Jakob Lindqvist

David Hagerman, Roman Naeem, Jakob Lindqvist et al.

Sparse vision transformers have gained popularity as efficient encoders for medical volumetric segmentation, with Swin emerging as a prominent choice. Swin uses local attention to reduce complexity and yields excellent performance for many tasks but still tends to overfit on small datasets. To mitigate this weakness, we propose a novel architecture that further enhances Swin's inductive bias by introducing Inception blocks in the feed-forward layers. The introduction of these multi-branch convolutions enables more direct reasoning over local, multi-scale features within the transformer block. We have also modified the decoder layers in order to capture finer details using fewer parameters. We demonstrate a performance improvement on eleven different medical datasets through extensive experimentation. We specifically showcase advancements over the previous state-of-the-art backbones on benchmark challenges like the Medical Segmentation Decathlon and Beyond the Cranial Vault. By showing that the existing inductive bias in Swin can be further improved, our work presents a promising avenue for enhancing the capabilities of sparse vision transformers for both medical and natural image segmentation tasks. Code and pre-trained weights can be accessed at https://github.com/Eiphodos/SwInception.

Anders Sjöberg, Jakob Lindqvist, Magnus Önnheim et al.

Diffusion models can be parameterized in terms of either a score or an energy function. The energy parameterization is attractive as it enables sampling procedures such as Markov Chain Monte Carlo (MCMC) that incorporates a Metropolis-Hastings (MH) correction step based on energy differences between proposed samples. Such corrections can significantly improve sampling quality, particularly in the context of model composition, where pre-trained models are combined to generate samples from novel distributions. Score-based diffusion models, on the other hand, are more widely adopted and come with a rich ecosystem of pre-trained models. However, they do not, in general, define an underlying energy function, making MH-based sampling inapplicable. In this work, we address this limitation by retaining the score parameterization and introducing a novel MH-like acceptance rule based on line integration of the score function. This allows the reuse of existing diffusion models while still combining the reverse process with various MCMC techniques, viewed as an instance of annealed MCMC. Through experiments on synthetic and real-world data, we show that our MH-like samplers offer comparable improvements to those obtained with energy-based models, without requiring explicit energy parameterization.

Amanda Olmin, Jakob Lindqvist, Lennart Svensson et al.

Annotating data for supervised learning can be costly. When the annotation budget is limited, active learning can be used to select and annotate those observations that are likely to give the most gain in model performance. We propose an active learning algorithm that, in addition to selecting which observation to annotate, selects the precision of the annotation that is acquired. Assuming that annotations with low precision are cheaper to obtain, this allows the model to explore a larger part of the input space, with the same annotation budget. We build our acquisition function on the previously proposed BALD objective for Gaussian Processes, and empirically demonstrate the gains of being able to adjust the annotation precision in the active learning loop.

Amanda Olmin, Jakob Lindqvist, Lennart Svensson et al.

Noise-contrastive estimation (NCE) is a popular method for estimating unnormalised probabilistic models, such as energy-based models, which are effective for modelling complex data distributions. Unlike classical maximum likelihood (ML) estimation that relies on importance sampling (resulting in ML-IS) or MCMC (resulting in contrastive divergence, CD), NCE uses a proxy criterion to avoid the need for evaluating an often intractable normalisation constant. Despite apparent conceptual differences, we show that two NCE criteria, ranking NCE (RNCE) and conditional NCE (CNCE), can be viewed as ML estimation methods. Specifically, RNCE is equivalent to ML estimation combined with conditional importance sampling, and both RNCE and CNCE are special cases of CD. These findings bridge the gap between the two method classes and allow us to apply techniques from the ML-IS and CD literature to NCE, offering several advantageous extensions.

Jakob Lindqvist, Amanda Olmin, Fredrik Lindsten et al.

Ensembles of neural networks have been shown to give better performance than single networks, both in terms of predictions and uncertainty estimation. Additionally, ensembles allow the uncertainty to be decomposed into aleatoric (data) and epistemic (model) components, giving a more complete picture of the predictive uncertainty. Ensemble distillation is the process of compressing an ensemble into a single model, often resulting in a leaner model that still outperforms the individual ensemble members. Unfortunately, standard distillation erases the natural uncertainty decomposition of the ensemble. We present a general framework for distilling both regression and classification ensembles in a way that preserves the decomposition. We demonstrate the desired behaviour of our framework and show that its predictive performance is on par with standard distillation.