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Andreas Hellander

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Published work

9 published item(s)

preprint2026arXiv

GeoFlowVLM: Geometry-Aware Joint Uncertainty for Frozen Vision-Language Embedding

Standard dual-encoder vision-language models that map images and text to deterministic points on a shared unit hypersphere through $\ell_2$ normalization typically expose neither \emph{aleatoric} uncertainty (cross-modal ambiguity) nor \emph{epistemic} uncertainty (lack of training-distribution support). Existing post-hoc methods either recover at most one of the two uncertainty components, or ignore the hyperspherical geometry of these models' embeddings. We propose \textbf{GeoFlowVLM} as a post-hoc adapter that learns the joint distribution of paired $\ell_2$-normalised dual-encoder VLM embeddings on the product hypersphere $\mathbb{S}^{d-1} \times \mathbb{S}^{d-1}$ via Riemannian flow matching with a single masked velocity field. A consistency result shows that, in the population limit, the trained network exposes the joint flow and both cross-modal conditional flows as valid Riemannian flow-matching velocity fields on their respective domains. We derive two quantities from this single model: a conditional retrieval entropy that quantifies aleatoric ambiguity with a decision-theoretic interpretation via a Fano-type bound, and a marginal-typicality epistemic score justified by an exact chain-rule decomposition of the joint NLL. This decomposition isolates a cross-modal pointwise-mutual-information term that is structurally discriminative rather than epistemic, and is empirically the only consistently uninformative standalone component. Empirically, the entropy tracks Recall@1 with near-ideal monotonic calibration across three retrieval benchmarks in both directions, and the marginal-typicality sum yields consistently calibrated selective accuracy across four zero-shot classification benchmarks.

preprint2022arXiv

FedQAS: Privacy-aware machine reading comprehension with federated learning

Machine reading comprehension (MRC) of text data is one important task in Natural Language Understanding. It is a complex NLP problem with a lot of ongoing research fueled by the release of the Stanford Question Answering Dataset (SQuAD) and Conversational Question Answering (CoQA). It is considered to be an effort to teach computers how to "understand" a text, and then to be able to answer questions about it using deep learning. However, until now large-scale training on private text data and knowledge sharing has been missing for this NLP task. Hence, we present FedQAS, a privacy-preserving machine reading system capable of leveraging large-scale private data without the need to pool those datasets in a central location. The proposed approach combines transformer models and federated learning technologies. The system is developed using the FEDn framework and deployed as a proof-of-concept alliance initiative. FedQAS is flexible, language-agnostic, and allows intuitive participation and execution of local model training. In addition, we present the architecture and implementation of the system, as well as provide a reference evaluation based on the SQUAD dataset, to showcase how it overcomes data privacy issues and enables knowledge sharing between alliance members in a Federated learning setting.

preprint2022arXiv

Scalable federated machine learning with FEDn

Federated machine learning has great promise to overcome the input privacy challenge in machine learning. The appearance of several projects capable of simulating federated learning has led to a corresponding rapid progress on algorithmic aspects of the problem. However, there is still a lack of federated machine learning frameworks that focus on fundamental aspects such as scalability, robustness, security, and performance in a geographically distributed setting. To bridge this gap we have designed and developed the FEDn framework. A main feature of FEDn is to support both cross-device and cross-silo training settings. This makes FEDn a powerful tool for researching a wide range of machine learning applications in a realistic setting.

preprint2020arXiv

Smart Resource Management for Data Streaming using an Online Bin-packing Strategy

Data stream processing frameworks provide reliable and efficient mechanisms for executing complex workflows over large datasets. A common challenge for the majority of currently available streaming frameworks is efficient utilization of resources. Most frameworks use static or semi-static settings for resource utilization that work well for established use cases but lead to marginal improvements for unseen scenarios. Another pressing issue is the efficient processing of large individual objects such as images and matrices typical for scientific datasets. HarmonicIO has proven to be a good solution for streams of relatively large individual objects, as demonstrated in a benchmark comparison with the Spark and Kafka streaming frameworks. We here present an extension of the HarmonicIO framework based on the online bin-packing algorithm, to allow for efficient utilization of resources. Based on a real world use case from large-scale microscopy pipelines, we compare results of the new system to Spark's auto-scaling mechanism.

preprint2019arXiv

Hierarchical Reaction-Diffusion Master Equation

We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh, while others live on a coarse-grained mesh. By allowing molecules to transfer from the fine levels to the coarse levels when appropriate, we show that we can save up to three orders of magnitude of computational time compared to microscopic simulations or highly resolved mesoscopic simulations, without losing significant accuracy. We demonstrate this in several numerical examples with systems that cannot be accurately simulated with a coarse-grained mesoscopic model.

preprint2015arXiv

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

preprint2015arXiv

Reaction rates for mesoscopic reaction-diffusion kinetics

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a mixed boundary condition at the reaction radius of two molecules. We also establish fundamental limits for the range of mesh resolutions for which this approach yields accurate results, and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics.

preprint2013arXiv

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

preprint2011arXiv

On the Reaction Diffusion Master Equation in the Microscopic Limit

Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice Reaction-Diffusion Master Equation (RDME) framework. As the mesh size goes from coarse to fine, the RDME initially becomes more accurate. However, recent developments have shown that it will become increasingly inaccurate compared to the Smoluchowski model as the lattice spacing becomes very fine. In this paper we give a new, general and simple argument for why the RDME breaks down. Our analysis reveals a hard limit on the voxel size for which no local RDME can agree with the Smoluchowski model.