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Payel Das

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32 papers

2 author rows

AAAI Conference 2026 Conference Paper

GP-MoLFormer-Sim: Test Time Molecular Optimization Through Contextual Similarity Guidance

Jiří Navrátil
Jarret Ross
Payel Das
Youssef Mroueh
Samuel C Hoffman
Vijil Chenthamarakshan
Brian Belgodere

The ability to design molecules while preserving similarity to a target molecule and/or property is crucial for various applications in drug discovery, chemical design, and biology. We introduce in this paper an efficient training-free method for navigating and sampling from the molecular space with a generative Chemical Language Model (CLM), while using the molecular similarity to the target as a guide. Our method leverages the contextual representations learned from the CLM itself to estimate the molecular similarity, which is then used to adjust the autoregressive sampling strategy of the CLM. At each step of the decoding process, the method tracks the distance of the current generations from the target and updates the logits to encourage the preservation of similarity in generations. We implement the method using a recently proposed ~47M parameter SMILES-based CLM, GP-MoLFormer, and therefore refer to the method as GP-MoLFormer-Sim, which enables a test-time update of the deep generative policy to reflect the contextual similarity to a set of guide molecules. The method is further integrated into a genetic algorithm (GA) and tested on a set of standard molecular optimization benchmarks involving property optimization, molecular rediscovery, and structure-based drug design. Results show that, GP-MoLFormer-Sim, combined with GA (GP-MoLFormer-Sim+GA) outperforms existing training-free baseline methods, when the oracle remains black-box. The findings in this work are a step forward in understanding and guiding the generative mechanisms of CLMs.

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ICML Conference 2025 Conference Paper

Aligning Protein Conformation Ensemble Generation with Physical Feedback

Jiarui Lu
Xiaoyin Chen
Stephen Zhewen Lu
Aurélie C. Lozano
Vijil Chenthamarakshan
Payel Das
Jian Tang 0005

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative modeling, particularly denoising diffusion models, have enabled efficient accurate protein structure prediction and conformation sampling by learning distributions over crystallographic structures. However, effectively integrating physical supervision into these data-driven approaches remains challenging, as standard energy-based objectives often lead to intractable optimization. In this paper, we introduce Energy-based Alignment (EBA), a method that aligns generative models with feedback from physical models, efficiently calibrating them to appropriately balance conformational states based on their energy differences. Experimental results on the MD ensemble benchmark demonstrate that EBA achieves state-of-the-art performance in generating high-quality protein ensembles. By improving the physical plausibility of generated structures, our approach enhances model predictions and holds promise for applications in structural biology and drug discovery.

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IJCAI Conference 2025 Conference Paper

Artificial Intelligence in Spectroscopy: Advancing Chemistry from Prediction To Generation and Beyond

Kehan Guo
Yili Shen
Gisela Abigail Gonzalez-Montiel
Yue Huang
Yujun Zhou
Mihir Surve
Zhichun Guo
Payel Das

The rapid advent of machine learning (ML) and artificial intelligence (AI) has catalyzed major transformations in chemistry, yet the application of these methods to spectroscopic and spectrometric data—termed Spectroscopy Machine Learning (SpectraML)—remains relatively underexplored. Modern spectroscopic techniques (MS, NMR, IR, Raman, UV-Vis) generate an ever-growing volume of high-dimensional data, creating a pressing need for automated and intelligent analysis beyond traditional expert-based workflows. In this survey, we provide a unified review of SpectraML, systematically examining state-of-the-art approaches for both forward tasks (molecule-to-spectrum prediction) and inverse tasks (spectrum-to-molecule inference). We trace the historical evolution of ML in spectroscopy—from early pattern recognition to the latest foundation models capable of advanced reasoning—and offer a taxonomy of representative neural architectures, including graph-based and transformer-based methods. Addressing key challenges such as data quality, multimodal integration, and computational scalability, we highlight emerging directions like synthetic data generation, large-scale pretraining, and few- or zero-shot learning. To foster reproducible research, we release an open-source repository containing curated datasets and code implementations. Our survey serves as a roadmap for researchers, guiding advancements at the intersection of spectroscopy and AI.

