We investigate the molecular gene expressions studies and public databases for disease modelling using Probabilistic Graphical Models and Bayesian Inference. A case study on Spinal Muscle Atrophy Genome-Wide Association Study results is modelled and analyzed. The genes up and down-regulated in two stages of the disease development are linked to prior knowledge published in the public domain and co-expressions network is created and analyzed. The Molecular Pathways triggered by these genes are identified. The Bayesian inference posteriors distributions are estimated using a variational analytical algorithm and a Markov chain Monte Carlo sampling algorithm. Assumptions, limitations and possible future work are concluded.

Hyperparameter Optimization (HPO) of Deep Learning-based models tends to be a compute resource intensive process as it usually requires to train the target model with many different hyperparameter configurations. We show that integrating model performance prediction with early stopping methods holds great potential to speed up the HPO process of deep learning models. Moreover, we propose a novel algorithm called Swift-Hyperband that can use either classical or quantum support vector regression for performance prediction and benefit from distributed High Performance Computing environments. This algorithm is tested not only for the Machine-Learned Particle Flow model used in High Energy Physics, but also for a wider range of target models from domains such as computer vision and natural language processing. Swift-Hyperband is shown to find comparable (or better) hyperparameters as well as using less computational resources in all test cases.

Prompt-based learning has been widely applied in many low-resource NLP tasks such as few-shot scenarios. However, this paradigm has been shown to be vulnerable to backdoor attacks. Most of the existing attack methods focus on inserting manually predefined templates as triggers in the pre-training phase to train the victim model and utilize the same triggers in the downstream task to perform inference, which tends to ignore the transferability and stealthiness of the templates. In this work, we propose a novel approach of TARGET (Template-trAnsfeRable backdoor attack aGainst prompt-basEd NLP models via GPT4), which is a data-independent attack method. Specifically, we first utilize GPT4 to reformulate manual templates to generate tone-strong and normal templates, and the former are injected into the model as a backdoor trigger in the pre-training phase. Then, we not only directly employ the above templates in the downstream task, but also use GPT4 to generate templates with similar tone to the above templates to carry out transferable attacks. Finally we have conducted extensive experiments on five NLP datasets and three BERT series models, with experimental results justifying that our TARGET method has better attack performance and stealthiness compared to the two-external baseline methods on direct attacks, and in addition achieves satisfactory attack capability in the unseen tone-similar templates.

The problem of firebreak placement is crucial for fire prevention, and its effectiveness at landscape scale will depend on their ability to impede the progress of future wildfires. To provide an adequate response, it is therefore necessary to consider the stochastic nature of fires, which are highly unpredictable from ignition to extinction. Thus, the placement of firebreaks can be considered a stochastic optimization problem where: (1) the objective function is to minimize the expected cells burnt of the landscape; (2) the decision variables being the location of firebreaks; and (3) the random variable being the spatial propagation/behavior of fires. In this paper, we propose a solution approach for the problem from the perspective of simulation-based optimization (SbO), where the objective function is not available (a black-box function), but can be computed (and/or approximated) by wildfire simulations. For this purpose, Genetic Algorithm and GRASP are implemented. The final implementation yielded favorable results for the Genetic Algorithm, demonstrating strong performance in scenarios with medium to high operational capacity, as well as medium levels of stochasticity

Monitoring wildfires is an essential step in minimizing their impact on the planet, understanding the many negative environmental, economic, and social consequences. Recent advances in remote sensing technology combined with the increasing application of artificial intelligence methods have improved real-time, high-resolution fire monitoring. This study explores two proposed approaches based on the U-Net model for automating and optimizing the burned-area mapping process. Denoted 128 and AllSizes (AS), they are trained on datasets with a different class balance by cropping input images to different sizes. They are then applied to Landsat imagery and time-series data from two fire-prone regions in Chile. The results obtained after enhancement of model performance by hyperparameter optimization demonstrate the effectiveness of both approaches. Tests based on 195 representative images of the study area show that increasing dataset balance using the AS model yields better performance. More specifically, AS exhibited a Dice Coefficient (DC) of 0.93, an Omission Error (OE) of 0.086, and a Commission Error (CE) of 0.045, while the 128 model achieved a DC of 0.86, an OE of 0.12, and a CE of 0.12. These findings should provide a basis for further development of scalable automatic burned-area mapping tools.

