Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with pre-defined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.

Pretrained large language models have revolutionized many applications but still face challenges related to cultural bias and a lack of cultural commonsense knowledge crucial for guiding cross-culture communication and interactions. Recognizing the shortcomings of existing methods in capturing the diverse and rich cultures across the world, this paper introduces a novel approach for massively multicultural knowledge acquisition. Specifically, our method strategically navigates from densely informative Wikipedia documents on cultural topics to an extensive network of linked pages. Leveraging this valuable source of data collection, we construct the CultureAtlas dataset, which covers a wide range of sub-country level geographical regions and ethnolinguistic groups, with data cleaning and preprocessing to ensure textual assertion sentence self-containment, as well as fine-grained cultural profile information extraction. Our dataset not only facilitates the evaluation of language model performance in culturally diverse contexts but also serves as a foundational tool for the development of culturally sensitive and aware language models. Our work marks an important step towards deeper understanding and bridging the gaps of cultural disparities in AI, to promote a more inclusive and balanced representation of global cultures in the digital domain.

Creating content for a specific identity (ID) has shown significant interest in the field of generative models. In the field of text-to-image generation (T2I), subject-driven content generation has achieved great progress with the ID in the images controllable. However, extending it to video generation is not well explored. In this work, we propose a simple yet effective subject identity controllable video generation framework, termed Video Custom Diffusion (VCD). With a specified subject ID defined by a few images, VCD reinforces the identity information extraction and injects frame-wise correlation at the initialization stage for stable video outputs with identity preserved to a large extent. To achieve this, we propose three novel components that are essential for high-quality ID preservation: 1) an ID module trained with the cropped identity by prompt-to-segmentation to disentangle the ID information and the background noise for more accurate ID token learning; 2) a text-to-video (T2V) VCD module with 3D Gaussian Noise Prior for better inter-frame consistency and 3) video-to-video (V2V) Face VCD and Tiled VCD modules to deblur the face and upscale the video for higher resolution. Despite its simplicity, we conducted extensive experiments to verify that VCD is able to generate stable and high-quality videos with better ID over the selected strong baselines. Besides, due to the transferability of the ID module, VCD is also working well with finetuned text-to-image models available publically, further improving its usability. The codes are available at https://github.com/Zhen-Dong/Magic-Me.

We present PECMAE, an interpretable model for music audio classification based on prototype learning. Our model is based on a previous method, APNet, which jointly learns an autoencoder and a prototypical network. Instead, we propose to decouple both training processes. This enables us to leverage existing self-supervised autoencoders pre-trained on much larger data (EnCodecMAE), providing representations with better generalization. APNet allows prototypes' reconstruction to waveforms for interpretability relying on the nearest training data samples. In contrast, we explore using a diffusion decoder that allows reconstruction without such dependency. We evaluate our method on datasets for music instrument classification (Medley-Solos-DB) and genre recognition (GTZAN and a larger in-house dataset), the latter being a more challenging task not addressed with prototypical networks before. We find that the prototype-based models preserve most of the performance achieved with the autoencoder embeddings, while the sonification of prototypes benefits understanding the behavior of the classifier.

Harmful algal blooms (HABs) are episodes of high concentrations of algae that are potentially toxic for human consumption. Mollusc farming can be affected by HABs because, as filter feeders, they can accumulate high concentrations of marine biotoxins in their tissues. To avoid the risk to human consumption, harvesting is prohibited when toxicity is detected. At present, the closure of production areas is based on expert knowledge and the existence of a predictive model would help when conditions are complex and sampling is not possible. Although the concentration of toxin in meat is the method most commonly used by experts in the control of shellfish production areas, it is rarely used as a target by automatic prediction models. This is largely due to the irregularity of the data due to the established sampling programs. As an alternative, the activity status of production areas has been proposed as a target variable based on whether mollusc meat has a toxicity level below or above the legal limit. This new option is the most similar to the actual functioning of the control of shellfish production areas. For this purpose, we have made a comparison between hybrid machine learning models like Neural-Network-Adding Bootstrap (BAGNET) and Discriminative Nearest Neighbor Classification (SVM-KNN) when estimating the state of production areas. The study has been carried out in several estuaries with different levels of complexity in the episodes of algal blooms to demonstrate the generalization capacity of the models in bloom detection. As a result, we could observe that, with an average recall value of 93.41% and without dropping below 90% in any of the estuaries, BAGNET outperforms the other models both in terms of results and robustness.

