Species distribution modeling is a highly versatile tool for understanding the intricate relationship between environmental conditions and species occurrences. However, the available data often lacks information on confirmed species absence and is limited to opportunistically sampled, presence-only observations. To overcome this limitation, a common approach is to employ pseudo-absences, which are specific geographic locations designated as negative samples. While pseudo-absences are well-established for single-species distribution models, their application in the context of multi-species neural networks remains underexplored. Notably, the significant class imbalance between species presences and pseudo-absences is often left unaddressed. Moreover, the existence of different types of pseudo-absences (e.g., random and target-group background points) adds complexity to the selection process. Determining the optimal combination of pseudo-absences types is difficult and depends on the characteristics of the data, particularly considering that certain types of pseudo-absences can be used to mitigate geographic biases. In this paper, we demonstrate that these challenges can be effectively tackled by integrating pseudo-absences in the training of multi-species neural networks through modifications to the loss function. This adjustment involves assigning different weights to the distinct terms of the loss function, thereby addressing both the class imbalance and the choice of pseudo-absence types. Additionally, we propose a strategy to set these loss weights using spatial block cross-validation with presence-only data. We evaluate our approach using a benchmark dataset containing independent presence-absence data from six different regions and report improved results when compared to competing approaches.

Self-supervised representation learning methods have achieved significant success in computer vision and natural language processing, where data samples exhibit explicit spatial or semantic dependencies. However, applying these methods to tabular data is challenging due to the less pronounced dependencies among data samples. In this paper, we address this limitation by introducing SwitchTab, a novel self-supervised method specifically designed to capture latent dependencies in tabular data. SwitchTab leverages an asymmetric encoder-decoder framework to decouple mutual and salient features among data pairs, resulting in more representative embeddings. These embeddings, in turn, contribute to better decision boundaries and lead to improved results in downstream tasks. To validate the effectiveness of SwitchTab, we conduct extensive experiments across various domains involving tabular data. The results showcase superior performance in end-to-end prediction tasks with fine-tuning. Moreover, we demonstrate that pre-trained salient embeddings can be utilized as plug-and-play features to enhance the performance of various traditional classification methods (e.g., Logistic Regression, XGBoost, etc.). Lastly, we highlight the capability of SwitchTab to create explainable representations through visualization of decoupled mutual and salient features in the latent space.

While alignment algorithms are now commonly used to tune pre-trained language models towards a user's preferences, we lack explanations for the underlying mechanisms in which models become ``aligned'', thus making it difficult to explain phenomena like jailbreaks. In this work we study a popular algorithm, direct preference optimization (DPO), and the mechanisms by which it reduces toxicity. Namely, we first study how toxicity is represented and elicited in a pre-trained language model, GPT2-medium. We then apply DPO with a carefully crafted pairwise dataset to reduce toxicity. We examine how the resulting model averts toxic outputs, and find that capabilities learned from pre-training are not removed, but rather bypassed. We use this insight to demonstrate a simple method to un-align the model, reverting it back to its toxic behavior.

This paper presents instruct-imagen, a model that tackles heterogeneous image generation tasks and generalizes across unseen tasks. We introduce *multi-modal instruction* for image generation, a task representation articulating a range of generation intents with precision. It uses natural language to amalgamate disparate modalities (e.g., text, edge, style, subject, etc.), such that abundant generation intents can be standardized in a uniform format. We then build instruct-imagen by fine-tuning a pre-trained text-to-image diffusion model with a two-stage framework. First, we adapt the model using the retrieval-augmented training, to enhance model's capabilities to ground its generation on external multimodal context. Subsequently, we fine-tune the adapted model on diverse image generation tasks that requires vision-language understanding (e.g., subject-driven generation, etc.), each paired with a multi-modal instruction encapsulating the task's essence. Human evaluation on various image generation datasets reveals that instruct-imagen matches or surpasses prior task-specific models in-domain and demonstrates promising generalization to unseen and more complex tasks.

According to the World Health Organization (WHO), air pollution kills seven million people every year. Outdoor air pollution is a major environmental health problem affecting low, middle, and high-income countries. In the past few years, the research community has explored IoT-enabled machine learning applications for outdoor air pollution prediction. The general objective of this paper is to systematically review applications of machine learning and Internet of Things (IoT) for outdoor air pollution prediction and the combination of monitoring sensors and input features used. Two research questions were formulated for this review. 1086 publications were collected in the initial PRISMA stage. After the screening and eligibility phases, 37 papers were selected for inclusion. A cost-based analysis was conducted on the findings to highlight high-cost monitoring, low-cost IoT and hybrid enabled prediction. Three methods of prediction were identified: time series, feature-based and spatio-temporal. This review's findings identify major limitations in applications found in the literature, namely lack of coverage, lack of diversity of data and lack of inclusion of context-specific features. This review proposes directions for future research and underlines practical implications in healthcare, urban planning, global synergy and smart cities.

