arXiv subjects

A. Aldo Faisal

Publications and source records attributed to A. Aldo Faisal.

At least 19 recordsLinked to original sources

arXiv2026

Pretraining EHR Foundation Models with Patient-Aware Sampling

Autoregressive foundation models for electronic health records (EHRs) typically inherit pretraining methods from language modeling, where patient trajectories are concatenated into a single token stream and windows are sampled from that stream. In EHR data, this choice is consequential: windows may mix multiple patients, and patients with longer records contribute more optimization updates, potentially introducing bias. We propose Patient Sampling, a pretraining sequence-construction method that allows us to control how training signal is distributed across patients. We compare this method to the standard approach, which we refer to as Global Stream. We show that stochastic Patient Sampling with controllable weighting improves performance on real-world EHR data. Across downstream clinical tasks on MIMIC-IV v2.2 and v3.1, Patient Sampling improves Macro AUROC and AUPRC over the Global Stream baseline. These results identify training and validation sequence construction as important and underexplored design choices for autoregressive EHR foundation models.

cs.LG↗

arXiv2026

Autoregressive EHR Foundation Models with Multimodal Inputs

Autoregressive foundation models trained on tokenized electronic health records (EHRs) can support zero-shot clinical prediction, yet most operate on structured event codes alone, and do not incorporate multiple modalities in a principled way. We present a framework for conditioning such models on auxiliary clinical modalities, including ECG waveforms, chest X-ray images, and clinical notes, using modality-specific latent compression and gated cross-attention with temporal alignment. We investigate two key design choices: (1) how to compress long per-modality sequences (e.g., ECG time series) before they enter the multi-modal cross-attention. This feature may be essential to reduce compute overheads and may be beneficial for generalization; (2) how the choice of pretrained encoder for each modality impacts downstream performance. Through controlled ablations on MIMIC-IV, we show that the best latent-compression configurations outperforms both uncompressed cross-attention and mean pooling. Encoder choice has a clear within-modality effect, with stronger pretrained encoders consistently outperforming weaker alternatives. We further show that merely adding auxiliary modalities does not guarantee improvement on ICU mortality prediction over an EHR-only baseline. This implies that careful design of the fusion architecture and an appropriate evaluation in the clinical context are required.

cs.LG↗

arXiv2025

Variational Uncertainty Decomposition for In-Context Learning

As large language models (LLMs) gain popularity in conducting prediction tasks in-context, understanding the sources of uncertainty in in-context learning becomes essential to ensuring reliability. The recent hypothesis of in-context learning performing predictive Bayesian inference opens the avenue for Bayesian uncertainty estimation, particularly for decomposing uncertainty into epistemic uncertainty due to lack of in-context data and aleatoric uncertainty inherent in the in-context prediction task. However, the decomposition idea remains under-explored due to the intractability of the latent parameter posterior from the underlying Bayesian model. In this work, we introduce a variational uncertainty decomposition framework for in-context learning without explicitly sampling from the latent parameter posterior, by optimising auxiliary queries as probes to obtain an upper bound to the aleatoric uncertainty of an LLM's in-context learning procedure, which also induces a lower bound to the epistemic uncertainty. Through experiments on synthetic and real-world tasks, we show quantitatively and qualitatively that the decomposed uncertainties obtained from our method exhibit desirable properties of epistemic and aleatoric uncertainty.

stat.ML↗

arXiv2025

Contrastive Representation Learning Helps Cross-institutional Knowledge Transfer: A Study in Pediatric Ventilation Management

Clinical machine learning deployment across institutions faces significant challenges when patient populations and clinical practices differ substantially. We present a systematic framework for cross-institutional knowledge transfer in clinical time series, demonstrated through pediatric ventilation management between a general pediatric intensive care unit (PICU) and a cardiac-focused unit. Using contrastive predictive coding (CPC) for representation learning, we investigate how different data regimes and fine-tuning strategies affect knowledge transfer across institutional boundaries. Our results show that while direct model transfer performs poorly, CPC with appropriate fine-tuning enables effective knowledge sharing between institutions, with benefits particularly evident in limited data scenarios. Analysis of transfer patterns reveals an important asymmetry: temporal progression patterns transfer more readily than point-of-care decisions, suggesting practical pathways for cross-institutional deployment. Through a systematic evaluation of fine-tuning approaches and transfer patterns, our work provides insights for developing more generalizable clinical decision support systems while enabling smaller specialized units to leverage knowledge from larger centers.

cs.LG↗

arXiv2024

Graph Neural Networks Uncover Geometric Neural Representations in Reinforcement-Based Motor Learning

