Node classification is the task of predicting the labels of unlabeled nodes in a graph. State-of-the-art methods based on graph neural networks achieve excellent performance when all labels are available during training. But in real-life, models are often applied on data with new classes, which can lead to massive misclassification and thus significantly degrade performance. Hence, developing open-set classification methods is crucial to determine if a given sample belongs to a known class. Existing methods for open-set node classification generally use transductive learning with part or all of the features of real unseen class nodes to help with open-set classification. In this paper, we propose a novel generative open-set node classification method, i.e. $\mathcal{G}^2Pxy$, which follows a stricter inductive learning setting where no information about unknown classes is available during training and validation. Two kinds of proxy unknown nodes, inter-class unknown proxies and external unknown proxies are generated via mixup to efficiently anticipate the distribution of novel classes. Using the generated proxies, a closed-set classifier can be transformed into an open-set one, by augmenting it with an extra proxy classifier. Under the constraints of both cross entropy loss and complement entropy loss, $\mathcal{G}^2Pxy$ achieves superior effectiveness for unknown class detection and known class classification, which is validated by experiments on benchmark graph datasets. Moreover, $\mathcal{G}^2Pxy$ does not have specific requirement on the GNN architecture and shows good generalizations.

The evolutionary distance between two species is proportional to some (unknown) function of the time of divergence from their common ancestor. One way to estimate this time is by comparing the underlying macromolecular sequences that cascade the information of accumulated evolutionary changes across DNA RNA Proteins (sequence structure function). Since the introduction of the molecular evolutionary clock by Zuckerkandl and Pauling (1965) to perform phylogenetic studies, several statistical models have been proposed to estimate the divergence of extant sequences from common ancestors, and to correlate the estimates of time from other sources of information (e.g., fossil records) when they exist (Sarich and Wilson, 1967). Such divergence time estimates require reliable statistical models of DNA/RNA/Proteins macromolecules (Bromham and Penny, 2003). For protein amino acid sequences, several statistical models have been proposed to explain sequence variation as a function of time. The point accepted mutation (PAM) matrix of Dayhoff et al. (1978) was the first successful model to explain the mutability of amino acid sequences. PAM is a stochastic (Markov) matrix defined in PAM (time) units where PAM-1 is a Markov matrix that embodies a 1% expected change to the amino acids. Subsequent studies highlighted the importance of incorporating evolutionary time-dependent substitution and gap models as an elegant way to model the divergent relationships of proteins (Holmes, 1998; Gonnet et al., 1992). The recent approach of Sumanaweera et al. (2022) derives a unified statistical model for quantifying the evolution of pairs of protein sequences

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deeplearning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging. Cell segmentation is a fundamental task that is universally required for biological image analysis across a large number of different experimental settings and imaging modalities. For example, in multiplexed fluorescence image-based cancer microenvironment analysis, cell segmentation is the prerequisite for the identification of tumor sub-types, composition, and organization, which can lead to important biological insights [1]-[3]. However, the development of a universal and automatic cell segmentation technique continues to pose significant challenges due to the extensive diversity observed in microscopy images. This diversity arises from variations in cell origins, microscopy types, staining techniques, and cell morphologies. Recent advances [4], [5] have successfully demonstrated the feasibility of automatic and precise cellular segmentation for specific microscopy image types and cell types, such as fluorescence and mass spectrometry images [6], [7], differential interference contrast images of platelets [8], bacteria images [9] and yeast images [10], [11], but the selection of appropriate segmentation models remains a non-trivial task for non-expert users in conventional biology laboratories. Efforts have been made towards the development of generalized cell segmentation algorithms [9], [12], [13]. However, these algorithms were primarily trained using datasets consisting of gray-scale images and two-channel fluorescent images, lacking the necessary diversity to ensure robust generalization across a wide range of imaging modalities. For example, the segmentation models have struggled to perform effectively on RGB images, such as bone marrow aspirate slides stained with Jenner-Giemsa. Furthermore, these models often require manual selection of both the model type and the specific image channel to be segmented, posing challenges for biologists with limited computational expertise. Biomedical image data science competitions have emerged as an effective way to accelerate the development of cutting-edge algorithms [14], [15].

Code summarization aims to generate concise natural language descriptions for source code. The prevailing approaches adopt transformer-based encoder-decoder architectures, where the Abstract Syntax Tree (AST) of the source code is utilized for encoding structural information. However, ASTs are much longer than the corresponding source code, and existing methods ignore this size constraint by directly feeding the entire linearized AST into the encoders. This simplistic approach makes it challenging to extract truly valuable dependency relations from the overlong input sequence and leads to significant computational overhead due to self-attention applied to all nodes in the AST. To address this issue effectively and efficiently, we present a model, AST-MHSA that uses multi-head attention to extract the important semantic information from the AST. The model consists of two main components: an encoder and a decoder. The encoder takes as input the abstract syntax tree (AST) of the code and generates a sequence of hidden states. The decoder then takes these hidden states as input and generates a natural language summary of the code. The multi-head attention mechanism allows the model to learn different representations of the input code, which can be combined to generate a more comprehensive summary. The model is trained on a dataset of code and summaries, and the parameters of the model are optimized to minimize the loss between the generated summaries and the ground-truth summaries.

