arXiv subjects

Inkit Padhi

Publications and source records attributed to Inkit Padhi.

33 records · Page 2Linked to original sources

arXiv2022

Cloud-Based Real-Time Molecular Screening Platform with MolFormer

With the prospect of automating a number of chemical tasks with high fidelity, chemical language processing models are emerging at a rapid speed. Here, we present a cloud-based real-time platform that allows users to virtually screen molecules of interest. For this purpose, molecular embeddings inferred from a recently proposed large chemical language model, named MolFormer, are leveraged. The platform currently supports three tasks: nearest neighbor retrieval, chemical space visualization, and property prediction. Based on the functionalities of this platform and results obtained, we believe that such a platform can play a pivotal role in automating chemistry and chemical engineering research, as well as assist in drug discovery and material design tasks. A demo of our platform is provided at \url{www.ibm.biz/molecular_demo}.

cs.LG↗

arXiv2021

ReGen: Reinforcement Learning for Text and Knowledge Base Generation using Pretrained Language Models

Automatic construction of relevant Knowledge Bases (KBs) from text, and generation of semantically meaningful text from KBs are both long-standing goals in Machine Learning. In this paper, we present ReGen, a bidirectional generation of text and graph leveraging Reinforcement Learning (RL) to improve performance. Graph linearization enables us to re-frame both tasks as a sequence to sequence generation problem regardless of the generative direction, which in turn allows the use of Reinforcement Learning for sequence training where the model itself is employed as its own critic leading to Self-Critical Sequence Training (SCST). We present an extensive investigation demonstrating that the use of RL via SCST benefits graph and text generation on WebNLG+ 2020 and TekGen datasets. Our system provides state-of-the-art results on WebNLG+ 2020 by significantly improving upon published results from the WebNLG 2020+ Challenge for both text-to-graph and graph-to-text generation tasks.

cs.CL↗

arXiv2021

Image Captioning as an Assistive Technology: Lessons Learned from VizWiz 2020 Challenge

Image captioning has recently demonstrated impressive progress largely owing to the introduction of neural network algorithms trained on curated dataset like MS-COCO. Often work in this field is motivated by the promise of deployment of captioning systems in practical applications. However, the scarcity of data and contexts in many competition datasets renders the utility of systems trained on these datasets limited as an assistive technology in real-world settings, such as helping visually impaired people navigate and accomplish everyday tasks. This gap motivated the introduction of the novel VizWiz dataset, which consists of images taken by the visually impaired and captions that have useful, task-oriented information. In an attempt to help the machine learning computer vision field realize its promise of producing technologies that have positive social impact, the curators of the VizWiz dataset host several competitions, including one for image captioning. This work details the theory and engineering from our winning submission to the 2020 captioning competition. Our work provides a step towards improved assistive image captioning systems.

cs.CV↗

arXiv2021

Generate Your Counterfactuals: Towards Controlled Counterfactual Generation for Text

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.

cs.CL↗

arXiv2021

Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics

De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled Latent attribute Space Sampling) - an efficient computational method for attribute-controlled generation of molecules, which leverages guidance from classifiers trained on an informative latent space of molecules modeled using a deep generative autoencoder. We screen the generated molecules for additional key attributes by using deep learning classifiers in conjunction with novel features derived from atomistic simulations. The proposed approach is demonstrated for designing non-toxic antimicrobial peptides (AMPs) with strong broad-spectrum potency, which are emerging drug candidates for tackling antibiotic resistance. Synthesis and testing of only twenty designed sequences identified two novel and minimalist AMPs with high potency against diverse Gram-positive and Gram-negative pathogens, including one multidrug-resistant and one antibiotic-resistant K. pneumoniae, via membrane pore formation. Both antimicrobials exhibit low in vitro and in vivo toxicity and mitigate the onset of drug resistance. The proposed approach thus presents a viable path for faster and efficient discovery of potent and selective broad-spectrum antimicrobials.

cs.LG↗

arXiv2021

Tabular Transformers for Modeling Multivariate Time Series

Tabular datasets are ubiquitous in data science applications. Given their importance, it seems natural to apply state-of-the-art deep learning algorithms in order to fully unlock their potential. Here we propose neural network models that represent tabular time series that can optionally leverage their hierarchical structure. This results in two architectures for tabular time series: one for learning representations that is analogous to BERT and can be pre-trained end-to-end and used in downstream tasks, and one that is akin to GPT and can be used for generation of realistic synthetic tabular sequences. We demonstrate our models on two datasets: a synthetic credit card transaction dataset, where the learned representations are used for fraud detection and synthetic data generation, and on a real pollution dataset, where the learned encodings are used to predict atmospheric pollutant concentrations. Code and data are available at https://github.com/IBM/TabFormer.

