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Probabilistic (Bayesian) modeling has experienced a surge of applications in almost all quantitative sciences and industrial areas. This development is driven by a combination of several factors, including better probabilistic estimation algorithms, flexible software, increased computing power, and a growing awareness of the benefits of probabilistic learning. However, a principled Bayesian model building workflow is far from complete and many challenges remain. To aid future research and applications of a principled Bayesian workflow, we ask and provide answers for what we perceive as two fundamental questions of Bayesian modeling, namely (a) "What actually is a Bayesian model?" and (b) "What makes a good Bayesian model?". As an answer to the first question, we propose the PAD model taxonomy that defines four basic kinds of Bayesian models, each representing some combination of the assumed joint distribution of all (known or unknown) variables (P), a posterior approximator (A), and training data (D). As an answer to the second question, we propose ten utility dimensions according to which we can evaluate Bayesian models holistically, namely, (1) causal consistency, (2) parameter recoverability, (3) predictive performance, (4) fairness, (5) structural faithfulness, (6) parsimony, (7) interpretability, (8) convergence, (9) estimation speed, and (10) robustness. Further, we propose two example utility decision trees that describe hierarchies and trade-offs between utilities depending on the inferential goals that drive model building and testing.

A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable longer, more naturalistic neuronal recordings. The implicit opportunity for understanding the self-organised brain calls for new analysis methods that link temporal scales: from the order of milliseconds over which neuronal dynamics evolve, to the order of minutes, days or even years over which experimental observations unfold. This review article demonstrates how hierarchical generative models and Bayesian inference help to characterise neuronal activity across different time scales. Crucially, these methods go beyond describing statistical associations among observations and enable inference about underlying mechanisms. We offer an overview of fundamental concepts in state-space modeling and suggest a taxonomy for these methods. Additionally, we introduce key mathematical principles that underscore a separation of temporal scales, such as the slaving principle, and review Bayesian methods that are being used to test hypotheses about the brain with multi-scale data. We hope that this review will serve as a useful primer for experimental and computational neuroscientists on the state of the art and current directions of travel in the complex systems modelling literature.

Parkinson's disease (PD) is a neurological disorder impacting a person's speech. Among automatic PD assessment methods, deep learning models have gained particular interest. Recently, the community has explored cross-pathology and cross-language models which can improve diagnostic accuracy even further. However, strict patient data privacy regulations largely prevent institutions from sharing patient speech data with each other. In this paper, we employ federated learning (FL) for PD detection using speech signals from 3 real-world language corpora of German, Spanish, and Czech, each from a separate institution. Our results indicate that the FL model outperforms all the local models in terms of diagnostic accuracy, while not performing very differently from the model based on centrally combined training sets, with the advantage of not requiring any data sharing among collaborators. This will simplify inter-institutional collaborations, resulting in enhancement of patient outcomes.

Accurate activity location prediction is a crucial component of many mobility applications and is particularly required to develop personalized, sustainable transportation systems. Despite the widespread adoption of deep learning models, next location prediction models lack a comprehensive discussion and integration of mobility-related spatio-temporal contexts. Here, we utilize a multi-head self-attentional (MHSA) neural network that learns location transition patterns from historical location visits, their visit time and activity duration, as well as their surrounding land use functions, to infer an individual's next location. Specifically, we adopt point-of-interest data and latent Dirichlet allocation for representing locations' land use contexts at multiple spatial scales, generate embedding vectors of the spatio-temporal features, and learn to predict the next location with an MHSA network. Through experiments on two large-scale GNSS tracking datasets, we demonstrate that the proposed model outperforms other state-of-the-art prediction models, and reveal the contribution of various spatio-temporal contexts to the model's performance. Moreover, we find that the model trained on population data achieves higher prediction performance with fewer parameters than individual-level models due to learning from collective movement patterns. We also reveal mobility conducted in the recent past and one week before has the largest influence on the current prediction, showing that learning from a subset of the historical mobility is sufficient to obtain an accurate location prediction result. We believe that the proposed model is vital for context-aware mobility prediction. The gained insights will help to understand location prediction models and promote their implementation for mobility applications.

Adverse drug reaction (ADR) detection is an essential task in the medical field, as ADRs have a gravely detrimental impact on patients' health and the healthcare system. Due to a large number of people sharing information on social media platforms, an increasing number of efforts focus on social media data to carry out effective ADR detection. Despite having achieved impressive performance, the existing methods of ADR detection still suffer from three main challenges. Firstly, researchers have consistently ignored the interaction between domain keywords and other words in the sentence. Secondly, social media datasets suffer from the challenges of low annotated data. Thirdly, the issue of sample imbalance is commonly observed in social media datasets. To solve these challenges, we propose the Knowledge Enhanced Shallow and Deep Transformer(KESDT) model for ADR detection. Specifically, to cope with the first issue, we incorporate the domain keywords into the Transformer model through a shallow fusion manner, which enables the model to fully exploit the interactive relationships between domain keywords and other words in the sentence. To overcome the low annotated data, we integrate the synonym sets into the Transformer model through a deep fusion manner, which expands the size of the samples. To mitigate the impact of sample imbalance, we replace the standard cross entropy loss function with the focal loss function for effective model training. We conduct extensive experiments on three public datasets including TwiMed, Twitter, and CADEC. The proposed KESDT outperforms state-of-the-art baselines on F1 values, with relative improvements of 4.87%, 47.83%, and 5.73% respectively, which demonstrates the effectiveness of our proposed KESDT.

