arXiv subjects

Payel Das

Publications and source records attributed to Payel Das.

At least 91 records · Page 5Linked to original sources

arXiv2022

Augmenting Molecular Deep Generative Models with Topological Data Analysis Representations

Deep generative models have emerged as a powerful tool for learning useful molecular representations and designing novel molecules with desired properties, with applications in drug discovery and material design. However, most existing deep generative models are restricted due to lack of spatial information. Here we propose augmentation of deep generative models with topological data analysis (TDA) representations, known as persistence images, for robust encoding of 3D molecular geometry. We show that the TDA augmentation of a character-based Variational Auto-Encoder (VAE) outperforms state-of-the-art generative neural nets in accurately modeling the structural composition of the QM9 benchmark. Generated molecules are valid, novel, and diverse, while exhibiting distinct electronic property distribution, namely higher sample population with small HOMO-LUMO gap. These results demonstrate that TDA features indeed provide crucial geometric signal for learning abstract structures, which is non-trivial for existing generative models operating on string, graph, or 3D point sets to capture.

physics.chem-ph↗

arXiv2021

Sample-Efficient Generation of Novel Photo-acid Generator Molecules using a Deep Generative Model

Photo-acid generators (PAGs) are compounds that release acids ($H^+$ ions) when exposed to light. These compounds are critical components of the photolithography processes that are used in the manufacture of semiconductor logic and memory chips. The exponential increase in the demand for semiconductors has highlighted the need for discovering novel photo-acid generators. While de novo molecule design using deep generative models has been widely employed for drug discovery and material design, its application to the creation of novel photo-acid generators poses several unique challenges, such as lack of property labels. In this paper, we highlight these challenges and propose a generative modeling approach that utilizes conditional generation from a pre-trained deep autoencoder and expert-in-the-loop techniques. The validity of the proposed approach was evaluated with the help of subject matter experts, indicating the promise of such an approach for applications beyond the creation of novel photo-acid generators.

cs.LG↗

arXiv2021

Mean-based Best Arm Identification in Stochastic Bandits under Reward Contamination

This paper investigates the problem of best arm identification in $\textit{contaminated}$ stochastic multi-arm bandits. In this setting, the rewards obtained from any arm are replaced by samples from an adversarial model with probability $\varepsilon$. A fixed confidence (infinite-horizon) setting is considered, where the goal of the learner is to identify the arm with the largest mean. Owing to the adversarial contamination of the rewards, each arm's mean is only partially identifiable. This paper proposes two algorithms, a gap-based algorithm and one based on the successive elimination, for best arm identification in sub-Gaussian bandits. These algorithms involve mean estimates that achieve the optimal error guarantee on the deviation of the true mean from the estimate asymptotically. Furthermore, these algorithms asymptotically achieve the optimal sample complexity. Specifically, for the gap-based algorithm, the sample complexity is asymptotically optimal up to constant factors, while for the successive elimination-based algorithm, it is optimal up to logarithmic factors. Finally, numerical experiments are provided to illustrate the gains of the algorithms compared to the existing baselines.

cs.LG↗

arXiv2021

Benchmarking deep generative models for diverse antibody sequence design

Computational protein design, i.e. inferring novel and diverse protein sequences consistent with a given structure, remains a major unsolved challenge. Recently, deep generative models that learn from sequences alone or from sequences and structures jointly have shown impressive performance on this task. However, those models appear limited in terms of modeling structural constraints, capturing enough sequence diversity, or both. Here we consider three recently proposed deep generative frameworks for protein design: (AR) the sequence-based autoregressive generative model, (GVP) the precise structure-based graph neural network, and Fold2Seq that leverages a fuzzy and scale-free representation of a three-dimensional fold, while enforcing structure-to-sequence (and vice versa) consistency. We benchmark these models on the task of computational design of antibody sequences, which demand designing sequences with high diversity for functional implication. The Fold2Seq framework outperforms the two other baselines in terms of diversity of the designed sequences, while maintaining the typical fold.