cs.LG↗

arXiv2020

Alleviating Noisy Data in Image Captioning with Cooperative Distillation

Image captioning systems have made substantial progress, largely due to the availability of curated datasets like Microsoft COCO or Vizwiz that have accurate descriptions of their corresponding images. Unfortunately, scarce availability of such cleanly labeled data results in trained algorithms producing captions that can be terse and idiosyncratically specific to details in the image. We propose a new technique, cooperative distillation that combines clean curated datasets with the web-scale automatically extracted captions of the Google Conceptual Captions dataset (GCC), which can have poor descriptions of images, but is abundant in size and therefore provides a rich vocabulary resulting in more expressive captions.

cs.CV↗

arXiv2020

DualTKB: A Dual Learning Bridge between Text and Knowledge Base

In this work, we present a dual learning approach for unsupervised text to path and path to text transfers in Commonsense Knowledge Bases (KBs). We investigate the impact of weak supervision by creating a weakly supervised dataset and show that even a slight amount of supervision can significantly improve the model performance and enable better-quality transfers. We examine different model architectures, and evaluation metrics, proposing a novel Commonsense KB completion metric tailored for generative models. Extensive experimental results show that the proposed method compares very favorably to the existing baselines. This approach is a viable step towards a more advanced system for automatic KB construction/expansion and the reverse operation of KB conversion to coherent textual descriptions.

cs.CL↗

arXiv2020

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

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.

cs.LG↗

arXiv2020

Learning Implicit Text Generation via Feature Matching

Generative feature matching network (GFMN) is an approach for training implicit generative models for images by performing moment matching on features from pre-trained neural networks. In this paper, we present new GFMN formulations that are effective for sequential data. Our experimental results show the effectiveness of the proposed method, SeqGFMN, for three distinct generation tasks in English: unconditional text generation, class-conditional text generation, and unsupervised text style transfer. SeqGFMN is stable to train and outperforms various adversarial approaches for text generation and text style transfer.

cs.CL↗

arXiv2019

Sobolev Independence Criterion

We propose the Sobolev Independence Criterion (SIC), an interpretable dependency measure between a high dimensional random variable X and a response variable Y . SIC decomposes to the sum of feature importance scores and hence can be used for nonlinear feature selection. SIC can be seen as a gradient regularized Integral Probability Metric (IPM) between the joint distribution of the two random variables and the product of their marginals. We use sparsity inducing gradient penalties to promote input sparsity of the critic of the IPM. In the kernel version we show that SIC can be cast as a convex optimization problem by introducing auxiliary variables that play an important role in feature selection as they are normalized feature importance scores. We then present a neural version of SIC where the critic is parameterized as a homogeneous neural network, improving its representation power as well as its interpretability. We conduct experiments validating SIC for feature selection in synthetic and real-world experiments. We show that SIC enables reliable and interpretable discoveries, when used in conjunction with the holdout randomization test and knockoffs to control the False Discovery Rate. Code is available at http://github.com/ibm/sic.

cs.LG↗

arXiv2019

Learning Implicit Generative Models by Matching Perceptual Features

Perceptual features (PFs) have been used with great success in tasks such as transfer learning, style transfer, and super-resolution. However, the efficacy of PFs as key source of information for learning generative models is not well studied. We investigate here the use of PFs in the context of learning implicit generative models through moment matching (MM). More specifically, we propose a new effective MM approach that learns implicit generative models by performing mean and covariance matching of features extracted from pretrained ConvNets. Our proposed approach improves upon existing MM methods by: (1) breaking away from the problematic min/max game of adversarial learning; (2) avoiding online learning of kernel functions; and (3) being efficient with respect to both number of used moments and required minibatch size. Our experimental results demonstrate that, due to the expressiveness of PFs from pretrained deep ConvNets, our method achieves state-of-the-art results for challenging benchmarks.

cs.CV↗

arXiv2018

PepCVAE: Semi-Supervised Targeted Design of Antimicrobial Peptide Sequences

Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model learns a rich latent space of the biological peptide context by taking advantage of abundant, unlabeled peptide sequences. The model further learns a disentangled antimicrobial attribute space by using the feedback from a jointly trained AMP classifier that uses limited labeled instances. The disentangled representation allows for controllable generation of AMPs. Extensive analysis of the PepCVAE-generated sequences reveals superior performance of our model in comparison to a plain VAE, as PepCVAE generates novel AMP sequences with higher long-range diversity, while being closer to the training distribution of biological peptides. These features are highly desired in next-generation antimicrobial design.

q-bio.QM↗

arXiv2018

Fighting Offensive Language on Social Media with Unsupervised Text Style Transfer

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.

cs.CL↗

arXiv2017

Improved Neural Text Attribute Transfer with Non-parallel Data

Text attribute transfer using non-parallel data requires methods that can perform disentanglement of content and linguistic attributes. In this work, we propose multiple improvements over the existing approaches that enable the encoder-decoder framework to cope with the text attribute transfer from non-parallel data. We perform experiments on the sentiment transfer task using two datasets. For both datasets, our proposed method outperforms a strong baseline in two of the three employed evaluation metrics.

cs.CL↗