WildGraph: Realistic Graph-based Trajectory Generation for Wildlife

Trajectory generation is an important task in movement studies; it circumvents the privacy, ethical, and technical challenges of collecting real trajectories from the target population. In particular, real trajectories in the wildlife domain are scarce as a result of ethical and environmental constraints of the collection process. In this paper, we consider the problem of generating long-horizon trajectories, akin to wildlife migration, based on a small set of real samples. We propose a hierarchical approach to learn the global movement characteristics of the real dataset and recursively refine localized regions. Our solution, WildGraph, discretizes the geographic path into a prototype network of H3 (https://www.uber.com/blog/h3/) regions and leverages a recurrent variational auto-encoder to probabilistically generate paths over the regions, based on occupancy. WildGraph successfully generates realistic months-long trajectories using a sample size as small as 60. Experiments performed on two wildlife migration datasets demonstrate that our proposed method improves the generalization of the generated trajectories in comparison to existing work while achieving superior or comparable performance in several benchmark metrics. Our code is published on the following repository: \url{https://github.com/aliwister/wildgraph}.

PEaCE: A Chemistry-Oriented Dataset for Optical Character Recognition on Scientific Documents

Optical Character Recognition (OCR) is an established task with the objective of identifying the text present in an image. While many off-the-shelf OCR models exist, they are often trained for either scientific (e.g., formulae) or generic printed English text. Extracting text from chemistry publications requires an OCR model that is capable in both realms. Nougat, a recent tool, exhibits strong ability to parse academic documents, but is unable to parse tables in PubMed articles, which comprises a significant part of the academic community and is the focus of this work. To mitigate this gap, we present the Printed English and Chemical Equations (PEaCE) dataset, containing both synthetic and real-world records, and evaluate the efficacy of transformer-based OCR models when trained on this resource. Given that real-world records contain artifacts not present in synthetic records, we propose transformations that mimic such qualities. We perform a suite of experiments to explore the impact of patch size, multi-domain training, and our proposed transformations, ultimately finding that models with a small patch size trained on multiple domains using the proposed transformations yield the best performance. Our dataset and code is available at https://github.com/ZN1010/PEaCE.

Automated Multi-Task Learning for Joint Disease Prediction on Electronic Health Records

In the realm of big data and digital healthcare, Electronic Health Records (EHR) have become a rich source of information with the potential to improve patient care and medical research. In recent years, machine learning models have proliferated for analyzing EHR data to predict patients future health conditions. Among them, some studies advocate for multi-task learning (MTL) to jointly predict multiple target diseases for improving the prediction performance over single task learning. Nevertheless, current MTL frameworks for EHR data have significant limitations due to their heavy reliance on human experts to identify task groups for joint training and design model architectures. To reduce human intervention and improve the framework design, we propose an automated approach named AutoDP, which can search for the optimal configuration of task grouping and architectures simultaneously. To tackle the vast joint search space encompassing task combinations and architectures, we employ surrogate model-based optimization, enabling us to efficiently discover the optimal solution. Experimental results on real-world EHR data demonstrate the efficacy of the proposed AutoDP framework. It achieves significant performance improvements over both hand-crafted and automated state-of-the-art methods, also maintains a feasible search cost at the same time.

Leveraging External Knowledge Resources to Enable Domain-Specific Comprehension

Machine Reading Comprehension (MRC) has been a long-standing problem in NLP and, with the recent introduction of the BERT family of transformer based language models, it has come a long way to getting solved. Unfortunately, however, when BERT variants trained on general text corpora are applied to domain-specific text, their performance inevitably degrades on account of the domain shift i.e. genre/subject matter discrepancy between the training and downstream application data. Knowledge graphs act as reservoirs for either open or closed domain information and prior studies have shown that they can be used to improve the performance of general-purpose transformers in domain-specific applications. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from knowledge graphs with the embeddings spaces of pre-trained language models (LMs). We fuse the aligned embeddings with open-domain LMs BERT and RoBERTa, and fine-tune them for two MRC tasks namely span detection (COVID-QA) and multiple-choice questions (PubMedQA). On the COVID-QA dataset, we see that our approach allows these models to perform similar to their domain-specific counterparts, Bio/Sci-BERT, as evidenced by the Exact Match (EM) metric. With regards to PubMedQA, we observe an overall improvement in accuracy while the F1 stays relatively the same over the domain-specific models.

Milestones in Bengali Sentiment Analysis leveraging Transformer-models: Fundamentals, Challenges and Future Directions

Sentiment Analysis (SA) refers to the task of associating a view polarity (usually, positive, negative, or neutral; or even fine-grained such as slightly angry, sad, etc.) to a given text, essentially breaking it down to a supervised (since we have the view labels apriori) classification task. Although heavily studied in resource-rich languages such as English thus pushing the SOTA by leaps and bounds, owing to the arrival of the Transformer architecture, the same cannot be said for resource-poor languages such as Bengali (BN). For a language spoken by roughly 300 million people, the technology enabling them to run trials on their favored tongue is severely lacking. In this paper, we analyze the SOTA for SA in Bengali, particularly, Transformer-based models. We discuss available datasets, their drawbacks, the nuances associated with Bengali i.e. what makes this a challenging language to apply SA on, and finally provide insights for future direction to mitigate the limitations in the field.

