Avishek Joey Bose

Avishek Joey Bose, Tara Akhound-Sadegh, Guillaume Huguet et al.

The computational design of novel protein structures has the potential to impact numerous scientific disciplines greatly. Toward this goal, we introduce FoldFlow, a series of novel generative models of increasing modeling power based on the flow-matching paradigm over $3\mathrm{D}$ rigid motions -- i.e. the group $\text{SE}(3)$ -- enabling accurate modeling of protein backbones. We first introduce FoldFlow-Base, a simulation-free approach to learning deterministic continuous-time dynamics and matching invariant target distributions on $\text{SE}(3)$. We next accelerate training by incorporating Riemannian optimal transport to create FoldFlow-OT, leading to the construction of both more simple and stable flows. Finally, we design FoldFlow-SFM, coupling both Riemannian OT and simulation-free training to learn stochastic continuous-time dynamics over $\text{SE}(3)$. Our family of FoldFlow, generative models offers several key advantages over previous approaches to the generative modeling of proteins: they are more stable and faster to train than diffusion-based approaches, and our models enjoy the ability to map any invariant source distribution to any invariant target distribution over $\text{SE}(3)$. Empirically, we validate FoldFlow, on protein backbone generation of up to $300$ amino acids leading to high-quality designable, diverse, and novel samples.

Marta Skreta, Lazar Atanackovic, Avishek Joey Bose et al.

The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable Itô density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, as well as improved conditional molecule generation and unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion

Tara Akhound-Sadegh, Jarrid Rector-Brooks, Avishek Joey Bose et al.

Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising Energy Matching (iDEM), an iterative algorithm that uses a novel stochastic score matching objective leveraging solely the energy function and its gradient -- and no data samples -- to train a diffusion-based sampler. Specifically, iDEM alternates between (I) sampling regions of high model density from a diffusion-based sampler and (II) using these samples in our stochastic matching objective to further improve the sampler. iDEM is scalable to high dimensions as the inner matching objective, is simulation-free, and requires no MCMC samples. Moreover, by leveraging the fast mode mixing behavior of diffusion, iDEM smooths out the energy landscape enabling efficient exploration and learning of an amortized sampler. We evaluate iDEM on a suite of tasks ranging from standard synthetic energy functions to invariant $n$-body particle systems. We show that the proposed approach achieves state-of-the-art performance on all metrics and trains $2-5\times$ faster, which allows it to be the first method to train using energy on the challenging $55$-particle Lennard-Jones system.

Kacper Kapuśniak, Peter Potaptchik, Teodora Reu et al.

Matching objectives underpin the success of modern generative models and rely on constructing conditional paths that transform a source distribution into a target distribution. Despite being a fundamental building block, conditional paths have been designed principally under the assumption of Euclidean geometry, resulting in straight interpolations. However, this can be particularly restrictive for tasks such as trajectory inference, where straight paths might lie outside the data manifold, thus failing to capture the underlying dynamics giving rise to the observed marginals. In this paper, we propose Metric Flow Matching (MFM), a novel simulation-free framework for conditional flow matching where interpolants are approximate geodesics learned by minimizing the kinetic energy of a data-induced Riemannian metric. This way, the generative model matches vector fields on the data manifold, which corresponds to lower uncertainty and more meaningful interpolations. We prescribe general metrics to instantiate MFM, independent of the task, and test it on a suite of challenging problems including LiDAR navigation, unpaired image translation, and modeling cellular dynamics. We observe that MFM outperforms the Euclidean baselines, particularly achieving SOTA on single-cell trajectory prediction.

Charlie B. Tan, Avishek Joey Bose, Chen Lin et al.

Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators tackle this problem by pairing normalizing flows with importance sampling to obtain uncorrelated samples under the target distribution. In this paper, we extend the Boltzmann generator framework with two key contributions, denoting our framework Sequential Boltzmann Generators (SBG). The first is a highly efficient Transformer-based normalizing flow operating directly on all-atom Cartesian coordinates. In contrast to the equivariant continuous flows of prior methods, we leverage exactly invertible non-equivariant architectures which are highly efficient during both sample generation and likelihood evaluation. This efficiency unlocks more sophisticated inference strategies beyond standard importance sampling. In particular, we perform inference-time scaling of flow samples using a continuous-time variant of sequential Monte Carlo, in which flow samples are transported towards the target distribution with annealed Langevin dynamics. SBG achieves state-of-the-art performance w.r.t. all metrics on peptide systems, demonstrating the first equilibrium sampling in Cartesian coordinates of tri-, tetra- and hexa-peptides that were thus far intractable for prior Boltzmann generators.

Oscar Davis, Michael S. Albergo, Nicholas M. Boffi et al.

Geometric data and purpose-built generative models on them have become ubiquitous in high-impact deep learning application domains, ranging from protein backbone generation and computational chemistry to geospatial data. Current geometric generative models remain computationally expensive at inference -- requiring many steps of complex numerical simulation -- as they are derived from dynamical measure transport frameworks such as diffusion and flow-matching on Riemannian manifolds. In this paper, we propose Generalised Flow Maps (GFM), a new class of few-step generative models that generalises the Flow Map framework in Euclidean spaces to arbitrary Riemannian manifolds. We instantiate GFMs with three self-distillation-based training methods: Generalised Lagrangian Flow Maps, Generalised Eulerian Flow Maps, and Generalised Progressive Flow Maps. We theoretically show that GFMs, under specific design decisions, unify and elevate existing Euclidean few-step generative models, such as consistency models, shortcut models, and meanflows, to the Riemannian setting. We benchmark GFMs against other geometric generative models on a suite of geometric datasets, including geospatial data, RNA torsion angles, and hyperbolic manifolds, and achieve state-of-the-art sample quality for single- and few-step evaluations, and superior or competitive log-likelihoods using the implicit probability flow.

Danyal Rehman, Oscar Davis, Jiarui Lu et al.

Simulation-free training frameworks have been at the forefront of the generative modelling revolution in continuous spaces, leading to large-scale diffusion and flow matching models. However, such modern generative models suffer from expensive inference, inhibiting their use in numerous scientific applications like Boltzmann Generators (BGs) for molecular conformations that require fast likelihood evaluation. In this paper, we revisit classical normalizing flows in the context of BGs that offer efficient sampling and likelihoods, but whose training via maximum likelihood is often unstable and computationally challenging. We propose Regression Training of Normalizing Flows (RegFlow), a novel and scalable regression-based training objective that bypasses the numerical instability and computational challenge of conventional maximum likelihood training in favour of a simple $\ell_2$-regression objective. Specifically, RegFlow maps prior samples under our flow to targets computed using optimal transport couplings or a pre-trained continuous normalizing flow (CNF). To enhance numerical stability, RegFlow employs effective regularization strategies such as a new forward-backward self-consistency loss that enjoys painless implementation. Empirically, we demonstrate that RegFlow unlocks a broader class of architectures that were previously intractable to train for BGs with maximum likelihood. We also show RegFlow exceeds the performance, computational cost, and stability of maximum likelihood training in equilibrium sampling in Cartesian coordinates of alanine dipeptide, tripeptide, and tetrapeptide, showcasing its potential in molecular systems.

Avishek Bose, Guojing Cong

Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. Despite having immense potential, GNN models lack performance when using datasets that contain high-dimensional, asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects are impractical. Therefore, an opportunity exists to address this challenge as multitarget prediction problems and predict all drug effects at a time. We developed standard and hybrid GNNs to perform two separate tasks: multiregression for continuous values and multilabel classification for categorical values contained in our datasets. Because multilabel classification makes the target data even more sparse and introduces asymmetric label co-occurrence, learning these models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multilabel classification performances on all the given imbalanced molecular graph datasets. Using the technique, we improve the data imbalance ratio of the drug effects while protecting the datasets' integrity. Finally, we evaluate the multilabel classification performance of the best-performing hybrid GNN model on all the oversampled datasets obtained from the proposed oversampling technique. In all the evaluation metrics (i.e., precision, recall, and F1 score), this model significantly outperforms other ML models, including GNN models when they are trained on the original datasets or oversampled datasets with MLSMOTE, which is a well-known oversampling technique.