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ICLR Conference 2025 Conference Paper

Large Language Models can Become Strong Self-Detoxifiers

Ching-Yun Ko
Pin-Yu Chen
Payel Das
Youssef Mroueh
Soham Dan
Georgios Kollias
Subhajit Chaudhury
Tejaswini Pedapati

Reducing the likelihood of generating harmful and toxic output is an essential task when aligning large language models (LLMs). Existing methods mainly rely on training an external reward model (i.e., another language model) or fine-tuning the LLM using self-generated data to influence the outcome. In this paper, we show that LLMs have the capability of self-detoxification without external reward model learning or retraining of the LM. We propose \textit{Self-disciplined Autoregressive Sampling (SASA)}, a lightweight controlled decoding algorithm for toxicity reduction of LLMs. SASA leverages the contextual representations from an LLM to learn linear subspaces from labeled data characterizing toxic v.s. non-toxic output in analytical forms. When auto-completing a response token-by-token, SASA dynamically tracks the margin of the current output to steer the generation away from the toxic subspace, by adjusting the autoregressive sampling strategy. Evaluated on LLMs of different scale and nature, namely Llama-3.1-Instruct (8B), Llama-2 (7B), and GPT2-L models with the RealToxicityPrompts, BOLD, and AttaQ benchmarks, SASA markedly enhances the quality of the generated sentences relative to the original models and attains comparable performance to state-of-the-art detoxification techniques, significantly reducing the toxicity level by only using the LLM's internal representations.

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ICLR Conference 2025 Conference Paper

SEAL: Safety-enhanced Aligned LLM Fine-tuning via Bilevel Data Selection

Han Shen
Pin-Yu Chen
Payel Das
Tianyi Chen

Fine-tuning on task-specific data to boost downstream performance is a crucial step for leveraging Large Language Models (LLMs). However, though fine-tuning enhances the model performance for specialized applications, previous studies have demonstrated that fine-tuning the models on several adversarial samples or even benign data can greatly comprise the model's pre-equipped alignment and safety capabilities. In this work, we propose SEAL, a novel framework to enhance safety in LLM fine-tuning. SEAL learns a data ranker based on the bilevel optimization to up rank the safe and high-quality fine-tuning data and down rank the unsafe or low-quality ones. Models trained with SEAL demonstrate superior quality over multiple baselines, with 8.5\% and 9.7\% win rate increase compared to random selection respectively on Llama-3-8b-Instruct and Merlinite-7b models. Our code is available on github https://github.com/hanshen95/SEAL.

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TMLR Journal 2024 Journal Article

Attribute Graphs Underlying Molecular Generative Models: Path to Learning with Limited Data

Samuel C Hoffman
Payel Das
Karthikeyan Shanmugam
Kahini Wadhawan
Prasanna Sattigeri

Training generative models that capture rich semantics of the data and interpreting the latent representations encoded by such models are very important problems in un-/self-supervised learning. In this work, we provide a simple algorithm that relies on perturbation experiments on latent codes of a pre-trained generative autoencoder to uncover an attribute graph that is implied by the generative model. We perform perturbation experiments to check for influence of a given latent variable on a subset of attributes. Given this, we show that one can fit an effective graphical model that models a structural equation model between latent codes taken as exogenous variables and attributes taken as observed variables. One interesting aspect is that a single latent variable controls multiple overlapping subsets of attributes unlike conventional approaches that try to impose full independence. Using a pre-trained generative autoencoder trained on a large dataset of small molecules, we demonstrate that the graphical model between various molecular attributes and latent codes learned by our algorithm can be used to predict a specific property for molecules which are drawn from a different distribution. We compare prediction models trained on various feature subsets chosen by simple baselines, as well as existing causal discovery and sparse learning/feature selection methods, with the ones in the derived Markov blanket from our method. Results show empirically that the predictor that relies on our Markov blanket attributes is robust to distribution shifts when transferred or fine-tuned with a few samples from the new distribution, especially when training data is limited.

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ICML Conference 2024 Conference Paper

Boundary Exploration for Bayesian Optimization With Unknown Physical Constraints

Yunsheng Tian
Ane Zuniga
Xinwei Zhang 0001
Johannes P. Dürholt
Payel Das
Jie Chen 0007
Wojciech Matusik
Mina Konakovic-Lukovic