q-bio.BM↗

arXiv2021

Predicting Deep Neural Network Generalization with Perturbation Response Curves

The field of Deep Learning is rich with empirical evidence of human-like performance on a variety of prediction tasks. However, despite these successes, the recent Predicting Generalization in Deep Learning (PGDL) NeurIPS 2020 competition suggests that there is a need for more robust and efficient measures of network generalization. In this work, we propose a new framework for evaluating the generalization capabilities of trained networks. We use perturbation response (PR) curves that capture the accuracy change of a given network as a function of varying levels of training sample perturbation. From these PR curves, we derive novel statistics that capture generalization capability. Specifically, we introduce two new measures for accurately predicting generalization gaps: the Gi-score and Pal-score, which are inspired by the Gini coefficient and Palma ratio (measures of income inequality), that accurately predict generalization gaps. Using our framework applied to intra and inter-class sample mixup, we attain better predictive scores than the current state-of-the-art measures on a majority of tasks in the PGDL competition. In addition, we show that our framework and the proposed statistics can be used to capture to what extent a trained network is invariant to a given parametric input transformation, such as rotation or translation. Therefore, these generalization gap prediction statistics also provide a useful means for selecting optimal network architectures and hyperparameters that are invariant to a certain perturbation.

cs.LG↗

arXiv2021

Optimizing Molecules using Efficient Queries from Property Evaluations

Machine learning based methods have shown potential for optimizing existing molecules with more desirable properties, a critical step towards accelerating new chemical discovery. Here we propose QMO, a generic query-based molecule optimization framework that exploits latent embeddings from a molecule autoencoder. QMO improves the desired properties of an input molecule based on efficient queries, guided by a set of molecular property predictions and evaluation metrics. We show that QMO outperforms existing methods in the benchmark tasks of optimizing small organic molecules for drug-likeness and solubility under similarity constraints. We also demonstrate significant property improvement using QMO on two new and challenging tasks that are also important in real-world discovery problems: (i) optimizing existing potential SARS-CoV-2 Main Protease inhibitors toward higher binding affinity; and (ii) improving known antimicrobial peptides towards lower toxicity. Results from QMO show high consistency with external validations, suggesting effective means to facilitate material optimization problems with design constraints.

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

Towards Interpreting Zoonotic Potential of Betacoronavirus Sequences With Attention

Current methods for viral discovery target evolutionarily conserved proteins that accurately identify virus families but remain unable to distinguish the zoonotic potential of newly discovered viruses. Here, we apply an attention-enhanced long-short-term memory (LSTM) deep neural net classifier to a highly conserved viral protein target to predict zoonotic potential across betacoronaviruses. The classifier performs with a 94% accuracy. Analysis and visualization of attention at the sequence and structure-level features indicate possible association between important protein-protein interactions governing viral replication in zoonotic betacoronaviruses and zoonotic transmission.

q-bio.QM↗

arXiv2021

Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design

Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the diversity of the sequences (therefore structures and functions) within a fold. To overcome these challenges, we propose Fold2Seq, a novel transformer-based generative framework for designing protein sequences conditioned on a specific target fold. To model the complex sequence--structure relationship, Fold2Seq jointly learns a sequence embedding using a transformer and a fold embedding from the density of secondary structural elements in 3D voxels. On test sets with single, high-resolution and complete structure inputs for individual folds, our experiments demonstrate improved or comparable performance of Fold2Seq in terms of speed, coverage, and reliability for sequence design, when compared to existing state-of-the-art methods that include data-driven deep generative models and physics-based RosettaDesign. The unique advantages of fold-based Fold2Seq, in comparison to a structure-based deep model and RosettaDesign, become more evident on three additional real-world challenges originating from low-quality, incomplete, or ambiguous input structures. Source code and data are available at https://github.com/IBM/fold2seq.

cs.LG↗

arXiv2021

Gi and Pal Scores: Deep Neural Network Generalization Statistics

The field of Deep Learning is rich with empirical evidence of human-like performance on a variety of regression, classification, and control tasks. However, despite these successes, the field lacks strong theoretical error bounds and consistent measures of network generalization and learned invariances. In this work, we introduce two new measures, the Gi-score and Pal-score, that capture a deep neural network's generalization capabilities. Inspired by the Gini coefficient and Palma ratio, measures of income inequality, our statistics are robust measures of a network's invariance to perturbations that accurately predict generalization gaps, i.e., the difference between accuracy on training and test sets.

