramaravind Kommiya Mothilal, Brij Mohan Lal Srivastava, Alok Sharma, Vishnu Prasad, Venkanna U, Kalika Bali
Date: 2022-11-29 00:00:00
Tasks: Machine Translation, Translation

The primary obstacle to developing technologies for low-resource languages is the lack of representative, usable data. In this paper, we report the deployment of technology-driven data collection methods for creating a corpus of more than 60,000 translations from Hindi to Gondi, a low-resource vulnerable language spoken by around 2.3 million tribal people in south and central India. During this process, we help expand information access in Gondi across 2 different dimensions (a) The creation of linguistic resources that can be used by the community, such as a dictionary, children's stories, Gondi translations from multiple sources and an Interactive Voice Response (IVR) based mass awareness platform; (b) Enabling its use in the digital domain by developing a Hindi-Gondi machine translation model, which is compressed by nearly 4 times to enable it's edge deployment on low-resource edge devices and in areas of little to no internet connectivity. We also present preliminary evaluations of utilizing the developed machine translation model to provide assistance to volunteers who are involved in collecting more data for the target language. Through these interventions, we not only created a refined and evaluated corpus of 26,240 Hindi-Gondi translations that was used for building the translation model but also engaged nearly 850 community members who can help take Gondi onto the internet.
Penalizing Confident Predictions on Largely Perturbed Inputs Does Not Improve Out-of-Distribution Generalization in Question Answering
Authors: Kazutoshi Shinoda, Saku Sugawara, Akiko Aizawa
Date: 2022-11-29 00:00:00
Tasks: Out-of-Distribution Generalization, Question Answering, Sentence

Question answering (QA) models are shown to be insensitive to large perturbations to inputs; that is, they make correct and confident predictions even when given largely perturbed inputs from which humans can not correctly derive answers. In addition, QA models fail to generalize to other domains and adversarial test sets, while humans maintain high accuracy. Based on these observations, we assume that QA models do not use intended features necessary for human reading but rely on spurious features, causing the lack of generalization ability. Therefore, we attempt to answer the question: If the overconfident predictions of QA models for various types of perturbations are penalized, will the out-of-distribution (OOD) generalization be improved? To prevent models from making confident predictions on perturbed inputs, we first follow existing studies and maximize the entropy of the output probability for perturbed inputs. However, we find that QA models trained to be sensitive to a certain perturbation type are often insensitive to unseen types of perturbations. Thus, we simultaneously maximize the entropy for the four perturbation types (i.e., word- and sentence-level shuffling and deletion) to further close the gap between models and humans. Contrary to our expectations, although models become sensitive to the four types of perturbations, we find that the OOD generalization is not improved. Moreover, the OOD generalization is sometimes degraded after entropy maximization. Making unconfident predictions on largely perturbed inputs per se may be beneficial to gaining human trust. However, our negative results suggest that researchers should pay attention to the side effect of entropy maximization.
Syntactic Substitutability as Unsupervised Dependency Syntax
Authors: Jasper Jian, Siva Reddy
Date: 2022-11-29 00:00:00
Tasks: Dependency Parsing, Language Modeling, Language Modelling

Syntax is a latent hierarchical structure which underpins the robust and compositional nature of human language. In this work, we explore the hypothesis that syntactic dependencies can be represented in language model attention distributions and propose a new method to induce these structures theory-agnostically. Instead of modeling syntactic relations as defined by annotation schemata, we model a more general property implicit in the definition of dependency relations, syntactic substitutability. This property captures the fact that words at either end of a dependency can be substituted with words from the same category. Substitutions can be used to generate a set of syntactically invariant sentences whose representations are then used for parsing. We show that increasing the number of substitutions used improves parsing accuracy on natural data. On long-distance subject-verb agreement constructions, our method achieves 79.5% recall compared to 8.9% using a previous method. Our method also provides improvements when transferred to a different parsing setup, demonstrating that it generalizes.
Diverse Multi-Answer Retrieval with Determinantal Point Processes
Authors: Poojitha Nandigam, Nikhil Rayaprolu, Manish Shrivastava
Date: 2022-11-29 00:00:00
Proceeding: COLING 2022 10
Tasks: Open-Domain Question Answering, Point Processes, Question Answering, Re-Ranking, Retrieval

Often questions provided to open-domain question answering systems are ambiguous. Traditional QA systems that provide a single answer are incapable of answering ambiguous questions since the question may be interpreted in several ways and may have multiple distinct answers. In this paper, we address multi-answer retrieval which entails retrieving passages that can capture majority of the diverse answers to the question. We propose a re-ranking based approach using Determinantal point processes utilizing BERT as kernels. Our method jointly considers query-passage relevance and passage-passage correlation to retrieve passages that are both query-relevant and diverse. Results demonstrate that our re-ranking technique outperforms state-of-the-art method on the AmbigQA dataset.
Textual Enhanced Contrastive Learning for Solving Math Word Problems
Authors: Yibin Shen, Qianying Liu, Zhuoyuan Mao, Fei Cheng, Sadao Kurohashi
Date: 2022-11-29 00:00:00
Tasks: Contrastive Learning, Math

Solving math word problems is the task that analyses the relation of quantities and requires an accurate understanding of contextual natural language information. Recent studies show that current models rely on shallow heuristics to predict solutions and could be easily misled by small textual perturbations. To address this problem, we propose a Textual Enhanced Contrastive Learning framework, which enforces the models to distinguish semantically similar examples while holding different mathematical logic. We adopt a self-supervised manner strategy to enrich examples with subtle textual variance by textual reordering or problem re-construction. We then retrieve the hardest to differentiate samples from both equation and textual perspectives and guide the model to learn their representations. Experimental results show that our method achieves state-of-the-art on both widely used benchmark datasets and also exquisitely designed challenge datasets in English and Chinese. \footnote{Our code and data is available at \url{https://github.com/yiyunya/Textual_CL_MWP}