Bayesian optimization has been successfully applied to optimize black-box functions where the number of evaluations is severely limited. However, in many real-world applications, it is hard or impossible to know in advance which designs are feasible due to some physical or system limitations. These issues lead to an even more challenging problem of optimizing an unknown function with unknown constraints. In this paper, we observe that in such scenarios optimal solution typically lies on the boundary between feasible and infeasible regions of the design space, making it considerably more difficult than that with interior optima. Inspired by this observation, we propose BE-CBO, a new Bayesian optimization method that efficiently explores the boundary between feasible and infeasible designs. To identify the boundary, we learn the constraints with an ensemble of neural networks that outperform the standard Gaussian Processes for capturing complex boundaries. Our method demonstrates superior performance against state-of-the-art methods through comprehensive experiments on synthetic and real-world benchmarks. Code available at: https: //github. com/yunshengtian/BE-CBO

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ICML Conference 2024 Conference Paper

Larimar: Large Language Models with Episodic Memory Control

Payel Das
Subhajit Chaudhury
Elliot Nelson
Igor Melnyk
Sarathkrishna Swaminathan
Sihui Dai
Aurélie C. Lozano
Georgios Kollias

Efficient and accurate updating of knowledge stored in Large Language Models (LLMs) is one of the most pressing research challenges today. This paper presents Larimar - a novel, brain-inspired architecture for enhancing LLMs with a distributed episodic memory. Larimar’s memory allows for dynamic, one-shot updates of knowledge without the need for computationally expensive re-training or fine-tuning. Experimental results on multiple fact editing benchmarks demonstrate that Larimar attains accuracy comparable to most competitive baselines, even in the challenging sequential editing setup, but also excels in speed—yielding speed-ups of 8-10x depending on the base LLM —as well as flexibility due to the proposed architecture being simple, LLM-agnostic, and hence general. We further provide mechanisms for selective fact forgetting, information leakage prevention, and input context length generalization with Larimar and show their effectiveness. Our code is available at https: //github. com/IBM/larimar.

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NeurIPS Conference 2024 Conference Paper

Multi-Scale Representation Learning for Protein Fitness Prediction

Zuobai Zhang
Pascal Notin
Yining Huang
Aurélie Lozano
Vijil Chenthamarakshan
Debora Marks
Payel Das
Jian Tang

Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets. While initial protein representation learning studies solely focused on either sequence or structural features, recent hybrid architectures have sought to merge these modalities to harness their respective strengths. However, these sequence-structure models have so far achieved only incremental improvements when compared to the leading sequence-only approaches, highlighting unresolved challenges effectively leveraging these modalities together. Moreover, the function of certain proteins is highly dependent on the granular aspects of their surface topology, which have been overlooked by prior models. To address these limitations, we introduce the Sequence-Structure-Surface Fitness ( S3F ) model — a novel multimodal representation learning framework that integrates protein features across several scales. Our approach combines sequence representations from a protein language model with Geometric Vector Perceptron networks encoding protein backbone and detailed surface topology. The proposed method achieves state-of-the-art fitness prediction on the ProteinGym benchmark encompassing 217 substitution deep mutational scanning assays, and provides insights into the determinants of protein function. Our code is at https: //github. com/DeepGraphLearning/S3F.

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ICML Conference 2024 Conference Paper

What Would Gauss Say About Representations? Probing Pretrained Image Models using Synthetic Gaussian Benchmarks

Ching-Yun Ko
Pin-Yu Chen
Payel Das
Jeet Mohapatra
Luca Daniel

Recent years have witnessed a paradigm shift in deep learning from task-centric model design to task-agnostic representation learning and task-specific fine-tuning. Pretrained model representations are commonly evaluated extensively across various real-world tasks and used as a foundation for different downstream tasks. This paper proposes a solution for assessing the quality of representations in a task-agnostic way. To circumvent the need for real-world data in evaluation, we explore the use of synthetic binary classification tasks with Gaussian mixtures to probe pretrained models and compare the robustness-accuracy performance on pretrained representations with an idealized reference. Our approach offers a holistic evaluation, revealing intrinsic model capabilities and reducing the dependency on real-life data for model evaluation. Evaluated with various pretrained image models, the experimental results confirm that our task-agnostic evaluation correlates with actual linear probing performance on downstream tasks and can also guide parameter choice in robust linear probing to achieve a better robustness-accuracy trade-off.

