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In biomedical research, computational methods have become indispensable and their use is increasing, making the efficient allocation of computing resources paramount. Practitioners routinely allocate resources far in excess of what is required for batch processing jobs, leading to not just inflated wait times and costs, but also unnecessary carbon emissions. This is not without reason however, as accurately determining resource needs is complex, affected by the nature of tools, data size, and analysis parameters, especially on popular servers that handle numerous jobs. The Galaxy platform, a web-based hub for biomedical analysis used globally by scientists, exemplifies this challenge. Serving nearly half a million registered users and managing around 2 million monthly jobs, Galaxy's growth outpaces the resources at its disposal. This is necessitating smarter resource utilization. To address this, we have developed a tool named Total Perspective Vortex (TPV) - a software package that right-sizes resource allocations for each job. TPV is able to dynamically set resource requirements for individual jobs and perform meta-scheduling across heterogeneous resources. It also includes a first-ever community-curated database of default resource requirements for nearly 1,000 popular bioinformatics tools. Deployments in Galaxy Australia and Europe demonstrate its effectiveness with meta-scheduling user jobs and an improved experience for systems administrators managing Galaxy servers.

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這個新版本的工具會議系列恢復了從1989年到2012年的50個會議的傳統。工具最初是“面向對象語言和系統的技術”,后來發展到包括軟件技術的所有創新方面。今天許多最重要的軟件概念都是在這里首次引入的。2019年TOOLS 50+1在俄羅斯喀山附近舉行,以同樣的創新精神、對所有與軟件相關的事物的熱情、科學穩健性和行業適用性的結合以及歡迎該領域所有趨勢和社區的開放態度,延續了該系列。 官網鏈接: · Learning · Weight · Extensibility · EASE ·
2024 年 1 月 25 日

Emotion recognition in conversation (ERC) has emerged as a research hotspot in domains such as conversational robots and question-answer systems. How to efficiently and adequately retrieve contextual emotional cues has been one of the key challenges in the ERC task. Existing efforts do not fully model the context and employ complex network structures, resulting in limited performance gains. In this paper, we propose a novel emotion recognition network based on curriculum learning strategy (ERNetCL). The proposed ERNetCL primarily consists of temporal encoder (TE), spatial encoder (SE), and curriculum learning (CL) loss. We utilize TE and SE to combine the strengths of previous methods in a simplistic manner to efficiently capture temporal and spatial contextual information in the conversation. To ease the harmful influence resulting from emotion shift and simulate the way humans learn curriculum from easy to hard, we apply the idea of CL to the ERC task to progressively optimize the network parameters. At the beginning of training, we assign lower learning weights to difficult samples. As the epoch increases, the learning weights for these samples are gradually raised. Extensive experiments on four datasets exhibit that our proposed method is effective and dramatically beats other baseline models.

In proof-theoretic semantics, meaning is based on inference. It may seen as the mathematical expression of the inferentialist interpretation of logic. Much recent work has focused on base-extension semantics, in which the validity of formulas is given by an inductive definition generated by provability in a `base' of atomic rules. Base-extension semantics for classical and intuitionistic propositional logic have been explored by several authors. In this paper, we develop base-extension semantics for the classical propositional modal systems K, KT , K4, and S4, with $\square$ as the primary modal operator. We establish appropriate soundness and completeness theorems and establish the duality between $\square$ and a natural presentation of $\lozenge$. We also show that our semantics is in its current form not complete with respect to euclidean modal logics. Our formulation makes essential use of relational structures on bases.

We propose a decoder-only language model, VoxtLM, that can perform four tasks: speech recognition, speech synthesis, text generation, and speech continuation. VoxtLM integrates text vocabulary with discrete speech tokens from self-supervised speech features and uses special tokens to enable multitask learning. Compared to a single-task model, VoxtLM exhibits a significant improvement in speech synthesis, with improvements in both speech intelligibility from 28.9 to 5.6 and objective quality from 2.68 to 3.90. VoxtLM also improves speech generation and speech recognition performance over the single-task counterpart. Further, VoxtLM is trained with publicly available data and training recipes and model checkpoints are open-sourced to make fully reproducible work.

In the rapidly evolving field of AI research, foundational models like BERT and GPT have significantly advanced language and vision tasks. The advent of pretrain-prompting models such as ChatGPT and Segmentation Anything Model (SAM) has further revolutionized image segmentation. However, their applications in specialized areas, particularly in nuclei segmentation within medical imaging, reveal a key challenge: the generation of high-quality, informative prompts is as crucial as applying state-of-the-art (SOTA) fine-tuning techniques on foundation models. To address this, we introduce Segment Any Cell (SAC), an innovative framework that enhances SAM specifically for nuclei segmentation. SAC integrates a Low-Rank Adaptation (LoRA) within the attention layer of the Transformer to improve the fine-tuning process, outperforming existing SOTA methods. It also introduces an innovative auto-prompt generator that produces effective prompts to guide segmentation, a critical factor in handling the complexities of nuclei segmentation in biomedical imaging. Our extensive experiments demonstrate the superiority of SAC in nuclei segmentation tasks, proving its effectiveness as a tool for pathologists and researchers. Our contributions include a novel prompt generation strategy, automated adaptability for diverse segmentation tasks, the innovative application of Low-Rank Attention Adaptation in SAM, and a versatile framework for semantic segmentation challenges.

