Mattias Ohlsson

Ola Hall, Mattias Ohlsson, Thortseinn Rögnvaldsson

Recent advances in artificial intelligence and machine learning have created a step change in how to measure human development indicators, in particular asset based poverty. The combination of satellite imagery and machine learning has the capability to estimate poverty at a level similar to what is achieved with workhorse methods such as face-to-face interviews and household surveys. An increasingly important issue beyond static estimations is whether this technology can contribute to scientific discovery and consequently new knowledge in the poverty and welfare domain. A foundation for achieving scientific insights is domain knowledge, which in turn translates into explainability and scientific consistency. We review the literature focusing on three core elements relevant in this context: transparency, interpretability, and explainability and investigate how they relates to the poverty, machine learning and satellite imagery nexus. Our review of the field shows that the status of the three core elements of explainable machine learning (transparency, interpretability and domain knowledge) is varied and does not completely fulfill the requirements set up for scientific insights and discoveries. We argue that explainability is essential to support wider dissemination and acceptance of this research, and explainability means more than just interpretability.

Abdallah Alabdallah, Omar Hamed, Mattias Ohlsson et al.

The Cox Proportional Hazards (CPH) model has long been the preferred survival model for its explainability. However, to increase its predictive power beyond its linear log-risk, it was extended to utilize deep neural networks, sacrificing its explainability. In this work, we explore the potential of self-explaining neural networks (SENN) for survival analysis. We propose a new locally explainable Cox proportional hazards model, named CoxSE, by estimating a locally-linear log-hazard function using the SENN. We also propose a modification to the Neural additive (NAM) model, hybrid with SENN, named CoxSENAM, which enables the control of the stability and consistency of the generated explanations. Several experiments using synthetic and real datasets are presented, benchmarking CoxSE and CoxSENAM against a NAM-based model, a DeepSurv model explained with SHAP, and a linear CPH model. The results show that, unlike the NAM-based model, the SENN-based model can provide more stable and consistent explanations while maintaining the predictive power of the black-box model. The results also show that, due to their structural design, NAM-based models demonstrate better robustness to non-informative features. Among the models, the hybrid model exhibits the best robustness.

Ali Amirahmadi, Gökçe Geylan, Leonardo De Maria et al.

Cyclic peptides are promising modalities for targeting intracellular sites; however, cell-membrane permeability remains a key bottleneck, exacerbated by limited public data and the need for well-calibrated uncertainty. Instead of relying on data-eager complex deep learning architecture, we propose a monomer-aware decoupled global alignment kernel (MD-GAK), which couples chemically meaningful residue-residue similarity with sequence alignment while decoupling local matches from gap penalties. MD-GAK is a relatively simple kernel. To further demonstrate the robustness of our framework, we also introduce a variant, PMD-GAK, which incorporates a triangular positional prior. As we will show in the experimental section, PMD-GAK can offer additional advantages over MD-GAK, particularly in reducing calibration errors. Since our focus is on uncertainty estimation, we use Gaussian Processes as the predictive model, as both MD-GAK and PMD-GAK can be directly applied within this framework. We demonstrate the effectiveness of our methods through an extensive set of experiments, comparing our fully reproducible approach against state-of-the-art models, and show that it outperforms them across all metrics.

Ali Amirahmadi, Mattias Ohlsson, Kobra Etminani et al.

Using electronic health records data and machine learning to guide future decisions needs to address challenges, including 1) long/short-term dependencies and 2) interactions between diseases and interventions. Bidirectional transformers have effectively addressed the first challenge. Here we tackled the latter challenge by masking one source (e.g., ICD10 codes) and training the transformer to predict it using other sources (e.g., ATC codes).

Hamid Sarmadi, Ola Hall, Thorsteinn Rögnvaldsson et al.