Despite showing increasingly human-like abilities, large language models (LLMs) often struggle with factual inaccuracies, i.e. "hallucinations", even when they hold relevant knowledge. To address these hallucinations, current approaches typically necessitate high-quality human factuality annotations. In this work, we explore Self-Alignment for Factuality, where we leverage the self-evaluation capability of an LLM to provide training signals that steer the model towards factuality. Specifically, we incorporate Self-Eval, a self-evaluation component, to prompt an LLM to validate the factuality of its own generated responses solely based on its internal knowledge. Additionally, we design Self-Knowledge Tuning (SK-Tuning) to augment the LLM's self-evaluation ability by improving the model's confidence estimation and calibration. We then utilize these self-annotated responses to fine-tune the model via Direct Preference Optimization algorithm. We show that the proposed self-alignment approach substantially enhances factual accuracy over Llama family models across three key knowledge-intensive tasks on TruthfulQA and BioGEN.

Mussel farming is one of the most important aquaculture industries. The main risk to mussel farming is harmful algal blooms (HABs), which pose a risk to human consumption. In Galicia, the Spanish main producer of cultivated mussels, the opening and closing of the production areas is controlled by a monitoring program. In addition to the closures resulting from the presence of toxicity exceeding the legal threshold, in the absence of a confirmatory sampling and the existence of risk factors, precautionary closures may be applied. These decisions are made by experts without the support or formalisation of the experience on which they are based. Therefore, this work proposes a predictive model capable of supporting the application of precautionary closures. Achieving sensitivity, accuracy and kappa index values of 97.34%, 91.83% and 0.75 respectively, the kNN algorithm has provided the best results. This allows the creation of a system capable of helping in complex situations where forecast errors are more common.

Temporal graph neural networks Tgnn have exhibited state-of-art performance in future-link prediction tasks. Training of these TGNNs is enumerated by uniform random sampling based unsupervised loss. During training, in the context of a positive example, the loss is computed over uninformative negatives, which introduces redundancy and sub-optimal performance. In this paper, we propose modified unsupervised learning of Tgnn, by replacing the uniform negative sampling with importance-based negative sampling. We theoretically motivate and define the dynamically computed distribution for a sampling of negative examples. Finally, using empirical evaluations over three real-world datasets, we show that Tgnn trained using loss based on proposed negative sampling provides consistent superior performance.

Mega-constellations of small satellites have evolved into a source of massive amount of valuable data. To manage this data efficiently, on-board federated learning (FL) enables satellites to train a machine learning (ML) model collaboratively without having to share the raw data. This paper introduces a scheme for scheduling on-board FL for constellations connected with intra-orbit inter-satellite links. The proposed scheme utilizes the predictable visibility pattern between satellites and ground station (GS), both at the individual satellite level and cumulatively within the entire orbit, to mitigate intermittent connectivity and best use of available time. To this end, two distinct schedulers are employed: one for coordinating the FL procedures among orbits, and the other for controlling those within each orbit. These two schedulers cooperatively determine the appropriate time to perform global updates in GS and then allocate suitable duration to satellites within each orbit for local training, proportional to usable time until next global update. This scheme leads to improved test accuracy within a shorter time.

Neural networks have proven to be a highly effective tool for solving complex problems in many areas of life. Recently, their importance and practical usability have further been reinforced with the advent of deep learning. One of the important conditions for the success of neural networks is the choice of an appropriate activation function introducing non-linearity into the model. Many types of these functions have been proposed in the literature in the past, but there is no single comprehensive source containing their exhaustive overview. The absence of this overview, even in our experience, leads to redundancy and the unintentional rediscovery of already existing activation functions. To bridge this gap, our paper presents an extensive survey involving 400 activation functions, which is several times larger in scale than previous surveys. Our comprehensive compilation also references these surveys; however, its main goal is to provide the most comprehensive overview and systematization of previously published activation functions with links to their original sources. The secondary aim is to update the current understanding of this family of functions.