arXiv subjects

Jakub M. Tomczak

Publications and source records attributed to Jakub M. Tomczak.

At least 19 recordsLinked to original sources

arXiv2026

Constructing VAE Latent Spaces with Prescribed Topology

Variational autoencoders (VAEs) learn low-dimensional latent representations of high-dimensional data. When the data lies on a manifold with non-Euclidean topology, the standard Gaussian prior introduces a topological mismatch that degrades reconstruction quality and prevents faithful representation. We present a constructive mathematical framework that resolves this mismatch for all manifolds that admit a product covering space. These are manifolds expressible as products of elementary factors (circles, intervals, or lines) or as quotients of such products by a finite symmetry group. The class includes cylinders, tori, Möbius strips, Klein bottles, and real projective spaces. Factorized distributions over the elementary factors yield product topologies with closed-form, decoupled KL divergences, so that each latent factor can be shaped independently while keeping training tractable. We catalogue reparametrizable encoder-prior pairs for periodic, bounded, and unbounded supports, and provide coordinate transformations that allow standard neural networks to output non-Euclidean parameters with smooth gradients. For quotient manifolds, the decoder receives group-invariant features of the covering-space coordinates, so that identified points produce identical outputs. Anchor constraints fix the coordinate system relative to the data or create soft topological holes. Experiments on synthetic manifolds and real-image datasets (rotated and cyclically shifted MNIST) confirm that a topology-matched prior aligns KL regularization with the data manifold. The resulting topology-aware models outperform the Gaussian baseline at all practically relevant regularization strengths. The code is available at https://github.com/JvHulst/VAE-Topology.

cs.LG↗

arXiv2026

Scalable Single-Cell Gene Expression Generation with Latent Diffusion Models

Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge. This difficulty arises from the count nature of gene expression data and complex latent dependencies among genes. Existing generative models often impose artificial gene orderings or rely on shallow neural network architectures. We introduce a scalable latent diffusion model for single-cell gene expression data, which we refer to as scLDM, that respects the fundamental exchangeability property of the data. Our VAE uses fixed-size latent variables leveraging a unified Multi-head Cross-Attention Block (MCAB) architecture, which serves dual roles: permutation-invariant pooling in the encoder and permutation-equivariant unpooling in the decoder. We enhance this framework by replacing the Gaussian prior with a latent diffusion model using Diffusion Transformers and linear interpolants, enabling high-quality generation with multi-conditional classifier-free guidance. We show its superior performance in a variety of experiments for both observational and perturbational single-cell data, as well as downstream tasks like cell-level classification.

stat.ML↗

arXiv2026

Synergistic Benefits of Joint Molecule Generation and Property Prediction

Modeling the joint distribution of data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic benefits reaching beyond purely generative or predictive models. However, training joint models presents daunting architectural and optimization challenges. Here, we propose Hyformer, a transformer-based joint model that successfully blends the generative and predictive functionalities, using an alternating attention mechanism and a joint pre-training scheme. We show that Hyformer is simultaneously optimized for molecule generation and property prediction, while exhibiting synergistic benefits in conditional sampling, out-of-distribution property prediction and representation learning. Finally, we demonstrate the benefits of joint learning in a drug design use case of discovering novel antimicrobial~peptides.

cs.LG↗

arXiv2025

Knowledge Graph-extended Retrieval Augmented Generation for Question Answering

Large Language Models (LLMs) and Knowledge Graphs (KGs) offer a promising approach to robust and explainable Question Answering (QA). While LLMs excel at natural language understanding, they suffer from knowledge gaps and hallucinations. KGs provide structured knowledge but lack natural language interaction. Ideally, an AI system should be both robust to missing facts as well as easy to communicate with. This paper proposes such a system that integrates LLMs and KGs without requiring training, ensuring adaptability across different KGs with minimal human effort. The resulting approach can be classified as a specific form of a Retrieval Augmented Generation (RAG) with a KG, thus, it is dubbed Knowledge Graph-extended Retrieval Augmented Generation (KG-RAG). It includes a question decomposition module to enhance multi-hop information retrieval and answer explainability. Using In-Context Learning (ICL) and Chain-of-Thought (CoT) prompting, it generates explicit reasoning chains processed separately to improve truthfulness. Experiments on the MetaQA benchmark show increased accuracy for multi-hop questions, though with a slight trade-off in single-hop performance compared to LLM with KG baselines. These findings demonstrate KG-RAG's potential to improve transparency in QA by bridging unstructured language understanding with structured knowledge retrieval.

cs.LG↗

arXiv2024

Hierarchical VAE with a Diffusion-based VampPrior

Deep hierarchical variational autoencoders (VAEs) are powerful latent variable generative models. In this paper, we introduce Hierarchical VAE with Diffusion-based Variational Mixture of the Posterior Prior (VampPrior). We apply amortization to scale the VampPrior to models with many stochastic layers. The proposed approach allows us to achieve better performance compared to the original VampPrior work and other deep hierarchical VAEs, while using fewer parameters. We empirically validate our method on standard benchmark datasets (MNIST, OMNIGLOT, CIFAR10) and demonstrate improved training stability and latent space utilization.