We study the task of gesture recognition from electromyography (EMG), with the goal of enabling expressive human-computer interaction at high accuracy, while minimizing the time required for new subjects to provide calibration data. To fulfill these goals, we define combination gestures consisting of a direction component and a modifier component. New subjects only demonstrate the single component gestures and we seek to extrapolate from these to all possible single or combination gestures. We extrapolate to unseen combination gestures by combining the feature vectors of real single gestures to produce synthetic training data. This strategy allows us to provide a large and flexible gesture vocabulary, while not requiring new subjects to demonstrate combinatorially many example gestures. We pre-train an encoder and a combination operator using self-supervision, so that we can produce useful synthetic training data for unseen test subjects. To evaluate the proposed method, we collect a real-world EMG dataset, and measure the effect of augmented supervision against two baselines: a partially-supervised model trained with only single gesture data from the unseen subject, and a fully-supervised model trained with real single and real combination gesture data from the unseen subject. We find that the proposed method provides a dramatic improvement over the partially-supervised model, and achieves a useful classification accuracy that in some cases approaches the performance of the fully-supervised model.

Adversarial testing of large language models (LLMs) is crucial for their safe and responsible deployment. We introduce a novel approach for automated generation of adversarial evaluation datasets to test the safety of LLM generations on new downstream applications. We call it AI-assisted Red-Teaming (AART) - an automated alternative to current manual red-teaming efforts. AART offers a data generation and augmentation pipeline of reusable and customizable recipes that reduce human effort significantly and enable integration of adversarial testing earlier in new product development. AART generates evaluation datasets with high diversity of content characteristics critical for effective adversarial testing (e.g. sensitive and harmful concepts, specific to a wide range of cultural and geographic regions and application scenarios). The data generation is steered by AI-assisted recipes to define, scope and prioritize diversity within the application context. This feeds into a structured LLM-generation process that scales up evaluation priorities. Compared to some state-of-the-art tools, AART shows promising results in terms of concept coverage and data quality.

Improper pain management can lead to severe physical or mental consequences, including suffering, and an increased risk of opioid dependency. Assessing the presence and severity of pain is imperative to prevent such outcomes and determine the appropriate intervention. However, the evaluation of pain intensity is challenging because different individuals experience pain differently. To overcome this, researchers have employed machine learning models to evaluate pain intensity objectively. However, these efforts have primarily focused on point estimation of pain, disregarding the inherent uncertainty and variability present in the data and model. Consequently, the point estimates provide only partial information for clinical decision-making. This study presents a neural network-based method for objective pain interval estimation, incorporating uncertainty quantification. This work explores three algorithms: the bootstrap method, lower and upper bound estimation (LossL) optimized by genetic algorithm, and modified lower and upper bound estimation (LossS) optimized by gradient descent algorithm. Our empirical results reveal that LossS outperforms the other two by providing a narrower prediction interval. As LossS outperforms, we assessed its performance in three different scenarios for pain assessment: (1) a generalized approach (single model for the entire population), (2) a personalized approach (separate model for each individual), and (3) a hybrid approach (separate model for each cluster of individuals). Our findings demonstrate the hybrid approach's superior performance, with notable practicality in clinical contexts. It has the potential to be a valuable tool for clinicians, enabling objective pain intensity assessment while taking uncertainty into account. This capability is crucial in facilitating effective pain management and reducing the risks associated with improper treatment.

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.

Inverse imaging problems that are ill-posed can be encountered across multiple domains of science and technology, ranging from medical diagnosis to astronomical studies. To reconstruct images from incomplete and distorted data, it is necessary to create algorithms that can take into account both, the physical mechanisms responsible for generating these measurements and the intrinsic characteristics of the images being analyzed. In this work, the sparse representation of images is reviewed, which is a realistic, compact and effective generative model for natural images inspired by the visual system of mammals. It enables us to address ill-posed linear inverse problems by training the model on a vast collection of images. Moreover, we extend the application of sparse coding to solve the non-linear and ill-posed problem in microwave tomography imaging, which could lead to a significant improvement of the state-of-the-arts algorithms.