Understanding the complex interactions within the microbiome is crucial for developing effective diagnostic and therapeutic strategies. Traditional machine learning models often lack interpretability, which is essential for clinical and biological insights. This paper explores the application of symbolic regression (SR) to microbiome relative abundance data, with a focus on colorectal cancer (CRC). SR, known for its high interpretability, is compared against traditional machine learning models, e.g., random forest, gradient boosting decision trees. These models are evaluated based on performance metrics such as F1 score and accuracy. We utilize 71 studies encompassing, from various cohorts, over 10,000 samples across 749 species features. Our results indicate that SR not only competes reasonably well in terms of predictive performance, but also excels in model interpretability. SR provides explicit mathematical expressions that offer insights into the biological relationships within the microbiome, a crucial advantage for clinical and biological interpretation. Our experiments also show that SR can help understand complex models like XGBoost via knowledge distillation. To aid in reproducibility and further research, we have made the code openly available at https://github.com/swag2198/microbiome-symbolic-regression .

Tables are ubiquitous across various domains for concisely representing structured information. Empowering large language models (LLMs) to reason over tabular data represents an actively explored direction. However, since typical LLMs only support one-dimensional~(1D) inputs, existing methods often flatten the two-dimensional~(2D) table structure into a sequence of tokens, which can severely disrupt the spatial relationships and result in an inevitable loss of vital contextual information. In this paper, we first empirically demonstrate the detrimental impact of such flattening operations on the performance of LLMs in capturing the spatial information of tables through two elaborate proxy tasks. Subsequently, we introduce a simple yet effective positional encoding method, termed ``2D-TPE'' (Two-Dimensional Table Positional Encoding), to address this challenge. 2D-TPE enables each attention head to dynamically select a permutation order of tokens within the context for attending to them, where each permutation represents a distinct traversal mode for the table, such as column-wise or row-wise traversal. 2D-TPE effectively mitigates the risk of losing essential spatial information while preserving computational efficiency, thus better preserving the table structure. Extensive experiments across five benchmarks demonstrate that 2D-TPE outperforms strong baselines, underscoring the importance of preserving the table structure for accurate table comprehension. Comprehensive analysis further reveals the substantially better scalability of 2D-TPE to large tables than baselines.

Large Language Models (LLMs) have demonstrated remarkable capabilities in generating coherent text but remain limited by the static nature of their training data. Retrieval Augmented Generation (RAG) addresses this issue by combining LLMs with up-to-date information retrieval, but also expand the attack surface of the system. This paper investigates prompt injection attacks on RAG, focusing on malicious objectives beyond misinformation, such as inserting harmful links, promoting unauthorized services, and initiating denial-of-service behaviors. We build upon existing corpus poisoning techniques and propose a novel backdoor attack aimed at the fine-tuning process of the dense retriever component. Our experiments reveal that corpus poisoning can achieve significant attack success rates through the injection of a small number of compromised documents into the retriever's corpus. In contrast, backdoor attacks demonstrate even higher success rates but necessitate a more complex setup, as the victim must fine-tune the retriever using the attacker's poisoned dataset.

Natural Language Processing (NLP) research on AI Safety and social bias in AI has focused on safety for humans and social bias against human minorities. However, some AI ethicists have argued that the moral significance of nonhuman animals has been ignored in AI research. Therefore, the purpose of this study is to investigate whether there is speciesism, i.e., discrimination against nonhuman animals, in NLP research. First, we explain why nonhuman animals are relevant in NLP research. Next, we survey the findings of existing research on speciesism in NLP researchers, data, and models and further investigate this problem in this study. The findings of this study suggest that speciesism exists within researchers, data, and models, respectively. Specifically, our survey and experiments show that (a) among NLP researchers, even those who study social bias in AI, do not recognize speciesism or speciesist bias; (b) among NLP data, speciesist bias is inherent in the data annotated in the datasets used to evaluate NLP models; (c) OpenAI GPTs, recent NLP models, exhibit speciesist bias by default. Finally, we discuss how we can reduce speciesism in NLP research.

As a promising paradigm to collaboratively train models with decentralized data, Federated Learning (FL) can be exploited to fine-tune Large Language Models (LLMs). While LLMs correspond to huge size, the scale of the training data significantly increases, which leads to tremendous amounts of computation and communication costs. The training data is generally non-Independent and Identically Distributed (non-IID), which requires adaptive data processing within each device. Although Low Rank Adaptation (LoRA) can significantly reduce the scale of parameters to update in the fine-tuning process, it still takes unaffordable time to transfer the low-rank parameters of all the layers in LLMs. In this paper, we propose a Fisher Information-based Efficient Curriculum Federated Learning framework (FibecFed) with two novel methods, i.e., adaptive federated curriculum learning and efficient sparse parameter update. First, we propose a fisher information-based method to adaptively sample data within each device to improve the effectiveness of the FL fine-tuning process. Second, we dynamically select the proper layers for global aggregation and sparse parameters for local update with LoRA so as to improve the efficiency of the FL fine-tuning process. Extensive experimental results based on 10 datasets demonstrate that FibecFed yields excellent performance (up to 45.35% in terms of accuracy) and superb fine-tuning speed (up to 98.61% faster) compared with 17 baseline approaches).