In many scientific disciplines, the features of interest cannot be observed directly, so must instead be inferred from observed behaviour. Latent variable analyses are increasingly employed to systematise these inferences, and Principal Components Analysis (PCA) is perhaps the simplest and most popular of these methods. Here, we examine how the assumptions that we are prepared to entertain, about the latent variable system, mediate the likelihood that PCA-derived components will capture the true sources of variance underlying data. As expected, we find that this likelihood is excellent in the best case, and robust to empirically reasonable levels of measurement noise, but best-case performance is also: (a) not robust to violations of the method's more prominent assumptions, of linearity and orthogonality; and also (b) requires that other subtler assumptions be made, such as that the latent variables should have varying importance, and that weights relating latent variables to observed data have zero mean. Neither variance explained, nor replication in independent samples, could reliably predict which (if any) PCA-derived components will capture true sources of variance in data. We conclude by describing a procedure to fit these inferences more directly to empirical data, and use it to find that components derived via PCA from two different empirical neuropsychological datasets, are less likely to have meaningful referents in the brain than we hoped.

Imitation learning, in which learning is performed by demonstration, has been studied and advanced for sequential decision-making tasks in which a reward function is not predefined. However, imitation learning methods still require numerous expert demonstration samples to successfully imitate an expert's behavior. To improve sample efficiency, we utilize self-supervised representation learning, which can generate vast training signals from the given data. In this study, we propose a self-supervised representation-based adversarial imitation learning method to learn state and action representations that are robust to diverse distortions and temporally predictive, on non-image control tasks. In particular, in comparison with existing self-supervised learning methods for tabular data, we propose a different corruption method for state and action representations that is robust to diverse distortions. We theoretically and empirically observe that making an informative feature manifold with less sample complexity significantly improves the performance of imitation learning. The proposed method shows a 39% relative improvement over existing adversarial imitation learning methods on MuJoCo in a setting limited to 100 expert state-action pairs. Moreover, we conduct comprehensive ablations and additional experiments using demonstrations with varying optimality to provide insights into a range of factors.

Deep neural network based recommendation systems have achieved great success as information filtering techniques in recent years. However, since model training from scratch requires sufficient data, deep learning-based recommendation methods still face the bottlenecks of insufficient data and computational inefficiency. Meta-learning, as an emerging paradigm that learns to improve the learning efficiency and generalization ability of algorithms, has shown its strength in tackling the data sparsity issue. Recently, a growing number of studies on deep meta-learning based recommenddation systems have emerged for improving the performance under recommendation scenarios where available data is limited, e.g. user cold-start and item cold-start. Therefore, this survey provides a timely and comprehensive overview of current deep meta-learning based recommendation methods. Specifically, we propose a taxonomy to discuss existing methods according to recommendation scenarios, meta-learning techniques, and meta-knowledge representations, which could provide the design space for meta-learning based recommendation methods. For each recommendation scenario, we further discuss technical details about how existing methods apply meta-learning to improve the generalization ability of recommendation models. Finally, we also point out several limitations in current research and highlight some promising directions for future research in this area.

For languages with no annotated resources, transferring knowledge from rich-resource languages is an effective solution for named entity recognition (NER). While all existing methods directly transfer from source-learned model to a target language, in this paper, we propose to fine-tune the learned model with a few similar examples given a test case, which could benefit the prediction by leveraging the structural and semantic information conveyed in such similar examples. To this end, we present a meta-learning algorithm to find a good model parameter initialization that could fast adapt to the given test case and propose to construct multiple pseudo-NER tasks for meta-training by computing sentence similarities. To further improve the model's generalization ability across different languages, we introduce a masking scheme and augment the loss function with an additional maximum term during meta-training. We conduct extensive experiments on cross-lingual named entity recognition with minimal resources over five target languages. The results show that our approach significantly outperforms existing state-of-the-art methods across the board.

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.

Recently, ensemble has been applied to deep metric learning to yield state-of-the-art results. Deep metric learning aims to learn deep neural networks for feature embeddings, distances of which satisfy given constraint. In deep metric learning, ensemble takes average of distances learned by multiple learners. As one important aspect of ensemble, the learners should be diverse in their feature embeddings. To this end, we propose an attention-based ensemble, which uses multiple attention masks, so that each learner can attend to different parts of the object. We also propose a divergence loss, which encourages diversity among the learners. The proposed method is applied to the standard benchmarks of deep metric learning and experimental results show that it outperforms the state-of-the-art methods by a significant margin on image retrieval tasks.

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