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NeurIPS Conference 2023 Conference Paper

Efficient Equivariant Transfer Learning from Pretrained Models

Sourya Basu
Pulkit Katdare
Prasanna Sattigeri
Vijil Chenthamarakshan
Katherine Driggs-Campbell
Payel Das
Lav R. Varshney

Efficient transfer learning algorithms are key to the success of foundation models on diverse downstream tasks even with limited data. Recent works of Basu et al. (2023) and Kaba et al. (2022) propose group averaging (equitune) and optimization-based methods, respectively, over features from group-transformed inputs to obtain equivariant outputs from non-equivariant neural networks. While Kaba et al. (2022) are only concerned with training from scratch, we find that equitune performs poorly on equivariant zero-shot tasks despite good finetuning results. We hypothesize that this is because pretrained models provide better quality features for certain transformations than others and simply averaging them is deleterious. Hence, we propose λ-equitune that averages the features using importance weights, λs. These weights are learned directly from the data using a small neural network, leading to excellent zero-shot and finetuned results that outperform equitune. Further, we prove that λ-equitune is equivariant and a universal approximator of equivariant functions. Additionally, we show that the method of Kaba et al. (2022) used with appropriate loss functions, which we call equizero, also gives excellent zero-shot and finetuned performance. Both equitune and equizero are special cases of λ- equitune. To show the simplicity and generality of our method, we validate on a wide range of diverse applications and models such as 1) image classification using CLIP, 2) deep Q-learning, 3) fairness in natural language generation (NLG), 4) compositional generalization in languages, and 5) image classification using pretrained CNNs such as Resnet and Alexnet.

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AAAI Conference 2023 Conference Paper

Equi-Tuning: Group Equivariant Fine-Tuning of Pretrained Models

Sourya Basu
Prasanna Sattigeri
Karthikeyan Natesan Ramamurthy
Vijil Chenthamarakshan
Kush R. Varshney
Lav R. Varshney
Payel Das

We introduce equi-tuning, a novel fine-tuning method that transforms (potentially non-equivariant) pretrained models into group equivariant models while incurring minimum L_2 loss between the feature representations of the pretrained and the equivariant models. Large pretrained models can be equi-tuned for different groups to satisfy the needs of various downstream tasks. Equi-tuned models benefit from both group equivariance as an inductive bias and semantic priors from pretrained models. We provide applications of equi-tuning on three different tasks: image classification, compositional generalization in language, and fairness in natural language generation (NLG). We also provide a novel group-theoretic definition for fairness in NLG. The effectiveness of this definition is shown by testing it against a standard empirical method of fairness in NLG. We provide experimental results for equi-tuning using a variety of pretrained models: Alexnet, Resnet, VGG, and Densenet for image classification; RNNs, GRUs, and LSTMs for compositional generalization; and GPT2 for fairness in NLG. We test these models on benchmark datasets across all considered tasks to show the generality and effectiveness of the proposed method.

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ICML Conference 2023 Conference Paper

Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction

Minghao Guo
Veronika Thost
Samuel W. Song
Adithya Balachandran
Payel Das
Jie Chen 0007
Wojciech Matusik

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are faced with a common challenge in practice: Labeled data are limited by the cost of manual extraction from literature and laborious experimentation. In this work, we propose a data-efficient property predictor by utilizing a learnable hierarchical molecular grammar that can generate molecules from grammar production rules. Such a grammar induces an explicit geometry of the space of molecular graphs, which provides an informative prior on molecular structural similarity. The property prediction is performed using graph neural diffusion over the grammar-induced geometry. On both small and large datasets, our evaluation shows that this approach outperforms a wide spectrum of baselines, including supervised and pre-trained graph neural networks. We include a detailed ablation study and further analysis of our solution, showing its effectiveness in cases with extremely limited data.

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NeurIPS Conference 2023 Conference Paper

Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction

Zuobai Zhang
Minghao Xu
Aurelie C. Lozano
Vijil Chenthamarakshan
Payel Das
Jian Tang

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Code will be released upon acceptance.

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ICLR Conference 2023 Conference Paper

Protein Representation Learning by Geometric Structure Pretraining

Zuobai Zhang
Minghao Xu
Arian Rokkum Jamasb
Vijil Chenthamarakshan
Aurélie C. Lozano
Payel Das
Jian Tang 0005

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

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ICML Conference 2023 Conference Paper

Reprogramming Pretrained Language Models for Antibody Sequence Infilling

Igor Melnyk
Vijil Chenthamarakshan
Pin-Yu Chen
Payel Das
Amit Dhurandhar
Inkit Padhi
Devleena Das

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https: //github. com/IBM/ReprogBERT

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NeurIPS Conference 2023 Conference Paper

