With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimization. This paper presents a transfer learning design of experiments workflow to make this development feasible. By combining a transfer learning surrogate model with Bayesian optimization, we show how the total number of experiments can be reduced by sharing information between optimization tasks. We demonstrate the reduction in the number of experiments using data from the development of DNA competitors for use in an amplification-based diagnostic assay. We use cross-validation to compare the predictive accuracy of different transfer learning models, and then compare the performance of the models for both single objective and penalized optimization tasks.

Experimental (design) optimization is a key driver in designing and discovering new products and processes. Bayesian Optimization (BO) is an effective tool for optimizing expensive and black-box experimental design processes. While Bayesian optimization is a principled data-driven approach to experimental optimization, it learns everything from scratch and could greatly benefit from the expertise of its human (domain) experts who often reason about systems at different abstraction levels using physical properties that are not necessarily directly measured (or measurable). In this paper, we propose a human-AI collaborative Bayesian framework to incorporate expert preferences about unmeasured abstract properties into the surrogate modeling to further boost the performance of BO. We provide an efficient strategy that can also handle any incorrect/misleading expert bias in preferential judgments. We discuss the convergence behavior of our proposed framework. Our experimental results involving synthetic functions and real-world datasets show the superiority of our method against the baselines.

Conventional causal discovery methods rely on centralized data, which is inconsistent with the decentralized nature of data in many real-world situations. This discrepancy has motivated the development of federated causal discovery (FCD) approaches. However, existing FCD methods may be limited by their potentially restrictive assumptions of identifiable functional causal models or homogeneous data distributions, narrowing their applicability in diverse scenarios. In this paper, we propose a novel FCD method attempting to accommodate arbitrary causal models and heterogeneous data. We first utilize a surrogate variable corresponding to the client index to account for the data heterogeneity across different clients. We then develop a federated conditional independence test (FCIT) for causal skeleton discovery and establish a federated independent change principle (FICP) to determine causal directions. These approaches involve constructing summary statistics as a proxy of the raw data to protect data privacy. Owing to the nonparametric properties, FCIT and FICP make no assumption about particular functional forms, thereby facilitating the handling of arbitrary causal models. We conduct extensive experiments on synthetic and real datasets to show the efficacy of our method. The code is available at https://github.com/lokali/FedCDH.git.

We introduce a modified incremental learning algorithm for evolving Granular Neural Network Classifiers (eGNN-C+). We use double-boundary hyper-boxes to represent granules, and customize the adaptation procedures to enhance the robustness of outer boxes for data coverage and noise suppression, while ensuring that inner boxes remain flexible to capture drifts. The classifier evolves from scratch, incorporates new classes on the fly, and performs local incremental feature weighting. As an application, we focus on the classification of emotion-related patterns within electroencephalogram (EEG) signals. Emotion recognition is crucial for enhancing the realism and interactivity of computer systems. We extract features from the Fourier spectrum of EEG signals obtained from 28 individuals engaged in playing computer games -- a public dataset. Each game elicits a different predominant emotion: boredom, calmness, horror, or joy. We analyze individual electrodes, time window lengths, and frequency bands to assess the accuracy and interpretability of resulting user-independent neural models. The findings indicate that both brain hemispheres assist classification, especially electrodes on the temporal (T8) and parietal (P7) areas, alongside contributions from frontal and occipital electrodes. While patterns may manifest in any band, the Alpha (8-13Hz), Delta (1-4Hz), and Theta (4-8Hz) bands, in this order, exhibited higher correspondence with the emotion classes. The eGNN-C+ demonstrates effectiveness in learning EEG data. It achieves an accuracy of 81.7% and a 0.0029 II interpretability using 10-second time windows, even in face of a highly-stochastic time-varying 4-class classification problem.

We characterise the likelihood function computed from a Bayesian network with latent variables as root nodes. We show that the marginal distribution over the remaining, manifest, variables also factorises as a Bayesian network, which we call empirical. A dataset of observations of the manifest variables allows us to quantify the parameters of the empirical Bayesian net. We prove that (i) the likelihood of such a dataset from the original Bayesian network is dominated by the global maximum of the likelihood from the empirical one; and that (ii) such a maximum is attained if and only if the parameters of the Bayesian network are consistent with those of the empirical model.