Graph Neural Networks (GNN) can capture the geometric properties of neural representations in EEG data. Here we utilise those to study how reinforcement-based motor learning affects neural activity patterns during motor planning, leveraging the inherent graph structure of EEG channels to capture the spatial relationships in brain activity. By exploiting task-specific symmetries, we define different pretraining strategies that not only improve model performance across all participant groups but also validate the robustness of the geometric representations. Explainability analysis based on the graph structures reveals consistent group-specific neural signatures that persist across pretraining conditions, suggesting stable geometric structures in the neural representations associated with motor learning and feedback processing. These geometric patterns exhibit partial invariance to certain task space transformations, indicating symmetries that enable generalisation across conditions while maintaining specificity to individual learning strategies. This work demonstrates how GNNs can uncover the effects of previous outcomes on motor planning, in a complex real-world task, providing insights into the geometric principles governing neural representations. Our experimental design bridges the gap between controlled experiments and ecologically valid scenarios, offering new insights into the organisation of neural representations during naturalistic motor learning, which may open avenues for exploring fundamental principles governing brain activity in complex tasks.

cs.LG↗

arXiv2024

Offline Bayesian Aleatoric and Epistemic Uncertainty Quantification and Posterior Value Optimisation in Finite-State MDPs

We address the challenge of quantifying Bayesian uncertainty and incorporating it in offline use cases of finite-state Markov Decision Processes (MDPs) with unknown dynamics. Our approach provides a principled method to disentangle epistemic and aleatoric uncertainty, and a novel technique to find policies that optimise Bayesian posterior expected value without relying on strong assumptions about the MDP's posterior distribution. First, we utilise standard Bayesian reinforcement learning methods to capture the posterior uncertainty in MDP parameters based on available data. We then analytically compute the first two moments of the return distribution across posterior samples and apply the law of total variance to disentangle aleatoric and epistemic uncertainties. To find policies that maximise posterior expected value, we leverage the closed-form expression for value as a function of policy. This allows us to propose a stochastic gradient-based approach for solving the problem. We illustrate the uncertainty quantification and Bayesian posterior value optimisation performance of our agent in simple, interpretable gridworlds and validate it through ground-truth evaluations on synthetic MDPs. Finally, we highlight the real-world impact and computational scalability of our method by applying it to the AI Clinician problem, which recommends treatment for patients in intensive care units and has emerged as a key use case of finite-state MDPs with offline data. We discuss the challenges that arise with Bayesian modelling of larger scale MDPs while demonstrating the potential to apply our methods rooted in Bayesian decision theory into the real world. We make our code available at https://github.com/filippovaldettaro/finite-state-mdps .

cs.LG↗

arXiv2024

The Sandwich meta-framework for architecture agnostic deep privacy-preserving transfer learning for non-invasive brainwave decoding

Machine learning has enhanced the performance of decoding signals indicating human behaviour. EEG decoding, as an exemplar indicating neural activity and human thoughts non-invasively, has been helpful in neural activity analysis and aiding patients via brain-computer interfaces. However, training machine learning algorithms on EEG encounters two primary challenges: variability across data sets and privacy concerns using data from individuals and data centres. Our objective is to address these challenges by integrating transfer learning for data variability and federated learning for data privacy into a unified approach. We introduce the Sandwich as a novel deep privacy-preserving meta-framework combining transfer learning and federated learning. The Sandwich framework comprises three components: federated networks (first layers) that handle data set differences at the input level, a shared network (middle layer) learning common rules and applying transfer learning, and individual classifiers (final layers) for specific tasks of each data set. It enables the central network (central server) to benefit from multiple data sets, while local branches (local servers) maintain data and label privacy. We evaluated the `Sandwich' meta-architecture in various configurations using the BEETL motor imagery challenge, a benchmark for heterogeneous EEG data sets. Compared with baseline models, our `Sandwich' implementations showed superior performance. The best-performing model, the Inception Sandwich with deep set alignment (Inception-SD-Deepset), exceeded baseline methods by 9%. The `Sandwich' framework demonstrates significant advancements in federated deep transfer learning for diverse tasks and data sets. It outperforms conventional deep learning methods, showcasing the potential for effective use of larger, heterogeneous data sets with enhanced privacy as a model-agnostic meta-framework.

eess.SP↗

arXiv2024

Speaker-Independent Dysarthria Severity Classification using Self-Supervised Transformers and Multi-Task Learning