Andjela Mladenovic, Avishek Joey Bose, Hugo Berard et al.

Adversarial attacks expose important vulnerabilities of deep learning models, yet little attention has been paid to settings where data arrives as a stream. In this paper, we formalize the online adversarial attack problem, emphasizing two key elements found in real-world use-cases: attackers must operate under partial knowledge of the target model, and the decisions made by the attacker are irrevocable since they operate on a transient data stream. We first rigorously analyze a deterministic variant of the online threat model by drawing parallels to the well-studied $k$-secretary problem in theoretical computer science and propose Virtual+, a simple yet practical online algorithm. Our main theoretical result shows Virtual+ yields provably the best competitive ratio over all single-threshold algorithms for $k<5$ -- extending the previous analysis of the $k$-secretary problem. We also introduce the \textit{stochastic $k$-secretary} -- effectively reducing online blackbox transfer attacks to a $k$-secretary problem under noise -- and prove theoretical bounds on the performance of Virtual+ adapted to this setting. Finally, we complement our theoretical results by conducting experiments on MNIST, CIFAR-10, and Imagenet classifiers, revealing the necessity of online algorithms in achieving near-optimal performance and also the rich interplay between attack strategies and online attack selection, enabling simple strategies like FGSM to outperform stronger adversaries.

Adedolapo Okanlawon, Huichen Yang, Avishek Bose et al.

We present a machine learning framework and a new test bed for data mining from the Slurm Workload Manager for high-performance computing (HPC) clusters. The focus was to find a method for selecting features to support decisions: helping users decide whether to resubmit failed jobs with boosted CPU and memory allocations or migrate them to a computing cloud. This task was cast as both supervised classification and regression learning, specifically, sequential problem solving suitable for reinforcement learning. Selecting relevant features can improve training accuracy, reduce training time, and produce a more comprehensible model, with an intelligent system that can explain predictions and inferences. We present a supervised learning model trained on a Simple Linux Utility for Resource Management (Slurm) data set of HPC jobs using three different techniques for selecting features: linear regression, lasso, and ridge regression. Our data set represented both HPC jobs that failed and those that succeeded, so our model was reliable, less likely to overfit, and generalizable. Our model achieved an R^2 of 95\% with 99\% accuracy. We identified five predictors for both CPU and memory properties.

Kian Ahrabian, Aarash Feizi, Yasmin Salehi et al.

Learning low-dimensional representations for entities and relations in knowledge graphs using contrastive estimation represents a scalable and effective method for inferring connectivity patterns. A crucial aspect of contrastive learning approaches is the choice of corruption distribution that generates hard negative samples, which force the embedding model to learn discriminative representations and find critical characteristics of observed data. While earlier methods either employ too simple corruption distributions, i.e. uniform, yielding easy uninformative negatives or sophisticated adversarial distributions with challenging optimization schemes, they do not explicitly incorporate known graph structure resulting in suboptimal negatives. In this paper, we propose Structure Aware Negative Sampling (SANS), an inexpensive negative sampling strategy that utilizes the rich graph structure by selecting negative samples from a node's k-hop neighborhood. Empirically, we demonstrate that SANS finds semantically meaningful negatives and is competitive with SOTA approaches while requires no additional parameters nor difficult adversarial optimization.

Avishek Joey Bose, Gauthier Gidel, Hugo Berard et al.