Noise-contrastive estimation (NCE) is a popular method for estimating unnormalised probabilistic models, such as energy-based models, which are effective for modelling complex data distributions. Unlike classical maximum likelihood (ML) estimation that relies on importance sampling (resulting in ML-IS) or MCMC (resulting in contrastive divergence, CD), NCE uses a proxy criterion to avoid the need for evaluating an often intractable normalisation constant. Despite apparent conceptual differences, we show that two NCE criteria, ranking NCE (RNCE) and conditional NCE (CNCE), can be viewed as ML estimation methods. Specifically, RNCE is equivalent to ML estimation combined with conditional importance sampling, and both RNCE and CNCE are special cases of CD. These findings bridge the gap between the two method classes and allow us to apply techniques from the ML-IS and CD literature to NCE, offering several advantageous extensions.

Performance degradation owing to data heterogeneity and low output interpretability are the most significant challenges faced by federated learning in practical applications. Personalized federated learning diverges from traditional approaches, as it no longer seeks to train a single model, but instead tailors a unique personalized model for each client. However, previous work focused only on personalization from the perspective of neural network parameters and lack of robustness and interpretability. In this work, we establish a novel framework for personalized federated learning, incorporating Bayesian methodology which enhances the algorithm's ability to quantify uncertainty. Furthermore, we introduce normalizing flow to achieve personalization from the parameter posterior perspective and theoretically analyze the impact of normalizing flow on out-of-distribution (OOD) detection for Bayesian neural networks. Finally, we evaluated our approach on heterogeneous datasets, and the experimental results indicate that the new algorithm not only improves accuracy but also outperforms the baseline significantly in OOD detection due to the reliable output of the Bayesian approach.

With the rise of increasingly powerful and user-facing NLP systems, there is growing interest in assessing whether they have a good representation of uncertainty by evaluating the quality of their predictive distribution over outcomes. We identify two main perspectives that drive starkly different evaluation protocols. The first treats predictive probability as an indication of model confidence; the second as an indication of human label variation. We discuss their merits and limitations, and take the position that both are crucial for trustworthy and fair NLP systems, but that exploiting a single predictive distribution is limiting. We recommend tools and highlight exciting directions towards models with disentangled representations of uncertainty about predictions and uncertainty about human labels.

Statistical heterogeneity of clients' local data is an important characteristic in federated learning, motivating personalized algorithms tailored to the local data statistics. Though there has been a plethora of algorithms proposed for personalized supervised learning, discovering the structure of local data through personalized unsupervised learning is less explored. We initiate a systematic study of such personalized unsupervised learning by developing algorithms based on optimization criteria inspired by a hierarchical Bayesian statistical framework. We develop adaptive algorithms that discover the balance between using limited local data and collaborative information. We do this in the context of two unsupervised learning tasks: personalized dimensionality reduction and personalized diffusion models. We develop convergence analyses for our adaptive algorithms which illustrate the dependence on problem parameters (e.g., heterogeneity, local sample size). We also develop a theoretical framework for personalized diffusion models, which shows the benefits of collaboration even under heterogeneity. We finally evaluate our proposed algorithms using synthetic and real data, demonstrating the effective sample amplification for personalized tasks, induced through collaboration, despite data heterogeneity.

Granger causality has been widely used in various application domains to capture lead-lag relationships amongst the components of complex dynamical systems, and the focus in extant literature has been on a single dynamical system. In certain applications in macroeconomics and neuroscience, one has access to data from a collection of related such systems, wherein the modeling task of interest is to extract the shared common structure that is embedded across them, as well as to identify the idiosyncrasies within individual ones. This paper introduces a Variational Autoencoder (VAE) based framework that jointly learns Granger-causal relationships amongst components in a collection of related-yet-heterogeneous dynamical systems, and handles the aforementioned task in a principled way. The performance of the proposed framework is evaluated on several synthetic data settings and benchmarked against existing approaches designed for individual system learning. The method is further illustrated on a real dataset involving time series data from a neurophysiological experiment and produces interpretable results.