cs.LG↗

arXiv2021

Characterizing the Latent Space of Molecular Deep Generative Models with Persistent Homology Metrics

Deep generative models are increasingly becoming integral parts of the in silico molecule design pipeline and have dual goals of learning the chemical and structural features that render candidate molecules viable while also being flexible enough to generate novel designs. Specifically, Variational Auto Encoders (VAEs) are generative models in which encoder-decoder network pairs are trained to reconstruct training data distributions in such a way that the latent space of the encoder network is smooth. Therefore, novel candidates can be found by sampling from this latent space. However, the scope of architectures and hyperparameters is vast and choosing the best combination for in silico discovery has important implications for downstream success. Therefore, it is important to develop a principled methodology for distinguishing how well a given generative model is able to learn salient molecular features. In this work, we propose a method for measuring how well the latent space of deep generative models is able to encode structural and chemical features of molecular datasets by correlating latent space metrics with metrics from the field of topological data analysis (TDA). We apply our evaluation methodology to a VAE trained on SMILES strings and show that 3D topology information is consistently encoded throughout the latent space of the model.

q-bio.BM↗

arXiv2021

Towards creativity characterization of generative models via group-based subset scanning

Deep generative models, such as Variational Autoencoders (VAEs), have been employed widely in computational creativity research. However, such models discourage out-of-distribution generation to avoid spurious sample generation, limiting their creativity. Thus, incorporating research on human creativity into generative deep learning techniques presents an opportunity to make their outputs more compelling and human-like. As we see the emergence of generative models directed to creativity research, a need for machine learning-based surrogate metrics to characterize creative output from these models is imperative. We propose group-based subset scanning to quantify, detect, and characterize creative processes by detecting a subset of anomalous node-activations in the hidden layers of generative models. Our experiments on original, typically decoded, and "creatively decoded" (Das et al 2020) image datasets reveal that the proposed subset scores distribution is more useful for detecting creative processes in the activation space rather than the pixel space. Further, we found that creative samples generate larger subsets of anomalies than normal or non-creative samples across datasets. The node activations highlighted during the creative decoding process are different from those responsible for normal sample generation.

cs.LG↗

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

Reprogramming Language Models for Molecular Representation Learning

Recent advancements in transfer learning have made it a promising approach for domain adaptation via transfer of learned representations. This is especially when relevant when alternate tasks have limited samples of well-defined and labeled data, which is common in the molecule data domain. This makes transfer learning an ideal approach to solve molecular learning tasks. While Adversarial reprogramming has proven to be a successful method to repurpose neural networks for alternate tasks, most works consider source and alternate tasks within the same domain. In this work, we propose a new algorithm, Representation Reprogramming via Dictionary Learning (R2DL), for adversarially reprogramming pretrained language models for molecular learning tasks, motivated by leveraging learned representations in massive state of the art language models. The adversarial program learns a linear transformation between a dense source model input space (language data) and a sparse target model input space (e.g., chemical and biological molecule data) using a k-SVD solver to approximate a sparse representation of the encoded data, via dictionary learning. R2DL achieves the baseline established by state of the art toxicity prediction models trained on domain-specific data and outperforms the baseline in a limited training-data setting, thereby establishing avenues for domain-agnostic transfer learning for tasks with molecule data.

cs.LG↗

arXiv2020

Towards Better Understanding of Adaptive Gradient Algorithms in Generative Adversarial Nets