The existence of adversarial examples capable of fooling trained neural network classifiers calls for a much better understanding of possible attacks to guide the development of safeguards against them. This includes attack methods in the challenging non-interactive blackbox setting, where adversarial attacks are generated without any access, including queries, to the target model. Prior attacks in this setting have relied mainly on algorithmic innovations derived from empirical observations (e.g., that momentum helps), lacking principled transferability guarantees. In this work, we provide a theoretical foundation for crafting transferable adversarial examples to entire hypothesis classes. We introduce Adversarial Example Games (AEG), a framework that models the crafting of adversarial examples as a min-max game between a generator of attacks and a classifier. AEG provides a new way to design adversarial examples by adversarially training a generator and a classifier from a given hypothesis class (e.g., architecture). We prove that this game has an equilibrium, and that the optimal generator is able to craft adversarial examples that can attack any classifier from the corresponding hypothesis class. We demonstrate the efficacy of AEG on the MNIST and CIFAR-10 datasets, outperforming prior state-of-the-art approaches with an average relative improvement of $29.9\%$ and $47.2\%$ against undefended and robust models (Table 2 & 3) respectively.

Avishek Joey Bose, Ariella Smofsky, Renjie Liao et al.

The choice of approximate posterior distributions plays a central role in stochastic variational inference (SVI). One effective solution is the use of normalizing flows \cut{defined on Euclidean spaces} to construct flexible posterior distributions. However, one key limitation of existing normalizing flows is that they are restricted to the Euclidean space and are ill-equipped to model data with an underlying hierarchical structure. To address this fundamental limitation, we present the first extension of normalizing flows to hyperbolic spaces. We first elevate normalizing flows to hyperbolic spaces using coupling transforms defined on the tangent bundle, termed Tangent Coupling ($\mathcal{TC}$). We further introduce Wrapped Hyperboloid Coupling ($\mathcal{W}\mathbb{H}C$), a fully invertible and learnable transformation that explicitly utilizes the geometric structure of hyperbolic spaces, allowing for expressive posteriors while being efficient to sample from. We demonstrate the efficacy of our novel normalizing flow over hyperbolic VAEs and Euclidean normalizing flows. Our approach achieves improved performance on density estimation, as well as reconstruction of real-world graph data, which exhibit a hierarchical structure. Finally, we show that our approach can be used to power a generative model over hierarchical data using hyperbolic latent variables.

Avishek Joey Bose, Ankit Jain, Piero Molino et al.

We consider the task of few shot link prediction on graphs. The goal is to learn from a distribution over graphs so that a model is able to quickly infer missing edges in a new graph after a small amount of training. We show that current link prediction methods are generally ill-equipped to handle this task. They cannot effectively transfer learned knowledge from one graph to another and are unable to effectively learn from sparse samples of edges. To address this challenge, we introduce a new gradient-based meta learning framework, Meta-Graph. Our framework leverages higher-order gradients along with a learned graph signature function that conditionally generates a graph neural network initialization. Using a novel set of few shot link prediction benchmarks, we show that Meta-Graph can learn to quickly adapt to a new graph using only a small sample of true edges, enabling not only fast adaptation but also improved results at convergence.

Patrick Nadeem Ward, Ariella Smofsky, Avishek Joey Bose

Deep Reinforcement Learning (DRL) algorithms for continuous action spaces are known to be brittle toward hyperparameters as well as \cut{being}sample inefficient. Soft Actor Critic (SAC) proposes an off-policy deep actor critic algorithm within the maximum entropy RL framework which offers greater stability and empirical gains. The choice of policy distribution, a factored Gaussian, is motivated by \cut{chosen due}its easy re-parametrization rather than its modeling power. We introduce Normalizing Flow policies within the SAC framework that learn more expressive classes of policies than simple factored Gaussians. \cut{We also present a series of stabilization tricks that enable effective training of these policies in the RL setting.}We show empirically on continuous grid world tasks that our approach increases stability and is better suited to difficult exploration in sparse reward settings.

Peng Xu, Hamidreza Saghir, Jin Sung Kang et al.

