arXiv subjects

Jan Olszewski

Publications and source records attributed to Jan Olszewski.

5 recordsLinked to original sources

arXiv2025

seqme: a Python library for evaluating biological sequence design

Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their attainment of desired properties. However, a single software library implementing these metrics was lacking. In this work we introduce seqme, a modular and highly extendable open-source Python library, containing model-agnostic metrics for evaluating computational methods for biological sequence design. seqme considers three groups of metrics: sequence-based, embedding-based, and property-based, and is applicable to a wide range of biological sequences: small molecules, DNA, ncRNA, mRNA, peptides and proteins. The library offers a number of embedding and property models for biological sequences, as well as diagnostics and visualization functions to inspect the results. seqme can be used to evaluate both one-shot and iterative computational design methods.

cs.LG↗

arXiv2025

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↗

arXiv2023

TORE: Token Recycling in Vision Transformers for Efficient Active Visual Exploration

Active Visual Exploration (AVE) optimizes the utilization of robotic resources in real-world scenarios by sequentially selecting the most informative observations. However, modern methods require a high computational budget due to processing the same observations multiple times through the autoencoder transformers. As a remedy, we introduce a novel approach to AVE called TOken REcycling (TORE). It divides the encoder into extractor and aggregator components. The extractor processes each observation separately, enabling the reuse of tokens passed to the aggregator. Moreover, to further reduce the computations, we decrease the decoder to only one block. Through extensive experiments, we demonstrate that TORE outperforms state-of-the-art methods while reducing computational overhead by up to 90\%.

cs.LG↗

arXiv2023

Beyond Grids: Exploring Elastic Input Sampling for Vision Transformers

Vision transformers have excelled in various computer vision tasks but mostly rely on rigid input sampling using a fixed-size grid of patches. It limits their applicability in real-world problems, such as active visual exploration, where patches have various scales and positions. Our paper addresses this limitation by formalizing the concept of input elasticity for vision transformers and introducing an evaluation protocol for measuring this elasticity. Moreover, we propose modifications to the transformer architecture and training regime, which increase its elasticity. Through extensive experimentation, we spotlight opportunities and challenges associated with such architecture.

cs.CV↗

arXiv2023

HashCC: Lightweight Method to Improve the Quality of the Camera-less NeRF Scene Generation

Neural Radiance Fields has become a prominent method of scene generation via view synthesis. A critical requirement for the original algorithm to learn meaningful scene representation is camera pose information for each image in a data set. Current approaches try to circumnavigate this assumption with moderate success, by learning approximate camera positions alongside learning neural representations of a scene. This requires complicated camera models, causing a long and complicated training process, or results in a lack of texture and sharp details in rendered scenes. In this work we introduce Hash Color Correction (HashCC) -- a lightweight method for improving Neural Radiance Fields rendered image quality, applicable also in situations where camera positions for a given set of images are unknown.

cs.CV↗