A dataset of primary nasopharyngeal carcinoma MRI with multi-modalities segmentation

Multi-modality magnetic resonance imaging data with various sequences facilitate the early diagnosis, tumor segmentation, and disease staging in the management of nasopharyngeal carcinoma (NPC). The lack of publicly available, comprehensive datasets limits advancements in diagnosis, treatment planning, and the development of machine learning algorithms for NPC. Addressing this critical need, we introduce the first comprehensive NPC MRI dataset, encompassing MR axial imaging of 277 primary NPC patients. This dataset includes T1-weighted, T2-weighted, and contrast-enhanced T1-weighted sequences, totaling 831 scans. In addition to the corresponding clinical data, manually annotated and labeled segmentations by experienced radiologists offer high-quality data resources from untreated primary NPC.

Guided Decoding for Robot Motion Generation and Adaption

We address motion generation for high-DoF robot arms in complex settings with obstacles, via points, etc. A significant advancement in this domain is achieved by integrating Learning from Demonstration (LfD) into the motion generation process. This integration facilitates rapid adaptation to new tasks and optimizes the utilization of accumulated expertise by allowing robots to learn and generalize from demonstrated trajectories. We train a transformer architecture on a large dataset of simulated trajectories. This architecture, based on a conditional variational autoencoder transformer, learns essential motion generation skills and adapts these to meet auxiliary tasks and constraints. Our auto-regressive approach enables real-time integration of feedback from the physical system, enhancing the adaptability and efficiency of motion generation. We show that our model can generate motion from initial and target points, but also that it can adapt trajectories in navigating complex tasks, including obstacle avoidance, via points, and meeting velocity and acceleration constraints, across platforms.

DomainLab: A modular Python package for domain generalization in deep learning

Poor generalization performance caused by distribution shifts in unseen domains often hinders the trustworthy deployment of deep neural networks. Many domain generalization techniques address this problem by adding a domain invariant regularization loss terms during training. However, there is a lack of modular software that allows users to combine the advantages of different methods with minimal effort for reproducibility. DomainLab is a modular Python package for training user specified neural networks with composable regularization loss terms. Its decoupled design allows the separation of neural networks from regularization loss construction. Hierarchical combinations of neural networks, different domain generalization methods, and associated hyperparameters, can all be specified together with other experimental setup in a single configuration file. Hierarchical combinations of neural networks, different domain generalization methods, and associated hyperparameters, can all be specified together with other experimental setup in a single configuration file. In addition, DomainLab offers powerful benchmarking functionality to evaluate the generalization performance of neural networks in out-of-distribution data. The package supports running the specified benchmark on an HPC cluster or on a standalone machine. The package is well tested with over 95 percent coverage and well documented. From the user perspective, it is closed to modification but open to extension. The package is under the MIT license, and its source code, tutorial and documentation can be found at https://github.com/marrlab/DomainLab.

M-HOF-Opt: Multi-Objective Hierarchical Output Feedback Optimization via Multiplier Induced Loss Landscape Scheduling

When a neural network parameterized loss function consists of many terms, the combinatorial choice of weight multipliers during the optimization process forms a challenging problem. To address this, we proposed a probabilistic graphical model (PGM) for the joint model parameter and multiplier evolution process, with a hypervolume based likelihood that promotes multi-objective descent of each loss term. The corresponding parameter and multiplier estimation as a sequential decision process is then cast into an optimal control problem, where the multi-objective descent goal is dispatched hierarchically into a series of constraint optimization sub-problems. The sub-problem constraint automatically adapts itself according to Pareto dominance and serves as the setpoint for the low level multiplier controller to schedule loss landscapes via output feedback of each loss term. Our method is multiplier-free and operates at the timescale of epochs, thus saves tremendous computational resources compared to full training cycle multiplier tuning. We applied it to domain invariant variational auto-encoding with 6 loss terms on the PACS domain generalization task, and observed robust performance across a range of controller hyperparameters, as well as different multiplier initial conditions, outperforming other multiplier scheduling methods. We offered modular implementation of our method, admitting custom definition of many loss terms for applying our multi-objective hierarchical output feedback training scheme to other deep learning fields.

Sequential Model for Predicting Patient Adherence in Subcutaneous Immunotherapy for Allergic Rhinitis

Objective: Subcutaneous Immunotherapy (SCIT) is the long-lasting causal treatment of allergic rhinitis. How to enhance the adherence of patients to maximize the benefit of allergen immunotherapy (AIT) plays a crucial role in the management of AIT. This study aims to leverage novel machine learning models to precisely predict the risk of non-adherence of patients and related systematic symptom scores, to provide a novel approach in the management of long-term AIT. Methods: The research develops and analyzes two models, Sequential Latent Actor-Critic (SLAC) and Long Short-Term Memory (LSTM), evaluating them based on scoring and adherence prediction capabilities. Results: Excluding the biased samples at the first time step, the predictive adherence accuracy of the SLAC models is from $60\,\%$ to $72\%$, and for LSTM models, it is $66\,\%$ to $84\,\%$, varying according to the time steps. The range of Root Mean Square Error (RMSE) for SLAC models is between $0.93$ and $2.22$, while for LSTM models it is between $1.09$ and $1.77$. Notably, these RMSEs are significantly lower than the random prediction error of $4.55$. Conclusion: We creatively apply sequential models in the long-term management of SCIT with promising accuracy in the prediction of SCIT nonadherence in Allergic Rhinitis (AR) patients. While LSTM outperforms SLAC in adherence prediction, SLAC excels in score prediction for patients undergoing SCIT for AR. The state-action-based SLAC adds flexibility, presenting a novel and effective approach for managing long-term AIT.