The Impact of Positional Encoding on Length Generalization in Transformers

Amirhossein Kazemnejad
Inkit Padhi
Karthikeyan Natesan Ramamurthy
Payel Das
Siva Reddy

Length generalization, the ability to generalize from small training context sizes to larger ones, is a critical challenge in the development of Transformer-based language models. Positional encoding (PE) has been identified as a major factor influencing length generalization, but the exact impact of different PE schemes on extrapolation in downstream tasks remains unclear. In this paper, we conduct a systematic empirical study comparing the length generalization performance of decoder-only Transformers with five different position encoding approaches including Absolute Position Embedding (APE), T5's Relative PE, ALiBi, and Rotary, in addition to Transformers without positional encoding (NoPE). Our evaluation encompasses a battery of reasoning and mathematical tasks. Our findings reveal that the most commonly used positional encoding methods, such as ALiBi, Rotary, and APE, are not well suited for length generalization in downstream tasks. More importantly, NoPE outperforms other explicit positional encoding methods while requiring no additional computation. We theoretically demonstrate that NoPE can represent both absolute and relative PEs, but when trained with SGD, it mostly resembles T5's relative PE attention patterns. Finally, we find that scratchpad is not always helpful to solve length generalization and its format highly impacts the model's performance. Overall, our work suggests that explicit position embeddings are not essential for decoder-only Transformers to generalize well to longer sequences.

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ICML Conference 2022 Conference Paper

Biological Sequence Design with GFlowNets

Moksh Jain
Emmanuel Bengio
Alex Hernández-García
Jarrid Rector-Brooks
Bonaventure F. P. Dossou
Chanakya Ekbote
Jie Fu 0001
Tianyu Zhang

Design of de novo biological sequences with desired properties, like protein and DNA sequences, often involves an active loop with several rounds of molecule ideation and expensive wet-lab evaluations. These experiments can consist of multiple stages, with increasing levels of precision and cost of evaluation, where candidates are filtered. This makes the diversity of proposed candidates a key consideration in the ideation phase. In this work, we propose an active learning algorithm leveraging epistemic uncertainty estimation and the recently proposed GFlowNets as a generator of diverse candidate solutions, with the objective to obtain a diverse batch of useful (as defined by some utility function, for example, the predicted anti-microbial activity of a peptide) and informative candidates after each round. We also propose a scheme to incorporate existing labeled datasets of candidates, in addition to a reward function, to speed up learning in GFlowNets. We present empirical results on several biological sequence design tasks, and we find that our method generates more diverse and novel batches with high scoring candidates compared to existing approaches.

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ICLR Conference 2022 Conference Paper

Data-Efficient Graph Grammar Learning for Molecular Generation

Minghao Guo
Veronika Thost
Beichen Li 0005
Payel Das
Jie Chen 0007
Wojciech Matusik

The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however, the size of class-specific chemical datasets is usually limited (e.g., dozens of samples) due to labor-intensive experimentation and data collection. Another major challenge is to generate only physically synthesizable molecules. This is a non-trivial task for neural network-based generative models since the relevant chemical knowledge can only be extracted and generalized from the limited training data. In this work, we propose a data-efficient generative model that can be learned from datasets with orders of magnitude smaller sizes than common benchmarks. At the heart of this method is a learnable graph grammar that generates molecules from a sequence of production rules. Without any human assistance, these production rules are automatically constructed from training data. Furthermore, additional chemical knowledge can be incorporated into the model by further grammar optimization. Our learned graph grammar yields state-of-the-art results on generating high-quality molecules for three monomer datasets that contain only ${\sim}20$ samples each. Our approach also achieves remarkable performance in a challenging polymer generation task with $only$ $117$ training samples and is competitive against existing methods using $81$k data points.

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AAAI Conference 2022 Conference Paper