Quantification of behavior is critical in applications ranging from neuroscience, veterinary medicine and animal conservation efforts. A common key step for behavioral analysis is first extracting relevant keypoints on animals, known as pose estimation. However, reliable inference of poses currently requires domain knowledge and manual labeling effort to build supervised models. We present a series of technical innovations that enable a new method, collectively called SuperAnimal, to develop and deploy deep learning models that require zero additional human labels and model training. SuperAnimal allows video inference on over 45 species with only two global classes of animal pose models. If the models need fine-tuning, we show SuperAnimal models are 10$\times$ more data efficient and outperform prior transfer-learning-based approaches. Moreover, we provide an unsupervised video-adaptation method to refine keypoints in videos. We illustrate the utility of our model in behavioral classification in mice and gait analysis in horses. Collectively, this presents a data-efficient solution for animal pose estimation for downstream behavioral analysis.

A central problem in computational statistics is to convert a procedure for sampling combinatorial from an objects into a procedure for counting those objects, and vice versa. Weconsider sampling problems coming from *Gibbs distributions*, which are probability distributions of the form $\mu^\Omega_\beta(\omega) \propto e^{\beta H(\omega)}$ for $\beta$ in an interval $[\beta_\min, \beta_\max]$ and $H( \omega ) \in \{0 \} \cup [1, n]$. The *partition function* is the normalization factor $Z(\beta)=\sum_{\omega \in\Omega}e^{\beta H(\omega)}$. Two important parameters are the log partition ratio $q = \log \tfrac{Z(\beta_\max)}{Z(\beta_\min)}$ and the vector of counts $c_x = |H^{-1}(x)|$. Our first result is an algorithm to estimate the counts $c_x$ using roughly $\tilde O( \frac{q}{\epsilon^2})$ samples for general Gibbs distributions and $\tilde O( \frac{n^2}{\epsilon^2} )$ samples for integer-valued distributions (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph. We develop a key subroutine for global estimation of the partition function. Specifically, we produce a data structure to estimate $Z(\beta)$ for \emph{all} values $\beta$, without further samples. Constructing the data structure requires $O(\frac{q \log n}{\epsilon^2})$ samples for general Gibbs distributions and $O(\frac{n^2 \log n}{\epsilon^2} + n \log q)$ samples for integer-valued distributions. This improves over a prior algorithm of Kolmogorov (2018) which computes the single point estimate $Z(\beta_\max)$ using $\tilde O(\frac{q}{\epsilon^2})$ samples. We also show that this complexity is optimal as a function of $n$ and $q$ up to logarithmic terms.

In light of the increasing adoption of edge computing in areas such as intelligent furniture, robotics, and smart homes, this paper introduces HyperSNN, an innovative method for control tasks that uses spiking neural networks (SNNs) in combination with hyperdimensional computing. HyperSNN substitutes expensive 32-bit floating point multiplications with 8-bit integer additions, resulting in reduced energy consumption while enhancing robustness and potentially improving accuracy. Our model was tested on AI Gym benchmarks, including Cartpole, Acrobot, MountainCar, and Lunar Lander. HyperSNN achieves control accuracies that are on par with conventional machine learning methods but with only 1.36% to 9.96% of the energy expenditure. Furthermore, our experiments showed increased robustness when using HyperSNN. We believe that HyperSNN is especially suitable for interactive, mobile, and wearable devices, promoting energy-efficient and robust system design. Furthermore, it paves the way for the practical implementation of complex algorithms like model predictive control (MPC) in real-world industrial scenarios.

The prevalence of machine learning in biomedical research is rapidly growing, yet the trustworthiness of such research is often overlooked. While some previous works have investigated the ability of adversarial attacks to degrade model performance in medical imaging, the ability to falsely improve performance via recently-developed "enhancement attacks" may be a greater threat to biomedical machine learning. In the spirit of developing attacks to better understand trustworthiness, we developed two techniques to drastically enhance prediction performance of classifiers with minimal changes to features: 1) general enhancement of prediction performance, and 2) enhancement of a particular method over another. Our enhancement framework falsely improved classifiers' accuracy from 50% to almost 100% while maintaining high feature similarities between original and enhanced data (Pearson's r's>0.99). Similarly, the method-specific enhancement framework was effective in falsely improving the performance of one method over another. For example, a simple neural network outperformed logistic regression by 17% on our enhanced dataset, although no performance differences were present in the original dataset. Crucially, the original and enhanced data were still similar (r=0.99). Our results demonstrate the feasibility of minor data manipulations to achieve any desired prediction performance, which presents an interesting ethical challenge for the future of biomedical machine learning. These findings emphasize the need for more robust data provenance tracking and other precautionary measures to ensure the integrity of biomedical machine learning research.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.