Dysarthria, a condition resulting from impaired control of the speech muscles due to neurological disorders, significantly impacts the communication and quality of life of patients. The condition's complexity, human scoring and varied presentations make its assessment and management challenging. This study presents a transformer-based framework for automatically assessing dysarthria severity from raw speech data. It can offer an objective, repeatable, accessible, standardised and cost-effective and compared to traditional methods requiring human expert assessors. We develop a transformer framework, called Speaker-Agnostic Latent Regularisation (SALR), incorporating a multi-task learning objective and contrastive learning for speaker-independent multi-class dysarthria severity classification. The multi-task framework is designed to reduce reliance on speaker-specific characteristics and address the intrinsic intra-class variability of dysarthric speech. We evaluated on the Universal Access Speech dataset using leave-one-speaker-out cross-validation, our model demonstrated superior performance over traditional machine learning approaches, with an accuracy of $70.48\%$ and an F1 score of $59.23\%$. Our SALR model also exceeded the previous benchmark for AI-based classification, which used support vector machines, by $16.58\%$. We open the black box of our model by visualising the latent space where we can observe how the model substantially reduces speaker-specific cues and amplifies task-specific ones, thereby showing its robustness. In conclusion, SALR establishes a new benchmark in speaker-independent multi-class dysarthria severity classification using generative AI. The potential implications of our findings for broader clinical applications in automated dysarthria severity assessments.

q-bio.NC↗

arXiv2023

Learning to Optimise Wind Farms with Graph Transformers

This work proposes a novel data-driven model capable of providing accurate predictions for the power generation of all wind turbines in wind farms of arbitrary layout, yaw angle configurations and wind conditions. The proposed model functions by encoding a wind farm into a fully-connected graph and processing the graph representation through a graph transformer. The graph transformer surrogate is shown to generalise well and is able to uncover latent structural patterns within the graph representation of wind farms. It is demonstrated how the resulting surrogate model can be used to optimise yaw angle configurations using genetic algorithms, achieving similar levels of accuracy to industrially-standard wind farm simulation tools while only taking a fraction of the computational cost.

cs.LG↗

arXiv2023

Towards AI-controlled FES-restoration of movements: Learning cycling stimulation pattern with reinforcement learning

Functional electrical stimulation (FES) has been increasingly integrated with other rehabilitation devices, including robots. FES cycling is one of the common FES applications in rehabilitation, which is performed by stimulating leg muscles in a certain pattern. The appropriate pattern varies across individuals and requires manual tuning which can be time-consuming and challenging for the individual user. Here, we present an AI-based method for finding the patterns, which requires no extra hardware or sensors. Our method has two phases, starting with finding model-based patterns using reinforcement learning and detailed musculoskeletal models. The models, built using open-source software, can be customised through our automated script and can be therefore used by non-technical individuals without extra cost. Next, our method fine-tunes the pattern using real cycling data. We test our both in simulation and experimentally on a stationary tricycle. In the simulation test, our method can robustly deliver model-based patterns for different cycling configurations. The experimental evaluation shows that our method can find a model-based pattern that induces higher cycling speed than an EMG-based pattern. By using just 100 seconds of cycling data, our method can deliver a fine-tuned pattern that gives better cycling performance. Beyond FES cycling, this work is a showcase, displaying the feasibility and potential of human-in-the-loop AI in real-world rehabilitation.

cs.RO↗

arXiv2023

Physics-informed reinforcement learning via probabilistic co-adjustment functions

Reinforcement learning of real-world tasks is very data inefficient, and extensive simulation-based modelling has become the dominant approach for training systems. However, in human-robot interaction and many other real-world settings, there is no appropriate one-model-for-all due to differences in individual instances of the system (e.g. different people) or necessary oversimplifications in the simulation models. This requires two approaches: 1. either learning the individual system's dynamics approximately from data which requires data-intensive training or 2. using a complete digital twin of the instances, which may not be realisable in many cases. We introduce two approaches: co-kriging adjustments (CKA) and ridge regression adjustment (RRA) as novel ways to combine the advantages of both approaches. Our adjustment methods are based on an auto-regressive AR1 co-kriging model that we integrate with GP priors. This yield a data- and simulation-efficient way of using simplistic simulation models (e.g., simple two-link model) and rapidly adapting them to individual instances (e.g., biomechanics of individual people). Using CKA and RRA, we obtain more accurate uncertainty quantification of the entire system's dynamics than pure GP-based and AR1 methods. We demonstrate the efficiency of co-kriging adjustment with an interpretable reinforcement learning control example, learning to control a biomechanical human arm using only a two-link arm simulation model (offline part) and CKA derived from a small amount of interaction data (on-the-fly online). Our method unlocks an efficient and uncertainty-aware way to implement reinforcement learning methods in real world complex systems for which only imperfect simulation models exist.