Effective collaboration requires groups to strategically regulate themselves to overcome challenges. Research has shown that groups may fail to regulate due to differences in members' perceptions of challenges which may benefit from external support. In this study, we investigated the potential of leveraging three distinct natural language processing models: an expert knowledge rule-based model, a supervised machine learning (ML) model and a Large Language model (LLM), in challenge detection and challenge dimension identification (cognitive, metacognitive, emotional and technical/other challenges) from student discourse, was investigated. The results show that the supervised ML and the LLM approaches performed considerably well in both tasks, in contrast to the rule-based approach, whose efficacy heavily relies on the engineered features by experts. The paper provides an extensive discussion of the three approaches' performance for automated detection and support of students' challenge moments in collaborative learning activities. It argues that, although LLMs provide many advantages, they are unlikely to be the panacea to issues of the detection and feedback provision of socially shared regulation of learning due to their lack of reliability, as well as issues of validity evaluation, privacy and confabulation. We conclude the paper with a discussion on additional considerations, including model transparency to explore feasible and meaningful analytical feedback for students and educators using LLMs.

In recent years, multi-parametric MRI has emerged as a powerful tool in the field of visual pathway (VP) segmentation Li et al. [2021]. By combining different imaging sequences, such as T1-weighted (T1-w) and fractional anisotropy (FA), researchers have been able to overcome the limitations of individual imaging sequences and gain a more comprehensive understanding of the VP. This can be a powerful tool in the diagnosis and treatment of various diseases affecting the visual system, including optic neuritis and optic nerve glioma. During the past years, deep learning (DL) approaches, such as convolutional neural networks (CNNs) and their variants, have shown significant advancements in multi-parametric MRI-based VP segmentation Li et al. [2021], Mansoor et al. [2016], Zhao et al. [2019], Xie et al. [2023a]. These methods can automatically learn hierarchical representations from the multi-parametric MR images and effectively capture the complementary characteristics. However, one of the major challenges in these DL-based methods is the laborious and time-consuming process of obtaining labeled training data Bai et al. [2023], Yu et al. [2019]. Manual annotation is prone to errors and requires significant expertise, making it impractical for large-scale studies. Therefore, there is a critical need to develop algorithms that can achieve accurate segmentation performance even in situations with limited labeled samples.

Large Language Models (LLMs) have exhibited remarkable capabilities in understanding and interacting with natural language across various sectors. However, their effectiveness is limited in specialized areas requiring high accuracy, such as plant science, due to a lack of specific expertise in these fields. This paper introduces PLLaMa, an open-source language model that evolved from LLaMa-2. It's enhanced with a comprehensive database, comprising more than 1.5 million scholarly articles in plant science. This development significantly enriches PLLaMa with extensive knowledge and proficiency in plant and agricultural sciences. Our initial tests, involving specific datasets related to plants and agriculture, show that PLLaMa substantially improves its understanding of plant science-related topics. Moreover, we have formed an international panel of professionals, including plant scientists, agricultural engineers, and plant breeders. This team plays a crucial role in verifying the accuracy of PLLaMa's responses to various academic inquiries, ensuring its effective and reliable application in the field. To support further research and development, we have made the model's checkpoints and source codes accessible to the scientific community. These resources are available for download at \url{https://github.com/Xianjun-Yang/PLLaMa}.

We present a deep learning model to automatically generate computer models of the human heart from patient imaging data with an emphasis on its capability to generate thin-walled cardiac structures. Our method works by deforming a template mesh to fit the cardiac structures to the given image. Compared with prior deep learning methods that adopted this approach, our framework is designed to minimize mesh self-penetration, which typically arises when deforming surface meshes separated by small distances. We achieve this by using a two-stage diffeomorphic deformation process along with a novel loss function derived from the kinematics of motion that penalizes surface contact and interpenetration. Our model demonstrates comparable accuracy with state-of-the-art methods while additionally producing meshes free of self-intersections. The resultant meshes are readily usable in physics based simulation, minimizing the need for post-processing and cleanup.

Accurate segmentation of clustered microcalcifications in mammography is crucial for the diagnosis and treatment of breast cancer. Despite exhibiting expert-level accuracy, recent deep learning advancements in medical image segmentation provide insufficient contribution to practical applications, due to the domain shift resulting from differences in patient postures, individual gland density, and imaging modalities of mammography etc. In this paper, a novel framework named MLN-net, which can accurately segment multi-source images using only single source images, is proposed for clustered microcalcification segmentation. We first propose a source domain image augmentation method to generate multi-source images, leading to improved generalization. And a structure of multiple layer normalization (LN) layers is used to construct the segmentation network, which can be found efficient for clustered microcalcification segmentation in different domains. Additionally, a branch selection strategy is designed for measuring the similarity of the source domain data and the target domain data. To validate the proposed MLN-net, extensive analyses including ablation experiments are performed, comparison of 12 baseline methods. Extensive experiments validate the effectiveness of MLN-net in segmenting clustered microcalcifications from different domains and the its segmentation accuracy surpasses state-of-the-art methods. Code will be available at https://github.com/yezanting/MLN-NET-VERSON1.