cs.LG↗

arXiv2024

Generative AI Systems: A Systems-based Perspective on Generative AI

Large Language Models (LLMs) have revolutionized AI systems by enabling communication with machines using natural language. Recent developments in Generative AI (GenAI) like Vision-Language Models (GPT-4V) and Gemini have shown great promise in using LLMs as multimodal systems. This new research line results in building Generative AI systems, GenAISys for short, that are capable of multimodal processing and content creation, as well as decision-making. GenAISys use natural language as a communication means and modality encoders as I/O interfaces for processing various data sources. They are also equipped with databases and external specialized tools, communicating with the system through a module for information retrieval and storage. This paper aims to explore and state new research directions in Generative AI Systems, including how to design GenAISys (compositionality, reliability, verifiability), build and train them, and what can be learned from the system-based perspective. Cross-disciplinary approaches are needed to answer open questions about the inner workings of GenAI systems.

cs.CL↗

arXiv2024

Mixed Models with Multiple Instance Learning

Predicting patient features from single-cell data can help identify 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 MixMIL, 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, MixMIL enhances computational efficiency and aligns with recent advancements in single-cell representation learning. Our empirical results reveal that MixMIL outperforms existing MIL models in single-cell datasets, uncovering new associations and elucidating biological mechanisms across different domains.

cs.LG↗

arXiv2024

Wavelet Networks: Scale-Translation Equivariant Learning From Raw Time-Series

Leveraging the symmetries inherent to specific data domains for the construction of equivariant neural networks has lead to remarkable improvements in terms of data efficiency and generalization. However, most existing research focuses on symmetries arising from planar and volumetric data, leaving a crucial data source largely underexplored: time-series. In this work, we fill this gap by leveraging the symmetries inherent to time-series for the construction of equivariant neural network. We identify two core symmetries: *scale and translation*, and construct scale-translation equivariant neural networks for time-series learning. Intriguingly, we find that scale-translation equivariant mappings share strong resemblance with the wavelet transform. Inspired by this resemblance, we term our networks Wavelet Networks, and show that they perform nested non-linear wavelet-like time-frequency transforms. Empirical results show that Wavelet Networks outperform conventional CNNs on raw waveforms, and match strongly engineered spectrogram techniques across several tasks and time-series types, including audio, environmental sounds, and electrical signals. Our code is publicly available at https://github.com/dwromero/wavelet_networks.

cs.LG↗

arXiv2023

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, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.

cs.LG↗

arXiv2023

Discouraging posterior collapse in hierarchical Variational Autoencoders using context

Hierarchical Variational Autoencoders (VAEs) are among the most popular likelihood-based generative models. There is a consensus that the top-down hierarchical VAEs allow effective learning of deep latent structures and avoid problems like posterior collapse. Here, we show that this is not necessarily the case, and the problem of collapsing posteriors remains. To discourage this issue, we propose a deep hierarchical VAE with a context on top. Specifically, we use a Discrete Cosine Transform to obtain the last latent variable. In a series of experiments, we observe that the proposed modification allows us to achieve better utilization of the latent space and does not harm the model's generative abilities.

cs.LG↗

arXiv2023

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 solve three neurosymbolic tasks with exponential combinatorial scaling. Finally, our experiments show that A-NeSI achieves explainability and safety without a penalty in performance.

cs.LG↗

arXiv2023

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.

cs.CV↗

arXiv2023

Learning Data Representations with Joint Diffusion Models

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 not only for generating but also predicting. We then propose to extend the vanilla diffusion model with a classifier that allows for stable joint end-to-end training with shared parameterization between those objectives. The resulting joint diffusion model outperforms recent state-of-the-art hybrid methods in terms of both classification and generation quality on all evaluated benchmarks. On top of our joint training approach, we present how we can directly benefit from shared generative and discriminative representations by introducing a method for visual counterfactual explanations.

cs.LG↗

arXiv2023

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.

cs.LG↗

arXiv2022

Alleviating Adversarial Attacks on Variational Autoencoders with MCMC

Variational autoencoders (VAEs) are latent variable models that can generate complex objects and provide meaningful latent representations. Moreover, they could 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 attack construction proposed previously and present a solution to alleviate the effect of these attacks. Our method utilizes the Markov Chain Monte Carlo (MCMC) technique in the inference step that we motivate with a theoretical analysis. Thus, we do not incorporate any extra costs during training, and the performance on non-attacked inputs is not decreased. We validate our approach on a variety of datasets (MNIST, Fashion MNIST, Color MNIST, CelebA) and VAE configurations ($β$-VAE, NVAE, $β$-TCVAE), and show that our approach consistently improves the model robustness to adversarial attacks.

cs.LG↗

arXiv2022

Hyperspherical Variational Auto-Encoders

The Variational Auto-Encoder (VAE) is one of the most used unsupervised machine learning models. But although the default choice of a Gaussian distribution for both the prior and posterior represents a mathematically convenient distribution often leading to competitive results, we show that this parameterization fails to model data with a latent hyperspherical structure. To address this issue we propose using a von Mises-Fisher (vMF) distribution instead, leading to a hyperspherical latent space. Through a series of experiments we show how such a hyperspherical VAE, or $\mathcal{S}$-VAE, is more suitable for capturing data with a hyperspherical latent structure, while outperforming a normal, $\mathcal{N}$-VAE, in low dimensions on other data types. Code at http://github.com/nicola-decao/s-vae-tf and https://github.com/nicola-decao/s-vae-pytorch

stat.ML↗

arXiv2022

Towards a General Purpose CNN for Long Range Dependencies in $N$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.

cs.LG↗

arXiv2022

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.

cs.LG↗