Probabilistic Dalek -- Emulator framework with probabilistic prediction for supernova tomography

Supernova spectral time series can be used to reconstruct a spatially resolved explosion model known as supernova tomography. In addition to an observed spectral time series, a supernova tomography requires a radiative transfer model to perform the inverse problem with uncertainty quantification for a reconstruction. The smallest parametrizations of supernova tomography models are roughly a dozen parameters with a realistic one requiring more than 100. Realistic radiative transfer models require tens of CPU minutes for a single evaluation making the problem computationally intractable with traditional means requiring millions of MCMC samples for such a problem. A new method for accelerating simulations known as surrogate models or emulators using machine learning techniques offers a solution for such problems and a way to understand progenitors/explosions from spectral time series. There exist emulators for the TARDIS supernova radiative transfer code but they only perform well on simplistic low-dimensional models (roughly a dozen parameters) with a small number of applications for knowledge gain in the supernova field. In this work, we present a new emulator for the radiative transfer code TARDIS that not only outperforms existing emulators but also provides uncertainties in its prediction. It offers the foundation for a future active-learning-based machinery that will be able to emulate very high dimensional spaces of hundreds of parameters crucial for unraveling urgent questions in supernovae and related fields.

Local distance preserving auto-encoders using Continuous k-Nearest Neighbours graphs

Auto-encoder models that preserve similarities in the data are a popular tool in representation learning. In this paper we introduce several auto-encoder models that preserve local distances when mapping from the data space to the latent space. We use a local distance preserving loss that is based on the continuous k-nearest neighbours graph which is known to capture topological features at all scales simultaneously. To improve training performance, we formulate learning as a constraint optimisation problem with local distance preservation as the main objective and reconstruction accuracy as a constraint. We generalise this approach to hierarchical variational auto-encoders thus learning generative models with geometrically consistent latent and data spaces. Our method provides state-of-the-art performance across several standard datasets and evaluation metrics.

Flat latent manifolds for music improvisation between human and machine

The use of machine learning in artistic music generation leads to controversial discussions of the quality of art, for which objective quantification is nonsensical. We therefore consider a music-generating algorithm as a counterpart to a human musician, in a setting where reciprocal improvisation is to lead to new experiences, both for the musician and the audience. To obtain this behaviour, we resort to the framework of recurrent Variational Auto-Encoders (VAE) and learn to generate music, seeded by a human musician. In the learned model, we generate novel musical sequences by interpolation in latent space. Standard VAEs however do not guarantee any form of smoothness in their latent representation. This translates into abrupt changes in the generated music sequences. To overcome these limitations, we regularise the decoder and endow the latent space with a flat Riemannian manifold, i.e., a manifold that is isometric to the Euclidean space. As a result, linearly interpolating in the latent space yields realistic and smooth musical changes that fit the type of machine--musician interactions we aim for. We provide empirical evidence for our method via a set of experiments on music datasets and we deploy our model for an interactive jam session with a professional drummer. The live performance provides qualitative evidence that the latent representation can be intuitively interpreted and exploited by the drummer to drive the interplay. Beyond the musical application, our approach showcases an instance of human-centred design of machine-learning models, driven by interpretability and the interaction with the end user.

Learning Flat Latent Manifolds with VAEs

Measuring the similarity between data points often requires domain knowledge. This can in parts be compensated by relying on unsupervised methods such as latent-variable models, where similarity/distance is estimated in a more compact latent space. Prevalent is the use of the Euclidean metric, which has the drawback of ignoring information about similarity of data stored in the decoder, as captured by the framework of Riemannian geometry. Alternatives---such as approximating the geodesic---are often computationally inefficient, rendering the methods impractical. We propose an extension to the framework of variational auto-encoders allows learning flat latent manifolds, where the Euclidean metric is a proxy for the similarity between data points. This is achieved by defining the latent space as a Riemannian manifold and by regularising the metric tensor to be a scaled identity matrix. Additionally, we replace the compact prior typically used in variational auto-encoders with a recently presented, more expressive hierarchical one---and formulate the learning problem as a constrained optimisation problem. We evaluate our method on a range of data-sets, including a video-tracking benchmark, where the performance of our unsupervised approach nears that of state-of-the-art supervised approaches, while retaining the computational efficiency of straight-line-based approaches.

Increasing the Generalisation Capacity of Conditional VAEs

We address the problem of one-to-many mappings in supervised learning, where a single instance has many different solutions of possibly equal cost. The framework of conditional variational autoencoders describes a class of methods to tackle such structured-prediction tasks by means of latent variables. We propose to incentivise informative latent representations for increasing the generalisation capacity of conditional variational autoencoders. To this end, we modify the latent variable model by defining the likelihood as a function of the latent variable only and introduce an expressive multimodal prior to enable the model for capturing semantically meaningful features of the data. To validate our approach, we train our model on the Cornell Robot Grasping dataset, and modified versions of MNIST and Fashion-MNIST obtaining results that show a significantly higher generalisation capability.