This study investigates the application of an artificial neural network framework for analysing water pollution caused by solids. Water pollution by suspended solids poses significant environmental and health risks. Traditional methods for assessing and predicting pollution levels are often time-consuming and resource-intensive. To address these challenges, we developed a model that leverages a comprehensive dataset of water quality from total suspended solids. A convolutional neural network was trained under a transfer learning approach using data corresponding to different total suspended solids concentrations, with the goal of accurately predicting low, medium and high pollution levels based on various input variables. Our model demonstrated high predictive accuracy, outperforming conventional statistical methods in terms of both speed and reliability. The results suggest that the artificial neural network framework can serve as an effective tool for real-time monitoring and management of water pollution, facilitating proactive decision-making and policy formulation. This approach not only enhances our understanding of pollution dynamics but also underscores the potential of machine learning techniques in environmental science.

Positional bias in large language models (LLMs) hinders their ability to effectively process long inputs. A prominent example is the "lost in the middle" phenomenon, where LLMs struggle to utilize relevant information situated in the middle of the input. While prior research primarily focuses on single pieces of relevant information, real-world applications often involve multiple relevant information pieces. To bridge this gap, we present LongPiBench, a benchmark designed to assess positional bias involving multiple pieces of relevant information. Thorough experiments are conducted with five commercial and six open-source models. These experiments reveal that while most current models are robust against the "lost in the middle" issue, there exist significant biases related to the spacing of relevant information pieces. These findings highlight the importance of evaluating and reducing positional biases to advance LLM's capabilities.

Misinformation spreads rapidly on social media, confusing the truth and targetting potentially vulnerable people. To effectively mitigate the negative impact of misinformation, it must first be accurately detected before applying a mitigation strategy, such as X's community notes, which is currently a manual process. This study takes a knowledge-based approach to misinformation detection, modelling the problem similarly to one of natural language inference. The EffiARA annotation framework is introduced, aiming to utilise inter- and intra-annotator agreement to understand the reliability of each annotator and influence the training of large language models for classification based on annotator reliability. In assessing the EffiARA annotation framework, the Russo-Ukrainian Conflict Knowledge-Based Misinformation Classification Dataset (RUC-MCD) was developed and made publicly available. This study finds that sample weighting using annotator reliability performs the best, utilising both inter- and intra-annotator agreement and soft-label training. The highest classification performance achieved using Llama-3.2-1B was a macro-F1 of 0.757 and 0.740 using TwHIN-BERT-large.

Knowledge Editing (KE) aims to correct and update factual information in Large Language Models (LLMs) to ensure accuracy and relevance without computationally expensive fine-tuning. Though it has been proven effective in several domains, limited work has focused on its application within the e-commerce sector. However, there are naturally occurring scenarios that make KE necessary in this domain, such as the timely updating of product features and trending purchase intentions by customers, which necessitate further exploration. In this paper, we pioneer the application of KE in the e-commerce domain by presenting ECOMEDIT, an automated e-commerce knowledge editing framework tailored for e-commerce-related knowledge and tasks. Our framework leverages more powerful LLMs as judges to enable automatic knowledge conflict detection and incorporates conceptualization to enhance the semantic coverage of the knowledge to be edited. Through extensive experiments, we demonstrate the effectiveness of ECOMEDIT in improving LLMs' understanding of product descriptions and purchase intentions. We also show that LLMs, after our editing, can achieve stronger performance on downstream e-commerce tasks.

We develop a novel data-driven framework as an alternative to dynamic flux balance analysis, bypassing the demand for deep domain knowledge and manual efforts to formulate the optimization problem. The proposed framework is end-toend, which trains a structured neural ODE process (SNODEP) model to estimate flux and balance samples using gene-expression time-series data. SNODEP is designed to circumvent the limitations of the standard neural ODE process model, including restricting the latent and decoder sampling distributions to be normal and lacking structure between context points for calculating the latent, thus more suitable for modeling the underlying dynamics of a metabolic system. Through comprehensive experiments (156 in total), we demonstrate that SNODEP not only predicts the unseen time points of real-world gene-expression data and the flux and balance estimates well but can even generalize to more challenging unseen knockout configurations and irregular data sampling scenarios, all essential for metabolic pathway analysis. We hope our work can serve as a catalyst for building more scalable and powerful models for genome-scale metabolic analysis. A distinctive characteristic of deep neural networks is their capability to implicitly learn complicated features and dynamics from data, significantly saving human effort in composing those handcrafted features and devising complex models. Therefore, there has been a growing interest in using them in a variety of scientific contexts, such as quantum chemistry (von Glehn et al., 2022), tokamak controller design (Degrave et al., 2022), climate sciences (Lam et al., 2022; Nguyen et al., 2023), molecule generation (Hoogeboom et al., 2022) and drug discovery (Askr et al., 2023), to name a few.