Fourier Representations for Black-Box Optimization over Categorical Variables

Hamid Dadkhahi
Jesus Rios
Karthikeyan Shanmugam
Payel Das

Optimization of real-world black-box functions defined over purely categorical variables is an active area of research. In particular, optimization and design of biological sequences with specific functional or structural properties have a profound impact in medicine, materials science, and biotechnology. Standalone search algorithms, such as simulated annealing (SA) and Monte Carlo tree search (MCTS), are typically used for such optimization problems. In order to improve the performance and sample efficiency of such algorithms, we propose to use existing methods in conjunction with a surrogate model for the black-box evaluations over purely categorical variables. To this end, we present two different representations, a grouptheoretic Fourier expansion and an abridged one-hot encoded Boolean Fourier expansion. To learn such representations, we consider two different settings to update our surrogate model. First, we utilize an adversarial online regression setting where Fourier characters of each representation are considered as experts and their respective coefficients are updated via an exponential weight update rule each time the black box is evaluated. Second, we consider a Bayesian setting where queries are selected via Thompson sampling and the posterior is updated via a sparse Bayesian regression model (over our proposed representation) with a regularized horseshoe prior. Numerical experiments over synthetic benchmarks as well as real-world RNA sequence optimization and design problems demonstrate the representational power of the proposed methods, which achieve competitive or superior performance compared to state-of-the-art counterparts, while improving the computation cost and/or sample efficiency, substantially.

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IJCAI Conference 2022 Conference Paper

Towards Creativity Characterization of Generative Models via Group-Based Subset Scanning

Celia Cintas
Payel Das
Brian Quanz
Girmaw Abebe Tadesse
Skyler Speakman
Pin-Yu Chen

Deep generative models, such as Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs), have been employed widely in computational creativity research. However, such models discourage out-of-distribution generation to avoid spurious sample generation, thereby 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 toward 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 identify, quantify, and characterize creative processes by detecting a subset of anomalous node-activations in the hidden layers of the generative models. Our experiments on the standard image benchmarks and their ``creatively generated'' variants reveal that the proposed subset scores distribution is more useful for detecting novelty in 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 the normal sample generation. Lastly, we assess if the images from the subsets selected by our method were also found creative by human evaluators, presenting a link between creativity perception in humans and node activations within deep neural nets.

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ICML Conference 2021 Conference Paper

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

Yue Cao 0010
Payel Das
Vijil Chenthamarakshan
Pin-Yu Chen
Igor Melnyk
Yang Shen 0001

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.

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NeurIPS Conference 2021 Conference Paper

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

Arpan Mukherjee
Ali Tajer
Pin-Yu Chen
Payel Das

This paper investigates the problem of best arm identification in {\sl 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.

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NeurIPS Conference 2021 Conference Paper

Predicting Deep Neural Network Generalization with Perturbation Response Curves

Yair Schiff
Brian Quanz
Payel Das
Pin-Yu Chen

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.

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AAAI Conference 2021 Conference Paper

Self-Progressing Robust Training

Minhao Cheng
Pin-Yu Chen
Sijia Liu
Shiyu Chang
Cho-Jui Hsieh
Payel Das

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. , L-inf-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, selfprogressing 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-infnorm 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.

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NeurIPS Conference 2020 Conference Paper

A Decentralized Parallel Algorithm for Training Generative Adversarial Nets

Mingrui Liu
Wei Zhang
Youssef Mroueh
Xiaodong Cui
Jarret Ross
Tianbao Yang
Payel Das

Generative Adversarial Networks (GANs) are a powerful class of generative models in the deep learning community. Current practice on large-scale GAN training utilizes large models and distributed large-batch training strategies, and is implemented on deep learning frameworks (e. g. , TensorFlow, PyTorch, etc. ) designed in a centralized manner. In the centralized network topology, every worker needs to either directly communicate with the central node or indirectly communicate with all other workers in every iteration. However, when the network bandwidth is low or network latency is high, the performance would be significantly degraded. Despite recent progress on decentralized algorithms for training deep neural networks, it remains unclear whether it is possible to train GANs in a decentralized manner. The main difficulty lies at handling the nonconvex-nonconcave min-max optimization and the decentralized communication simultaneously. In this paper, we address this difficulty by designing the \textbf{first gradient-based decentralized parallel algorithm} which allows workers to have multiple rounds of communications in one iteration and to update the discriminator and generator simultaneously, and this design makes it amenable for the convergence analysis of the proposed decentralized algorithm. Theoretically, our proposed decentralized algorithm is able to solve a class of non-convex non-concave min-max problems with provable non-asymptotic convergence to first-order stationary point. Experimental results on GANs demonstrate the effectiveness of the proposed algorithm.