Adaptive gradient algorithms perform gradient-based updates using the history of gradients and are ubiquitous in training deep neural networks. While adaptive gradient methods theory is well understood for minimization problems, the underlying factors driving their empirical success in min-max problems such as GANs remain unclear. In this paper, we aim at bridging this gap from both theoretical and empirical perspectives. First, we analyze a variant of Optimistic Stochastic Gradient (OSG) proposed in~\citep{daskalakis2017training} for solving a class of non-convex non-concave min-max problem and establish $O(ε^{-4})$ complexity for finding $ε$-first-order stationary point, in which the algorithm only requires invoking one stochastic first-order oracle while enjoying state-of-the-art iteration complexity achieved by stochastic extragradient method by~\citep{iusem2017extragradient}. Then we propose an adaptive variant of OSG named Optimistic Adagrad (OAdagrad) and reveal an \emph{improved} adaptive complexity $O\left(ε^{-\frac{2}{1-α}}\right)$, where $α$ characterizes the growth rate of the cumulative stochastic gradient and $0\leq α\leq 1/2$. To the best of our knowledge, this is the first work for establishing adaptive complexity in non-convex non-concave min-max optimization. Empirically, our experiments show that indeed adaptive gradient algorithms outperform their non-adaptive counterparts in GAN training. Moreover, this observation can be explained by the slow growth rate of the cumulative stochastic gradient, as observed empirically.

math.OC↗

arXiv2020

Self-Progressing Robust Training

Enhancing model robustness under new and even adversarial environments is a crucial milestone toward building trustworthy machine learning systems. Current robust training methods such as adversarial training explicitly uses an "attack" (e.g., $\ell_{\infty}$-norm bounded perturbation) to generate adversarial examples during model training for improving adversarial robustness. In this paper, we take a different perspective and propose a new framework called SPROUT, self-progressing robust training. During model training, SPROUT progressively adjusts training label distribution via our proposed parametrized label smoothing technique, making training free of attack generation and more scalable. We also motivate SPROUT using a general formulation based on vicinity risk minimization, which includes many robust training methods as special cases. Compared with state-of-the-art adversarial training methods (PGD-l_inf and TRADES) under l_inf-norm bounded attacks and various invariance tests, SPROUT consistently attains superior performance and is more scalable to large neural networks. Our results shed new light on scalable, effective and attack-independent robust training methods.

cs.LG↗

arXiv2020

Using heritability of stellar chemistry to reveal the history of the Milky Way

Since chemical abundances are inherited between generations of stars, we use them to trace the evolutionary history of our Galaxy. We present a robust methodology for creating a phylogenetic tree, a biological tool used for centuries to study heritability. Combining our phylogeny with information on stellar ages and dynamical properties, we reconstruct the shared history of 78 stars in the Solar Neighbourhood. The branching pattern in our tree supports a scenario in which the thick disk is an ancestral population of the thin disk. The transition from thick to thin disk shows an anomaly, which we attribute to a star formation burst. Our tree shows a further signature of the variability in stars similar to the Sun, perhaps linked to a minor star formation enhancement creating our Solar System. In this paper, we demonstrate the immense potential of a phylogenetic perspective and interdisciplinary collaboration, where with borrowed techniques from biology we can study key processes that have contributed to the evolution of the Milky Way.

astro-ph.GA↗

arXiv2020

Optimizing Mode Connectivity via Neuron Alignment

The loss landscapes of deep neural networks are not well understood due to their high nonconvexity. Empirically, the local minima of these loss functions can be connected by a learned curve in model space, along which the loss remains nearly constant; a feature known as mode connectivity. Yet, current curve finding algorithms do not consider the influence of symmetry in the loss surface created by model weight permutations. We propose a more general framework to investigate the effect of symmetry on landscape connectivity by accounting for the weight permutations of the networks being connected. To approximate the optimal permutation, we introduce an inexpensive heuristic referred to as neuron alignment. Neuron alignment promotes similarity between the distribution of intermediate activations of models along the curve. We provide theoretical analysis establishing the benefit of alignment to mode connectivity based on this simple heuristic. We empirically verify that the permutation given by alignment is locally optimal via a proximal alternating minimization scheme. Empirically, optimizing the weight permutation is critical for efficiently learning a simple, planar, low-loss curve between networks that successfully generalizes. Our alignment method can significantly alleviate the recently identified robust loss barrier on the path connecting two adversarial robust models and find more robust and accurate models on the path.

cs.LG↗