Attention-based Multi-instance Mixed Models

Predicting patient features from single-cell data can unveil cellular states implicated in health and disease. Linear models and average cell type expressions are typically favored for this task for their efficiency and robustness, but they overlook the rich cell heterogeneity inherent in single-cell data. To address this gap, we introduce GMIL, a framework integrating Generalized Linear Mixed Models (GLMM) and Multiple Instance Learning (MIL), upholding the advantages of linear models while modeling cell-state heterogeneity. By leveraging predefined cell embeddings, GMIL enhances computational efficiency and aligns with recent advancements in single-cell representation learning. Our empirical results reveal that GMIL outperforms existing MIL models in single-cell datasets, uncovering new associations and elucidating biological mechanisms across different domains.

De Novo Drug Design with Joint Transformers

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, a Transformer encoder, and a predictor in a joint generative model with shared weights. We show that training the model with a penalized log-likelihood objective results in state-of-the-art performance in molecule generation, while decreasing the prediction error on newly sampled molecules, as compared to a fine-tuned decoder-only Transformer, by 42%. Finally, we propose a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties, as compared to the training data, outperforming other SMILES-based optimization methods in de novo drug design.

Exploring Continual Learning of Diffusion Models

Diffusion models have achieved remarkable success in generating high-quality images thanks to their novel training procedures applied to unprecedented amounts of data. However, training a diffusion model from scratch is computationally expensive. This highlights the need to investigate the possibility of training these models iteratively, reusing computation while the data distribution changes. In this study, we take the first step in this direction and evaluate the continual learning (CL) properties of diffusion models. We begin by benchmarking the most common CL methods applied to Denoising Diffusion Probabilistic Models (DDPMs), where we note the strong performance of the experience replay with the reduced rehearsal coefficient. Furthermore, we provide insights into the dynamics of forgetting, which exhibit diverse behavior across diffusion timesteps. We also uncover certain pitfalls of using the bits-per-dimension metric for evaluating CL.

Analyzing the Posterior Collapse in Hierarchical Variational Autoencoders

Hierarchical Variational Autoencoders (VAEs) are among the most popular likelihood-based generative models. There is rather a consensus that the top-down hierarchical VAEs allow to effectively learn deep latent structures and avoid problems like the posterior collapse. Here, we show that it is not necessarily the case and the problem of collapsing posteriors remains. To discourage the posterior collapse, we propose a new deep hierarchical VAE with a partly fixed encoder, specifically, we use Discrete Cosine Transform to obtain top latent variables. In a series of experiments, we observe that the proposed modification allows us to achieve better utilization of the latent space. Further, we demonstrate that the proposed approach can be useful for compression and robustness to adversarial attacks.

Learning Data Representations with Joint Diffusion Models

We introduce a joint diffusion model that simultaneously learns meaningful internal representations fit for both generative and predictive tasks. Joint machine learning models that allow synthesizing and classifying data often offer uneven performance between those tasks or are unstable to train. In this work, we depart from a set of empirical observations that indicate the usefulness of internal representations built by contemporary deep diffusion-based generative models in both generative and predictive settings. We then introduce an extension of the vanilla diffusion model with a classifier that allows for stable joint training with shared parametrization between those objectives. The resulting joint diffusion model offers superior performance across various tasks, including generative modeling, semi-supervised classification, and domain adaptation.

Modelling Long Range Dependencies in N-D: From Task-Specific to a General Purpose CNN

Performant Convolutional Neural Network (CNN) architectures must be tailored to specific tasks in order to consider the length, resolution, and dimensionality of the input data. In this work, we tackle the need for problem-specific CNN architectures. We present the Continuous Convolutional Neural Network (CCNN): a single CNN able to process data of arbitrary resolution, dimensionality and length without any structural changes. Its key component are its continuous convolutional kernels which model long-range dependencies at every layer, and thus remove the need of current CNN architectures for task-dependent downsampling and depths. We showcase the generality of our method by using the same architecture for tasks on sequential ($1{\rm D}$), visual ($2{\rm D}$) and point-cloud ($3{\rm D}$) data. Our CCNN matches and often outperforms the current state-of-the-art across all tasks considered.