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ICLR Conference 2020 Conference Paper

Bridging Mode Connectivity in Loss Landscapes and Adversarial Robustness

Pu Zhao 0001
Pin-Yu Chen
Payel Das
Karthikeyan Natesan Ramamurthy
Xue Lin 0001

Mode connectivity provides novel geometric insights on analyzing loss landscapes and enables building high-accuracy pathways between well-trained neural networks. In this work, we propose to employ mode connectivity in loss landscapes to study the adversarial robustness of deep neural networks, and provide novel methods for improving this robustness. Our experiments cover various types of adversarial attacks applied to different network architectures and datasets. When network models are tampered with backdoor or error-injection attacks, our results demonstrate that the path connection learned using limited amount of bonafide data can effectively mitigate adversarial effects while maintaining the original accuracy on clean data. Therefore, mode connectivity provides users with the power to repair backdoored or error-injected models. We also use mode connectivity to investigate the loss landscapes of regular and robust models against evasion attacks. Experiments show that there exists a barrier in adversarial robustness loss on the path connecting regular and adversarially-trained models. A high correlation is observed between the adversarial robustness loss and the largest eigenvalue of the input Hessian matrix, for which theoretical justifications are provided. Our results suggest that mode connectivity offers a holistic tool and practical means for evaluating and improving adversarial robustness.

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NeurIPS Conference 2020 Conference Paper

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

Vijil Chenthamarakshan
Payel Das
Samuel Hoffman
Hendrik Strobelt
Inkit Padhi
Kar Wai Lim
Benjamin Hoover
Matteo Manica

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. We applied the CogMol framework 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 the 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 predicted parent molecule and metabolite toxicity and high predicted synthetic feasibility. In summary, CogMol can handle multi-constraint design of synthesizable, low-toxic, drug-like molecules with high target specificity and selectivity, even to novel protein target sequences, and does not need target-dependent fine-tuning of the framework or target structure information.

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NeurIPS Conference 2020 Conference Paper

Optimizing Mode Connectivity via Neuron Alignment

Norman Tatro
Pin-Yu Chen
Payel Das
Igor Melnyk
Prasanna Sattigeri
Rongjie Lai

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 a model along the curve with that of the endpoint models. 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.

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IJCAI Conference 2020 Conference Paper

Toward a neuro-inspired creative decoder

Payel Das
Brian Quanz
Pin-Yu Chen
Jae-wook Ahn
Dhruv Shah

Creativity, a process that generates novel and meaningful ideas, involves increased association between task-positive (control) and task-negative (default) networks in the human brain. Inspired by this seminal finding, in this study we propose a creative decoder within a deep generative framework, which involves direct modulation of the neuronal activation pattern after sampling from the learned latent space. The proposed approach is fully unsupervised and can be used off- the-shelf. Several novelty metrics and human evaluation were used to evaluate the creative capacity of the deep decoder. Our experiments on different image datasets (MNIST, FMNIST, MNIST+FMNIST, WikiArt and CelebA) reveal that atypical co-activation of highly activated and weakly activated neurons in a deep decoder promotes generation of novel and meaningful artifacts.

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ICLR Conference 2020 Conference Paper

Towards Better Understanding of Adaptive Gradient Algorithms in Generative Adversarial Nets

Mingrui Liu
Youssef Mroueh
Jerret Ross
Wei Zhang 0022
Xiaodong Cui
Payel Das
Tianbao Yang

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 $O(\epsilon^{-4})$ complexity for finding $\epsilon$-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 $O\left(\epsilon^{-\frac{2}{1-\alpha}}\right)$, where $\alpha$ characterizes the growth rate of the cumulative stochastic gradient and $0\leq \alpha\leq 1/2$. 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.

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NeurIPS Conference 2018 Conference Paper

Explanations based on the Missing: Towards Contrastive Explanations with Pertinent Negatives

Amit Dhurandhar
Pin-Yu Chen
Ronny Luss
Chun-Chen Tu
Paishun Ting
Karthikeyan Shanmugam
Payel Das

In this paper we propose a novel method that provides contrastive explanations justifying the classification of an input by a black box classifier such as a deep neural network. Given an input we find what should be minimally and sufficiently present (viz. important object pixels in an image) to justify its classification and analogously what should be minimally and necessarily \emph{absent} (viz. certain background pixels). We argue that such explanations are natural for humans and are used commonly in domains such as health care and criminology. What is minimally but critically \emph{absent} is an important part of an explanation, which to the best of our knowledge, has not been explicitly identified by current explanation methods that explain predictions of neural networks. We validate our approach on three real datasets obtained from diverse domains; namely, a handwritten digits dataset MNIST, a large procurement fraud dataset and a brain activity strength dataset. In all three cases, we witness the power of our approach in generating precise explanations that are also easy for human experts to understand and evaluate.

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