Automated medical report generation has become increasingly important in medical analysis. It can produce computer-aided diagnosis descriptions and thus significantly alleviate the doctors' work. Inspired by the huge success of neural machine translation and image captioning, various deep learning methods have been proposed for medical report generation. However, due to the inherent properties of medical data, including data imbalance and the length and correlation between report sequences, the generated reports by existing methods may exhibit linguistic fluency but lack adequate clinical accuracy. In this work, we propose an image-to-indicator hierarchical transformer (IIHT) framework for medical report generation. It consists of three modules, i.e., a classifier module, an indicator expansion module and a generator module. The classifier module first extracts image features from the input medical images and produces disease-related indicators with their corresponding states. The disease-related indicators are subsequently utilised as input for the indicator expansion module, incorporating the "data-text-data" strategy. The transformer-based generator then leverages these extracted features along with image features as auxiliary information to generate final reports. Furthermore, the proposed IIHT method is feasible for radiologists to modify disease indicators in real-world scenarios and integrate the operations into the indicator expansion module for fluent and accurate medical report generation. Extensive experiments and comparisons with state-of-the-art methods under various evaluation metrics demonstrate the great performance of the proposed method.

Large skew-t factor copula models are attractive for the modeling of financial data because they allow for asymmetric and extreme tail dependence. We show that the copula implicit in the skew-t distribution of Azzalini and Capitanio (2003) allows for a higher level of pairwise asymmetric dependence than two popular alternative skew-t copulas. Estimation of this copula in high dimensions is challenging, and we propose a fast and accurate Bayesian variational inference (VI) approach to do so. The method uses a conditionally Gaussian generative representation of the skew-t distribution to define an augmented posterior that can be approximated accurately. A fast stochastic gradient ascent algorithm is used to solve the variational optimization. The new methodology is used to estimate copula models for intraday returns from 2017 to 2021 on 93 U.S. equities. The copula captures substantial heterogeneity in asymmetric dependence over equity pairs, in addition to the variability in pairwise correlations. We show that intraday predictive densities from the skew-t copula are more accurate than from some other copula models, while portfolio selection strategies based on the estimated pairwise tail dependencies improve performance relative to the benchmark index.

Explainable AI has the potential to support more interactive and fluid co-creative AI systems which can creatively collaborate with people. To do this, creative AI models need to be amenable to debugging by offering eXplainable AI (XAI) features which are inspectable, understandable, and modifiable. However, currently there is very little XAI for the arts. In this work, we demonstrate how a latent variable model for music generation can be made more explainable; specifically we extend MeasureVAE which generates measures of music. We increase the explainability of the model by: i) using latent space regularisation to force some specific dimensions of the latent space to map to meaningful musical attributes, ii) providing a user interface feedback loop to allow people to adjust dimensions of the latent space and observe the results of these changes in real-time, iii) providing a visualisation of the musical attributes in the latent space to help people understand and predict the effect of changes to latent space dimensions. We suggest that in doing so we bridge the gap between the latent space and the generated musical outcomes in a meaningful way which makes the model and its outputs more explainable and more debuggable. The code repository can be found at: https://github.com/bbanar2/

Over the last decade, Q&A platforms have played a crucial role in how programmers seek help online. The emergence of ChatGPT, however, is causing a shift in this pattern. Despite ChatGPT's popularity, there hasn't been a thorough investigation into the quality and usability of its responses to software engineering queries. To address this gap, we undertook a comprehensive analysis of ChatGPT's replies to 517 questions from Stack Overflow (SO). We assessed the correctness, consistency, comprehensiveness, and conciseness of these responses. Additionally, we conducted an extensive linguistic analysis and a user study to gain insights into the linguistic and human aspects of ChatGPT's answers. Our examination revealed that 52% of ChatGPT's answers contain inaccuracies and 77% are verbose. Nevertheless, users still prefer ChatGPT's responses 39.34% of the time due to their comprehensiveness and articulate language style. These findings underscore the need for meticulous error correction in ChatGPT while also raising awareness among users about the potential risks associated with seemingly accurate answers.

Understanding code is challenging, especially when working in new and complex development environments. Code comments and documentation can help, but are typically scarce or hard to navigate. Large language models (LLMs) are revolutionizing the process of writing code. Can they do the same for helping understand it? In this study, we provide a first investigation of an LLM-based conversational UI built directly in the IDE that is geared towards code understanding. Our IDE plugin queries OpenAI's GPT-3.5 and GPT-4 models with four high-level requests without the user having to write explicit prompts: to explain a highlighted section of code, provide details of API calls used in the code, explain key domain-specific terms, and provide usage examples for an API. The plugin also allows for open-ended prompts, which are automatically contextualized to the LLM with the program being edited. We evaluate this system in a user study with 32 participants, which confirms that using our plugin can aid task completion more than web search. We additionally provide a thorough analysis of the ways developers use, and perceive the usefulness of, our system, among others finding that the usage and benefits differ significantly between students and professionals. We conclude that in-IDE prompt-less interaction with LLMs is a promising future direction for tool builders.

The 2023 World Scrabble Championship, held last month in Las Vegas, was an instant classic. The best-of-seven finals went the distance, with tense games, obscure words, strategic genius, and a Scrabble-record audience of 900 watching on Twitch. The winner was David Eldar, 33, of Melbourne, Australia, who defeated Harshan Lamabadusuriya, 44, a pediatrician who lives in Southmoor, England, to capture the $10,000 first prize. To reach the finals, they topped a field of 134 players from 29 countries--from Poland to Pakistan, Singapore to Sierra Leone--in a four-day, 32-game tournament. Game 6 of the finals was hailed by Scrabble experts as one of most exciting high-stakes games ever. I discussed it online with the two competitors. Our conversation has been edited and condensed for clarity. Note: The event used the international-English Scrabble dictionary, which includes substantially more words than the lexicon governing competitive play in North America. To avoid confusion, words acceptable only in the international word list are marked with a #. Stefan Fatsis: David, you trail three games to two and are up first in Game 6.