Coherence is an important aspect of text quality and is crucial for ensuring its readability. One important limitation of existing coherence models is that training on one domain does not easily generalize to unseen categories of text. Previous work advocates for generative models for cross-domain generalization, because for discriminative models, the space of incoherent sentence orderings to discriminate against during training is prohibitively large. In this work, we propose a local discriminative neural model with a much smaller negative sampling space that can efficiently learn against incorrect orderings. The proposed coherence model is simple in structure, yet it significantly outperforms previous state-of-art methods on a standard benchmark dataset on the Wall Street Journal corpus, as well as in multiple new challenging settings of transfer to unseen categories of discourse on Wikipedia articles.

Avishek Joey Bose, Andre Cianflone, William L. Hamilton

Adversarial attacks on deep neural networks traditionally rely on a constrained optimization paradigm, where an optimization procedure is used to obtain a single adversarial perturbation for a given input example. In this work we frame the problem as learning a distribution of adversarial perturbations, enabling us to generate diverse adversarial distributions given an unperturbed input. We show that this framework is domain-agnostic in that the same framework can be employed to attack different input domains with minimal modification. Across three diverse domains---images, text, and graphs---our approach generates whitebox attacks with success rates that are competitive with or superior to existing approaches, with a new state-of-the-art achieved in the graph domain. Finally, we demonstrate that our framework can efficiently generate a diverse set of attacks for a single given input, and is even capable of attacking \textit{unseen} test instances in a zero-shot manner, exhibiting attack generalization.

Avishek Joey Bose, William L. Hamilton

Learning high-quality node embeddings is a key building block for machine learning models that operate on graph data, such as social networks and recommender systems. However, existing graph embedding techniques are unable to cope with fairness constraints, e.g., ensuring that the learned representations do not correlate with certain attributes, such as age or gender. Here, we introduce an adversarial framework to enforce fairness constraints on graph embeddings. Our approach is compositional---meaning that it can flexibly accommodate different combinations of fairness constraints during inference. For instance, in the context of social recommendations, our framework would allow one user to request that their recommendations are invariant to both their age and gender, while also allowing another user to request invariance to just their age. Experiments on standard knowledge graph and recommender system benchmarks highlight the utility of our proposed framework.

Avishek Joey Bose, Huan Ling, Yanshuai Cao

Learning by contrasting positive and negative samples is a general strategy adopted by many methods. Noise contrastive estimation (NCE) for word embeddings and translating embeddings for knowledge graphs are examples in NLP employing this approach. In this work, we view contrastive learning as an abstraction of all such methods and augment the negative sampler into a mixture distribution containing an adversarially learned sampler. The resulting adaptive sampler finds harder negative examples, which forces the main model to learn a better representation of the data. We evaluate our proposal on learning word embeddings, order embeddings and knowledge graph embeddings and observe both faster convergence and improved results on multiple metrics.

Avishek Bose, Arslan Munir, Neda Shabani

The hospitality industry is one of the data-rich industries that receives huge Volumes of data streaming at high Velocity with considerably Variety, Veracity, and Variability. These properties make the data analysis in the hospitality industry a big data problem. Meeting the customers' expectations is a key factor in the hospitality industry to grasp the customers' loyalty. To achieve this goal, marketing professionals in this industry actively look for ways to utilize their data in the best possible manner and advance their data analytic solutions, such as identifying a unique market segmentation clustering and developing a recommendation system. In this paper, we present a comprehensive literature review of existing big data clustering algorithms and their advantages and disadvantages for various use cases. We implement the existing big data clustering algorithms and provide a quantitative comparison of the performance of different clustering algorithms for different scenarios. We also present our insights and recommendations regarding the suitability of different big data clustering algorithms for different use cases. These recommendations will be helpful for hoteliers in selecting the appropriate market segmentation clustering algorithm for different clustering datasets to improve the customer experience and maximize the hotel revenue.