A-NeSI: A Scalable Approximate Method for Probabilistic Neurosymbolic Inference

We study the problem of combining neural networks with symbolic reasoning. Recently introduced frameworks for Probabilistic Neurosymbolic Learning (PNL), such as DeepProbLog, perform exponential-time exact inference, limiting the scalability of PNL solutions. We introduce Approximate Neurosymbolic Inference (A-NeSI): a new framework for PNL that uses neural networks for scalable approximate inference. A-NeSI 1) performs approximate inference in polynomial time without changing the semantics of probabilistic logics; 2) is trained using data generated by the background knowledge; 3) can generate symbolic explanations of predictions; and 4) can guarantee the satisfaction of logical constraints at test time, which is vital in safety-critical applications. Our experiments show that A-NeSI is the first end-to-end method to scale the Multi-digit MNISTAdd benchmark to sums of 15 MNIST digits, up from 4 in competing systems. Finally, our experiments show that A-NeSI achieves explainability and safety without a penalty in performance.

Towards a General Purpose CNN for Long Range Dependencies in $\mathrm{N}$D

The use of Convolutional Neural Networks (CNNs) is widespread in Deep Learning due to a range of desirable model properties which result in an efficient and effective machine learning framework. However, performant CNN architectures must be tailored to specific tasks in order to incorporate considerations such as the input length, resolution, and dimentionality. In this work, we overcome the need for problem-specific CNN architectures with our Continuous Convolutional Neural Network (CCNN): a single CNN architecture equipped with continuous convolutional kernels that can be used for tasks on data of arbitrary resolution, dimensionality and length without structural changes. Continuous convolutional kernels model long range dependencies at every layer, and remove the need for downsampling layers and task-dependent depths needed in current CNN architectures. We show the generality of our approach by applying the same CCNN to a wide set of tasks on sequential (1$\mathrm{D}$) and visual data (2$\mathrm{D}$). Our CCNN performs competitively and often outperforms the current state-of-the-art across all tasks considered.

On Analyzing Generative and Denoising Capabilities of Diffusion-based Deep Generative Models

Diffusion-based Deep Generative Models (DDGMs) offer state-of-the-art performance in generative modeling. Their main strength comes from their unique setup in which a model (the backward diffusion process) is trained to reverse the forward diffusion process, which gradually adds noise to the input signal. Although DDGMs are well studied, it is still unclear how the small amount of noise is transformed during the backward diffusion process. Here, we focus on analyzing this problem to gain more insight into the behavior of DDGMs and their denoising and generative capabilities. We observe a fluid transition point that changes the functionality of the backward diffusion process from generating a (corrupted) image from noise to denoising the corrupted image to the final sample. Based on this observation, we postulate to divide a DDGM into two parts: a denoiser and a generator. The denoiser could be parameterized by a denoising auto-encoder, while the generator is a diffusion-based model with its own set of parameters. We experimentally validate our proposition, showing its pros and cons.

Defending Variational Autoencoders from Adversarial Attacks with MCMC

Variational autoencoders (VAEs) are deep generative models used in various domains. VAEs can generate complex objects and provide meaningful latent representations, which can be further used in downstream tasks such as classification. As previous work has shown, one can easily fool VAEs to produce unexpected latent representations and reconstructions for a visually slightly modified input. Here, we examine several objective functions for adversarial attacks construction, suggest metrics assess the model robustness, and propose a solution to alleviate the effect of an attack. Our method utilizes the Markov Chain Monte Carlo (MCMC) technique in the inference step and is motivated by our theoretical analysis. Thus, we do not incorporate any additional costs during training or we do not decrease the performance on non-attacked inputs. We validate our approach on a variety of datasets (MNIST, Fashion MNIST, Color MNIST, CelebA) and VAE configurations ($\beta$-VAE, NVAE, TC-VAE) and show that it consistently improves the model robustness to adversarial attacks.