cs.LG↗

arXiv2023

EEG Decoding for Datasets with Heterogenous Electrode Configurations using Transfer Learning Graph Neural Networks

Brain-Machine Interfacing (BMI) has greatly benefited from adopting machine learning methods for feature learning that require extensive data for training, which are often unavailable from a single dataset. Yet, it is difficult to combine data across labs or even data within the same lab collected over the years due to the variation in recording equipment and electrode layouts resulting in shifts in data distribution, changes in data dimensionality, and altered identity of data dimensions. Our objective is to overcome this limitation and learn from many different and diverse datasets across labs with different experimental protocols. To tackle the domain adaptation problem, we developed a novel machine learning framework combining graph neural networks (GNNs) and transfer learning methodologies for non-invasive Motor Imagery (MI) EEG decoding, as an example of BMI. Empirically, we focus on the challenges of learning from EEG data with different electrode layouts and varying numbers of electrodes. We utilise three MI EEG databases collected using very different numbers of EEG sensors (from 22 channels to 64) and layouts (from custom layouts to 10-20). Our model achieved the highest accuracy with lower standard deviations on the testing datasets. This indicates that the GNN-based transfer learning framework can effectively aggregate knowledge from multiple datasets with different electrode layouts, leading to improved generalization in subject-independent MI EEG classification. The findings of this study have important implications for Brain-Computer-Interface (BCI) research, as they highlight a promising method for overcoming the limitations posed by non-unified experimental setups. By enabling the integration of diverse datasets with varying electrode layouts, our proposed approach can help advance the development and application of BMI technologies.

eess.SP↗

arXiv2023

Towards AI-controlled FES-restoration of arm movements: neuromechanics-based reinforcement learning for 3-D reaching

Reaching disabilities affect the quality of life. Functional Electrical Stimulation (FES) can restore lost motor functions. Yet, there remain challenges in controlling FES to induce desired movements. Neuromechanical models are valuable tools for developing FES control methods. However, focusing on the upper extremity areas, several existing models are either overly simplified or too computationally demanding for control purposes. Besides the model-related issues, finding a general method for governing the control rules for different tasks and subjects remains an engineering challenge. Here, we present our approach toward FES-based restoration of arm movements to address those fundamental issues in controlling FES. Firstly, we present our surface-FES-oriented neuromechanical models of human arms built using well-accepted, open-source software. The models are designed to capture significant dynamics in FES controls with minimal computational cost. Our models are customisable and can be used for testing different control methods. Secondly, we present the application of reinforcement learning (RL) as a general method for governing the control rules. In combination, our customisable models and RL-based control method open the possibility of delivering customised FES controls for different subjects and settings with minimal engineering intervention. We demonstrate our approach in planar and 3D settings.

eess.SY↗

arXiv2023

Towards AI-controlled FES-restoration of arm movements: Controlling for progressive muscular fatigue with Gaussian state-space models

Reaching disability limits an individual's ability in performing daily tasks. Surface Functional Electrical Stimulation (FES) offers a non-invasive solution to restore the lost abilities. However, inducing desired movements using FES is still an open engineering problem. This problem is accentuated by the complexities of human arms' neuromechanics and the variations across individuals. Reinforcement Learning (RL) emerges as a promising approach to govern customised control rules for different subjects and settings. Yet, one remaining challenge of using RL to control FES is unobservable muscle fatigue that progressively changes as an unknown function of the stimulation, breaking the Markovian assumption of RL. In this work, we present a method to address the unobservable muscle fatigue issue, allowing our RL controller to achieve higher control performances. Our method is based on a Gaussian State-Space Model (GSSM) that utilizes recurrent neural networks to learn Markovian state-spaces from partial observations. The GSSM is used as a filter that converts the observations into the state-space representation for RL to preserve the Markovian assumption. Here, we start with presenting the modification of the original GSSM to address an overconfident issue. We then present the interaction between RL and the modified GSSM, followed by the setup for FES control learning. We test our RL-GSSM system on a planar reaching setting in simulation using a detailed neuromechanical model and show that the GSSM can help RL maintain its control performance against the fatigue.

