Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort and domain expertise. In this paper, we propose a novel structural representation method for phylogenetic inference based on learnable topological features. By combining the raw node features that minimize the Dirichlet energy with modern graph representation learning techniques, our learnable topological features can provide efficient structural information of phylogenetic trees that automatically adapts to different downstream tasks without requiring domain expertise. We demonstrate the effectiveness and efficiency of our method on a simulated data tree probability estimation task and a benchmark of challenging real data variational Bayesian phylogenetic inference problems. Phylogenetics is an important discipline of computational biology where the goal is to identify the evolutionary history and relationships among individuals or groups of biological entities. In statistical approaches to phylogenetics, this has been formulated as an inference problem on hypotheses of shared history, i.e., phylogenetic trees, based on observed sequence data (e.g., DNA, RNA, or protein sequences) under a model of evolution.

There are many libraries in python available for making charts from the data. By which you can create charts and derive underlying information from the data. Plotly and Matplotlib are two of the libraries for it. Let's see the comparison between Plotly vs Matplotlib and see which is best for performing the best data visualization in python. Matplotlib is the library for plotting static visualizations in Python.

Deep recommender systems (DRS) are critical for current commercial online service providers, which address the issue of information overload by recommending items that are tailored to the user's interests and preferences. They have unprecedented feature representations effectiveness and the capacity of modeling the non-linear relationships between users and items. Despite their advancements, DRS models, like other deep learning models, employ sophisticated neural network architectures and other vital components that are typically designed and tuned by human experts. This article will give a comprehensive summary of automated machine learning (AutoML) for developing DRS models. We first provide an overview of AutoML for DRS models and the related techniques. Then we discuss the state-of-the-art AutoML approaches that automate the feature selection, feature embeddings, feature interactions, and model training in DRS. We point out that the existing AutoML-based recommender systems are developing to a multi-component joint search with abstract search space and efficient search algorithm. Finally, we discuss appealing research directions and summarize the survey.

We introduce a Bayesian perspective for the structured matrix factorization problem. The proposed framework provides a probabilistic interpretation for existing geometric methods based on determinant minimization. We model input data vectors as linear transformations of latent vectors drawn from a distribution uniform over a particular domain reflecting structural assumptions, such as the probability simplex in Nonnegative Matrix Factorization and polytopes in Polytopic Matrix Factorization. We represent the rows of the linear transformation matrix as vectors generated independently from a normal distribution whose covariance matrix is inverse Wishart distributed. We show that the corresponding maximum a posteriori estimation problem boils down to the robust determinant minimization approach for structured matrix factorization, providing insights about parameter selections and potential algorithmic extensions.

Memes have gained popularity as a means to share visual ideas through the Internet and social media by mixing text, images and videos, often for humorous purposes. Research enabling automated analysis of memes has gained attention in recent years, including among others the task of classifying the emotion expressed in memes. In this paper, we propose a novel model, cluster-based deep ensemble learning (CDEL), for emotion classification in memes. CDEL is a hybrid model that leverages the benefits of a deep learning model in combination with a clustering algorithm, which enhances the model with additional information after clustering memes with similar facial features. We evaluate the performance of CDEL on a benchmark dataset for emotion classification, proving its effectiveness by outperforming a wide range of baseline models and achieving state-of-the-art performance. Further evaluation through ablated models demonstrates the effectiveness of the different components of CDEL.

Knowledge distillation has been widely adopted in a variety of tasks and has achieved remarkable successes. Since its inception, many researchers have been intrigued by the dark knowledge hidden in the outputs of the teacher model. Recently, a study has demonstrated that knowledge distillation and label smoothing can be unified as learning from soft labels. Consequently, how to measure the effectiveness of the soft labels becomes an important question. Most existing theories have stringent constraints on the teacher model or data distribution, and many assumptions imply that the soft labels are close to the ground-truth labels. This paper studies whether biased soft labels are still effective. We present two more comprehensive indicators to measure the effectiveness of such soft labels. Based on the two indicators, we give sufficient conditions to ensure biased soft label based learners are classifier-consistent and ERM learnable. The theory is applied to three weakly-supervised frameworks. Experimental results validate that biased soft labels can also teach good students, which corroborates the soundness of the theory.

This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they can be instructed by prompts to solve new tasks without any fine-tuning. Moreover, they can be applied to a wide range of different media and problem domains, ranging from image and video processing to robot control learning. Because they provide a blueprint for solving many tasks in artificial intelligence, they have been called Foundation Models. After a brief introduction to basic NLP models the main pre-trained language models BERT, GPT and sequence-to-sequence transformer are described, as well as the concepts of self-attention and context-sensitive embedding. Then, different approaches to improving these models are discussed, such as expanding the pre-training criteria, increasing the length of input texts, or including extra knowledge. An overview of the best-performing models for about twenty application areas is then presented, e.g., question answering, translation, story generation, dialog systems, generating images from text, etc. For each application area, the strengths and weaknesses of current models are discussed, and an outlook on further developments is given. In addition, links are provided to freely available program code. A concluding chapter summarizes the economic opportunities, mitigation of risks, and potential developments of AI.

Personalized prediction of responses for individual entities caused by external drivers is vital across many disciplines. Recent machine learning (ML) advances have led to new state-of-the-art response prediction models. Models built at a population level often lead to sub-optimal performance in many personalized prediction settings due to heterogeneity in data across entities (tasks). In personalized prediction, the goal is to incorporate inherent characteristics of different entities to improve prediction performance. In this survey, we focus on the recent developments in the ML community for such entity-aware modeling approaches. ML algorithms often modulate the network using these entity characteristics when they are readily available. However, these entity characteristics are not readily available in many real-world scenarios, and different ML methods have been proposed to infer these characteristics from the data. In this survey, we have organized the current literature on entity-aware modeling based on the availability of these characteristics as well as the amount of training data. We highlight how recent innovations in other disciplines, such as uncertainty quantification, fairness, and knowledge-guided machine learning, can improve entity-aware modeling.

In deep active learning, it is especially important to choose multiple examples to markup at each step to work efficiently, especially on large datasets. At the same time, existing solutions to this problem in the Bayesian setup, such as BatchBALD, have significant limitations in selecting a large number of examples, associated with the exponential complexity of computing mutual information for joint random variables. We, therefore, present the Large BatchBALD algorithm, which gives a well-grounded approximation to the BatchBALD method that aims to achieve comparable quality while being more computationally efficient. We provide a complexity analysis of the algorithm, showing a reduction in computation time, especially for large batches. Furthermore, we present an extensive set of experimental results on image and text data, both on toy datasets and larger ones such as CIFAR-100.

This paper describes the participation of our NUAA-QMUL-AIIT team in the Memotion 3 shared task on meme emotion analysis. We propose a novel multi-modal fusion method, Squeeze-and-Excitation Fusion (SEFusion), and embed it into our system for emotion classification in memes. SEFusion is a simple fusion method that employs fully connected layers, reshaping, and matrix multiplication. SEFusion learns a weight for each modality and then applies it to its own modality feature. We evaluate the performance of our system on the three Memotion 3 sub-tasks. Among all participating systems in this Memotion 3 shared task, our system ranked first on task A, fifth on task B, and second on task C. Our proposed SEFusion provides the flexibility to fuse any features from different modalities.