WildGEN: Long-horizon Trajectory Generation for Wildlife

Trajectory generation is an important concern in pedestrian, vehicle, and wildlife movement studies. Generated trajectories help enrich the training corpus in relation to deep learning applications, and may be used to facilitate simulation tasks. This is especially significant in the wildlife domain, where the cost of obtaining additional real data can be prohibitively expensive, time-consuming, and bear ethical considerations. In this paper, we introduce WildGEN: a conceptual framework that addresses this challenge by employing a Variational Auto-encoders (VAEs) based method for the acquisition of movement characteristics exhibited by wild geese over a long horizon using a sparse set of truth samples. A subsequent post-processing step of the generated trajectories is performed based on smoothing filters to reduce excessive wandering. Our evaluation is conducted through visual inspection and the computation of the Hausdorff distance between the generated and real trajectories. In addition, we utilize the Pearson Correlation Coefficient as a way to measure how realistic the trajectories are based on the similarity of clusters evaluated on the generated and real trajectories.

FaMeSumm: Investigating and Improving Faithfulness of Medical Summarization

Summaries of medical text shall be faithful by being consistent and factual with source inputs, which is an important but understudied topic for safety and efficiency in healthcare. In this paper, we investigate and improve faithfulness in summarization on a broad range of medical summarization tasks. Our investigation reveals that current summarization models often produce unfaithful outputs for medical input text. We then introduce FaMeSumm, a framework to improve faithfulness by fine-tuning pre-trained language models based on medical knowledge. FaMeSumm performs contrastive learning on designed sets of faithful and unfaithful summaries, and it incorporates medical terms and their contexts to encourage faithful generation of medical terms. We conduct comprehensive experiments on three datasets in two languages: health question and radiology report summarization datasets in English, and a patient-doctor dialogue dataset in Chinese. Results demonstrate that FaMeSumm is flexible and effective by delivering consistent improvements over mainstream language models such as BART, T5, mT5, and PEGASUS, yielding state-of-the-art performances on metrics for faithfulness and general quality. Human evaluation by doctors also shows that FaMeSumm generates more faithful outputs. Our code is available at https://github.com/psunlpgroup/FaMeSumm .

Quality > Quantity: Synthetic Corpora from Foundation Models for Closed-Domain Extractive Question Answering

Domain adaptation, the process of training a model in one domain and applying it to another, has been extensively explored in machine learning. While training a domain-specific foundation model (FM) from scratch is an option, recent methods have focused on adapting pre-trained FMs for domain-specific tasks. However, our experiments reveal that either approach does not consistently achieve state-of-the-art (SOTA) results in the target domain. In this work, we study extractive question answering within closed domains and introduce the concept of targeted pre-training. This involves determining and generating relevant data to further pre-train our models, as opposed to the conventional philosophy of utilizing domain-specific FMs trained on a wide range of data. Our proposed framework uses Galactica to generate synthetic, ``targeted'' corpora that align with specific writing styles and topics, such as research papers and radiology reports. This process can be viewed as a form of knowledge distillation. We apply our method to two biomedical extractive question answering datasets, COVID-QA and RadQA, achieving a new benchmark on the former and demonstrating overall improvements on the latter. Code available at https://github.com/saptarshi059/CDQA-v1-Targetted-PreTraining/tree/main.

Analysis of Elephant Movement in Sub-Saharan Africa: Ecological, Climatic, and Conservation Perspectives

The interaction between elephants and their environment has profound implications for both ecology and conservation strategies. This study presents an analytical approach to decipher the intricate patterns of elephant movement in Sub-Saharan Africa, concentrating on key ecological drivers such as seasonal variations and rainfall patterns. Despite the complexities surrounding these influential factors, our analysis provides a holistic view of elephant migratory behavior in the context of the dynamic African landscape. Our comprehensive approach enables us to predict the potential impact of these ecological determinants on elephant migration, a critical step in establishing informed conservation strategies. This projection is particularly crucial given the impacts of global climate change on seasonal and rainfall patterns, which could substantially influence elephant movements in the future. The findings of our work aim to not only advance the understanding of movement ecology but also foster a sustainable coexistence of humans and elephants in Sub-Saharan Africa. By predicting potential elephant routes, our work can inform strategies to minimize human-elephant conflict, effectively manage land use, and enhance anti-poaching efforts. This research underscores the importance of integrating movement ecology and climatic variables for effective wildlife management and conservation planning.