eess.SY↗

arXiv2023

Federated deep transfer learning for EEG decoding using multiple BCI tasks

Deep learning has been successful in BCI decoding. However, it is very data-hungry and requires pooling data from multiple sources. EEG data from various sources decrease the decoding performance due to negative transfer. Recently, transfer learning for EEG decoding has been suggested as a remedy and become subject to recent BCI competitions (e.g. BEETL), but there are two complications in combining data from many subjects. First, privacy is not protected as highly personal brain data needs to be shared (and copied across increasingly tight information governance boundaries). Moreover, BCI data are collected from different sources and are often based on different BCI tasks, which has been thought to limit their reusability. Here, we demonstrate a federated deep transfer learning technique, the Multi-dataset Federated Separate-Common-Separate Network (MF-SCSN) based on our previous work of SCSN, which integrates privacy-preserving properties into deep transfer learning to utilise data sets with different tasks. This framework trains a BCI decoder using different source data sets obtained from different imagery tasks (e.g. some data sets with hands and feet, vs others with single hands and tongue, etc). Therefore, by introducing privacy-preserving transfer learning techniques, we unlock the reusability and scalability of existing BCI data sets. We evaluated our federated transfer learning method on the NeurIPS 2021 BEETL competition BCI task. The proposed architecture outperformed the baseline decoder by 3%. Moreover, compared with the baseline and other transfer learning algorithms, our method protects the privacy of the brain data from different data centres.

eess.SP↗

arXiv2022

Neuromuscular Reinforcement Learning to Actuate Human Limbs through FES

Functional Electrical Stimulation (FES) is a technique to evoke muscle contraction through low-energy electrical signals. FES can animate paralysed limbs. Yet, an open challenge remains on how to apply FES to achieve desired movements. This challenge is accentuated by the complexities of human bodies and the non-stationarities of the muscles' responses. The former causes difficulties in performing inverse dynamics, and the latter causes control performance to degrade over extended periods of use. Here, we engage the challenge via a data-driven approach. Specifically, we learn to control FES through Reinforcement Learning (RL) which can automatically customise the stimulation for the patients. However, RL typically has Markovian assumptions while FES control systems are non-Markovian because of the non-stationarities. To deal with this problem, we use a recurrent neural network to create Markovian state representations. We cast FES controls into RL problems and train RL agents to control FES in different settings in both simulations and the real world. The results show that our RL controllers can maintain control performances over long periods and have better stimulation characteristics than PID controllers.

cs.LG↗

arXiv2022

Enabling risk-aware Reinforcement Learning for medical interventions through uncertainty decomposition

Reinforcement Learning (RL) is emerging as tool for tackling complex control and decision-making problems. However, in high-risk environments such as healthcare, manufacturing, automotive or aerospace, it is often challenging to bridge the gap between an apparently optimal policy learnt by an agent and its real-world deployment, due to the uncertainties and risk associated with it. Broadly speaking RL agents face two kinds of uncertainty, 1. aleatoric uncertainty, which reflects randomness or noise in the dynamics of the world, and 2. epistemic uncertainty, which reflects the bounded knowledge of the agent due to model limitations and finite amount of information/data the agent has acquired about the world. These two types of uncertainty carry fundamentally different implications for the evaluation of performance and the level of risk or trust. Yet these aleatoric and epistemic uncertainties are generally confounded as standard and even distributional RL is agnostic to this difference. Here we propose how a distributional approach (UA-DQN) can be recast to render uncertainties by decomposing the net effects of each uncertainty. We demonstrate the operation of this method in grid world examples to build intuition and then show a proof of concept application for an RL agent operating as a clinical decision support system in critical care

cs.AI↗

arXiv2022

The role of haptic communication in dyadic collaborative object manipulation tasks

Intuitive and efficient physical human-robot collaboration relies on the mutual observability of the human and the robot, i.e. the two entities being able to interpret each other's intentions and actions. This is remedied by a myriad of methods involving human sensing or intention decoding, as well as human-robot turn-taking and sequential task planning. However, the physical interaction establishes a rich channel of communication through forces, torques and haptics in general, which is often overlooked in industrial implementations of human-robot interaction. In this work, we investigate the role of haptics in human collaborative physical tasks, to identify how to integrate physical communication in human-robot teams. We present a task to balance a ball at a target position on a board either bimanually by one participant, or dyadically by two participants, with and without haptic information. The task requires that the two sides coordinate with each other, in real-time, to balance the ball at the target. We found that with training the completion time and number of velocity peaks of the ball decreased, and that participants gradually became consistent in their braking strategy. Moreover we found that the presence of haptic information improved the performance (decreased completion time) and led to an increase in overall cooperative movements. Overall, our results show that humans can better coordinate with one another when haptic feedback is available. These results also highlight the likely importance of haptic communication in human-robot physical interaction, both as a tool to infer human intentions and to make the robot behaviour interpretable to humans.

cs.RO↗