Data Mining Practical Machine Learning Tools and Techniques

“Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks”の学習報告

5分で分かる!? 有名論文ナナメ読み：Jacob Devlin et al. : BERT : Pre-training of Deep Bidirectional Transformers for Language Understanding

Pre-trained text encoders have rapidly advanced the state of the art on many NLP tasks. We focus on one such model, BERT, and aim to quantify where linguistic information is captured within the network. We find that the model represents the steps of the traditional NLP pipeline in an interpretable and localizable way, and that the regions responsible for each step appear in the expected sequence: POS tagging, parsing, NER, semantic roles, then coreference. Qualitative analysis reveals that the model can and often does adjust this pipeline dynamically, revising lower-level decisions on the basis of disambiguating information from higher-level representations.

BERT Rediscovers the Classical NLP Pipeline

This paper investigates the ability of artificial neural networks to judge the grammatical acceptability of a sentence, with the goal of testing their linguistic competence. We introduce the Corpus of Linguistic Acceptability (CoLA), a set of 10,657 English sentences labeled as grammatical or ungrammatical from published linguistics literature. As baselines, we train several recurrent neural network models on acceptability classification, and find that our models outperform unsupervised models by Lau et al. (2016) on CoLA. Error-analysis on specific grammatical phenomena reveals that both Lau et al.’s models and ours learn systematic generalizations like subject-verb-object order. However, all models we test perform far below human level on a wide range of grammatical constructions.

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Neural Network Acceptability Judgments

We investigate whether a neural, encoderdecoder translation system learns syntactic information on the source side as a by-product of training. We propose two methods to detect whether the encoder has learned local and global source syntax. A fine-grained analysis of the syntactic structure learned by the encoder reveals which kinds of syntax are learned and which are missing.

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Does String-Based Neural MT Learn Source Syntax?

We introduce a new approach to tackle the problem of offensive language in online social media. Our approach uses unsupervised text style transfer to translate offensive sentences into non-offensive ones. We propose a new method for training encoder-decoders using non-parallel data that combines a collaborative classifier, attention and the cycle consistency loss. Experimental results on data from Twitter and Reddit show that our method outperforms a state-of-the-art text style transfer system in two out of three quantitative metrics and produces reliable non-offensive transferred sentences.

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Fighting Offensive Language on Social Media with Unsupervised Text Style Transfer.

The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report an efficient computational method for the generation of antimicrobials with desired attributes. The method leverages guidance from classifiers trained on an informative latent space of molecules modelled using a deep generative autoencoder, and screens the generated molecules using deep-learning classifiers as well as physicochemical features derived from high-throughput molecular dynamics simulations. Within 48 days, we identified, synthesized and experimentally tested 20 candidate antimicrobial peptides, of which two displayed high potency against diverse Gram-positive and Gram-negative pathogens (including multidrug-resistant Klebsiella pneumoniae) and a low propensity to induce drug resistance in Escherichia coli. Both peptides have low toxicity, as validated in vitro and in mice. We also show using live-cell confocal imaging that the bactericidal mode of action of the peptides involves the formation of membrane pores. The combination of deep learning and molecular dynamics may accelerate the discovery of potent and selective broad-spectrum antimicrobials. A computational method leveraging deep learning and molecular dynamics simulations enables the rapid discovery of antimicrobial peptides with low toxicity and with high potency against diverse Gram-positive and Gram-negative pathogens.

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Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations.

The novel nature of SARS-CoV-2 calls for the development of efficient de novo drug design approaches. In this study, we propose an end-to-end framework, named CogMol (Controlled Generation of Molecules), for designing new drug-like small molecules targeting novel viral proteins with high affinity and off-target selectivity. CogMol combines adaptive pre-training of a molecular SMILES Variational Autoencoder (VAE) and an efficient multi-attribute controlled sampling scheme that uses guidance from attribute predictors trained on latent features. To generate novel and optimal drug-like molecules for unseen viral targets, CogMol leverages a protein-molecule binding affinity predictor that is trained using SMILES VAE embeddings and protein sequence embeddings learned unsupervised from a large corpus. CogMol framework is applied to three SARS-CoV-2 target proteins: main protease, receptor-binding domain of the spike protein, and non-structural protein 9 replicase. The generated candidates are novel at both molecular and chemical scaffold levels when compared to the training data. CogMol also includes insilico screening for assessing toxicity of parent molecules and their metabolites with a multi-task toxicity classifier, synthetic feasibility with a chemical retrosynthesis predictor, and target structure binding with docking simulations. Docking reveals favorable binding of generated molecules to the target protein structure, where 87-95 % of high affinity molecules showed docking free energy < -6 kcal/mol. When compared to approved drugs, the majority of designed compounds show low parent molecule and metabolite toxicity and high synthetic feasibility. In summary, CogMol handles multi-constraint design of synthesizable, low-toxic, drug-like molecules with high target specificity and selectivity, and does not need target-dependent fine-tuning of the framework or target structure information.

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CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models

Machine Learning has seen tremendous growth recently, which has led to larger adoption of ML systems for educational assessments, credit risk, healthcare, employment, criminal justice, to name a few. The trustworthiness of ML and NLP systems is a crucial aspect and requires a guarantee that the decisions they make are fair and robust. Aligned with this, we propose a framework GYC, to generate a set of counterfactual text samples, which are crucial for testing these ML systems. Our main contributions include a) We introduce GYC, a framework to generate counterfactual samples such that the generation is plausible, diverse, goal-oriented, and effective, b) We generate counterfactual samples, that can direct the generation towards a corresponding condition such as named-entity tag, semantic role label, or sentiment. Our experimental results on various domains show that GYC generates counterfactual text samples exhibiting the above four properties. GYC generates counterfactuals that can act as test cases to evaluate a model and any text debiasing algorithm.

Inkit Padhi

Papers

Does String-Based Neural MT Learn Source Syntax?

Fighting Offensive Language on Social Media with Unsupervised Text Style Transfer.

Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations.

CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models

Generate Your Counterfactuals: Towards Controlled Counterfactual Generation for Text