This paper investigates the novel application of Large Language Models (LLMs) with vision capabilities to analyze satellite imagery for village-level poverty prediction. Although LLMs were originally designed for natural language understanding, their adaptability to multimodal tasks, including geospatial analysis, has opened new frontiers in data-driven research. By leveraging advancements in vision-enabled LLMs, we assess their ability to provide interpretable, scalable, and reliable insights into human poverty from satellite images. Using a pairwise comparison approach, we demonstrate that ChatGPT can rank satellite images based on poverty levels with accuracy comparable to domain experts. These findings highlight both the promise and the limitations of LLMs in socioeconomic research, providing a foundation for their integration into poverty assessment workflows. This study contributes to the ongoing exploration of unconventional data sources for welfare analysis and opens pathways for cost-effective, large-scale poverty monitoring.

Abdallah Alabdallah, Mattias Ohlsson, Sepideh Pashami et al.

The Concordance Index (C-index) is a commonly used metric in Survival Analysis for evaluating the performance of a prediction model. In this paper, we propose a decomposition of the C-index into a weighted harmonic mean of two quantities: one for ranking observed events versus other observed events, and the other for ranking observed events versus censored cases. This decomposition enables a finer-grained analysis of the relative strengths and weaknesses between different survival prediction methods. The usefulness of this decomposition is demonstrated through benchmark comparisons against classical models and state-of-the-art methods, together with the new variational generative neural-network-based method (SurVED) proposed in this paper. The performance of the models is assessed using four publicly available datasets with varying levels of censoring. Using the C-index decomposition and synthetic censoring, the analysis shows that deep learning models utilize the observed events more effectively than other models. This allows them to keep a stable C-index in different censoring levels. In contrast to such deep learning methods, classical machine learning models deteriorate when the censoring level decreases due to their inability to improve on ranking the events versus other events.

Alexander Galozy, Slawomir Nowaczyk, Mattias Ohlsson

We propose a new sequential decision-making setting, combining key aspects of two established online learning problems with bandit feedback. The optimal action to play at any given moment is contingent on an underlying changing state which is not directly observable by the agent. Each state is associated with a context distribution, possibly corrupted, allowing the agent to identify the state. Furthermore, states evolve in a Markovian fashion, providing useful information to estimate the current state via state history. In the proposed problem setting, we tackle the challenge of deciding on which of the two sources of information the agent should base its arm selection. We present an algorithm that uses a referee to dynamically combine the policies of a contextual bandit and a multi-armed bandit. We capture the time-correlation of states through iteratively learning the action-reward transition model, allowing for efficient exploration of actions. Our setting is motivated by adaptive mobile health (mHealth) interventions. Users transition through different, time-correlated, but only partially observable internal states, determining their current needs. The side information associated with each internal state might not always be reliable, and standard approaches solely rely on the context risk of incurring high regret. Similarly, some users might exhibit weaker correlations between subsequent states, leading to approaches that solely rely on state transitions risking the same. We analyze our setting and algorithm in terms of regret lower bound and upper bounds and evaluate our method on simulated medication adherence intervention data and several real-world data sets, showing improved empirical performance compared to several popular algorithms.

Najmeh Abiri, Björn Linse, Patrik Edén et al.

Dealing with missing data in data analysis is inevitable. Although powerful imputation methods that address this problem exist, there is still much room for improvement. In this study, we examined single imputation based on deep autoencoders, motivated by the apparent success of deep learning to efficiently extract useful dataset features. We have developed a consistent framework for both training and imputation. Moreover, we benchmarked the results against state-of-the-art imputation methods on different data sizes and characteristics. The work was not limited to the one-type variable dataset; we also imputed missing data with multi-type variables, e.g., a combination of binary, categorical, and continuous attributes. To evaluate the imputation methods, we randomly corrupted the complete data, with varying degrees of corruption, and then compared the imputed and original values. In all experiments, the developed autoencoder obtained the smallest error for all ranges of initial data corruption.

Najmeh Abiri, Mattias Ohlsson

We propose a new structure for the variational auto-encoders (VAEs) prior, with the weakly informative multivariate Student's t-distribution. In the proposed model all distribution parameters are trained, thereby allowing for a more robust approximation of the underlying data distribution. We used Fashion-MNIST data in two experiments to compare the proposed VAEs with the standard Gaussian priors. Both experiments showed a better reconstruction of the images with VAEs using Student's t-prior distribution.