Transformers have become the gold standard for many natural language processing tasks and, in particular, for multi-hop question answering (MHQA). This task includes processing a long document and reasoning over the multiple parts of it. The landscape of MHQA approaches can be classified into two primary categories. The first group focuses on extracting supporting evidence, thereby constraining the QA model's context to predicted facts. Conversely, the second group relies on the attention mechanism of the long input encoding model to facilitate multi-hop reasoning. However, attention-based token representations lack explicit global contextual information to connect reasoning steps. To address these issues, we propose GEMFormer, a two-stage method that first collects relevant information over the entire document to the memory and then combines it with local context to solve the task. Our experimental results show that fine-tuning a pre-trained model with memory-augmented input, including the most certain global elements, improves the model's performance on three MHQA datasets compared to the baseline. We also found that the global explicit memory contains information from supporting facts required for the correct answer.

The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM) of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. Results: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52%) corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578.

Background: Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster density and boundaries for sets of potentially related sequences of genes with variable degrees of polymorphism remains a significant challenge. The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets. Results: A novel method that combines the linear mapping hash function and multiple sequence alignment (MSA) was developed. This method takes advantage of the already sorted by similarity sequences from the MSA output, and identifies the optimal number of clusters, clusters cut-offs, and clusters centroids that can represent reference gene vouchers for the different species. The linear mapping hash function can map an already ordered by similarity distance matrix to indices to reveal gaps in the values around which the optimal cut-offs of the different clusters can be identified. The method was evaluated using sets of closely related (16S rRNA gene sequences of Nocardia species) and highly variable (VP1 genomic region of Enterovirus 71) sequences and outperformed existing unsupervised machine learning clustering methods and dimensionality reduction methods. This method does not require prior knowledge of the number of clusters or the distance between clusters, handles clusters of different sizes and shapes, and scales linearly with the dataset. Conclusions: The combination of MSA with the linear mapping hash function is a computationally efficient way of gene sequence clustering and can be a valuable tool for the assessment of similarity, clustering of different microbial genomes, identifying reference sequences, and for the study of evolution of bacteria and viruses.

Recent studies attempted to utilize multilayer perceptrons (MLPs) to solve semisupervised node classification on graphs, by training a student MLP by knowledge distillation from a teacher graph neural network (GNN). While previous studies have focused mostly on training the student MLP by matching the output probability distributions between the teacher and student models during distillation, it has not been systematically studied how to inject the structural information in an explicit and interpretable manner. Inspired by GNNs that separate feature transformation $T$ and propagation $\Pi$, we re-frame the distillation process as making the student MLP learn both $T$ and $\Pi$. Although this can be achieved by applying the inverse propagation $\Pi^{-1}$ before distillation from the teacher, it still comes with a high computational cost from large matrix multiplications during training. To solve this problem, we propose Propagate & Distill (P&D), which propagates the output of the teacher before distillation, which can be interpreted as an approximate process of the inverse propagation. We demonstrate that P&D can readily improve the performance of the student MLP.

In this paper, we address the limitations of existing text-to-image diffusion models in generating demographically fair results when given human-related descriptions. These models often struggle to disentangle the target language context from sociocultural biases, resulting in biased image generation. To overcome this challenge, we propose Fair Mapping, a general, model-agnostic, and lightweight approach that modifies a pre-trained text-to-image model by controlling the prompt to achieve fair image generation. One key advantage of our approach is its high efficiency. The training process only requires updating a small number of parameters in an additional linear mapping network. This not only reduces the computational cost but also accelerates the optimization process. We first demonstrate the issue of bias in generated results caused by language biases in text-guided diffusion models. By developing a mapping network that projects language embeddings into an unbiased space, we enable the generation of relatively balanced demographic results based on a keyword specified in the prompt. With comprehensive experiments on face image generation, we show that our method significantly improves image generation performance when prompted with descriptions related to human faces. By effectively addressing the issue of bias, we produce more fair and diverse image outputs. This work contributes to the field of text-to-image generation by enhancing the ability to generate images that accurately reflect the intended demographic characteristics specified in the text.

Understanding time is a pivotal aspect of human cognition, crucial in the broader framework of grasping the intricacies of the world. Previous studies typically focus on specific aspects of time, lacking a comprehensive temporal reasoning benchmark. To address this issue, we propose TimeBench, a comprehensive hierarchical temporal reasoning benchmark that covers a broad spectrum of temporal reasoning phenomena, which provides a thorough evaluation for investigating the temporal reasoning capabilities of large language models. We conduct extensive experiments on popular LLMs, such as GPT-4, LLaMA2, and Mistral, incorporating chain-of-thought prompting. Our experimental results indicate a significant performance gap between the state-of-the-art LLMs and humans, highlighting that there is still a considerable distance to cover in temporal reasoning. We aspire for TimeBench to serve as a comprehensive benchmark, fostering research in temporal reasoning for LLMs. Our resource is available at https://github.com/zchuz/TimeBench

Community Question Answering (CQA) becomes increasingly prevalent in recent years. However, there are a large number of answers, which is difficult for users to select the relevant answers. Therefore, answer selection is a very significant subtask of CQA. In this paper, we first propose the Question-Answer cross attention networks (QAN) with pre-trained models for answer selection and utilize large language model (LLM) to perform answer selection with knowledge augmentation. Specifically, we apply the BERT model as the encoder layer to do pre-training for question subjects, question bodies and answers, respectively, then the cross attention mechanism selects the most relevant answer for different questions. Experiments show that the QAN model achieves state-of-the-art performance on two datasets, SemEval2015 and SemEval2017. Moreover, we use the LLM to generate external knowledge from questions and correct answers to achieve knowledge augmentation for the answer selection task by LLM, while optimizing the prompt of LLM in different aspects. The results show that the introduction of external knowledge can improve the correct answer selection rate of LLM on datasets SemEval2015 and SemEval2017. Meanwhile, LLM can also select the correct answer on more questions by optimized prompt.

Instruction-based multitasking has played a critical role in the success of large language models (LLMs) in multi-turn dialog applications. While publicly available LLMs have shown promising performance, when exposed to complex instructions with multiple constraints, they lag against state-of-the-art models like ChatGPT. In this work, we hypothesize that the availability of large-scale complex demonstrations is crucial in bridging this gap. Focusing on dialog applications, we propose a novel framework, CESAR, that unifies a large number of dialog tasks in the same format and allows programmatic induction of complex instructions without any manual effort. We apply CESAR on InstructDial, a benchmark for instruction-based dialog tasks. We further enhance InstructDial with new datasets and tasks and utilize CESAR to induce complex tasks with compositional instructions. This results in a new benchmark called InstructDial++, which includes 63 datasets with 86 basic tasks and 68 composite tasks. Through rigorous experiments, we demonstrate the scalability of CESAR in providing rich instructions. Models trained on InstructDial++ can follow compositional prompts, such as prompts that ask for multiple stylistic constraints.

Multivariate time series have many applications, from healthcare and meteorology to life science. Although deep learning models have shown excellent predictive performance for time series, they have been criticised for being "black-boxes" or non-interpretable. This paper proposes a novel modular neural network model for multivariate time series prediction that is interpretable by construction. A recurrent neural network learns the temporal dependencies in the data while an attention-based feature selection component selects the most relevant features and suppresses redundant features used in the learning of the temporal dependencies. A modular deep network is trained from the selected features independently to show the users how features influence outcomes, making the model interpretable. Experimental results show that this approach can outperform state-of-the-art interpretable Neural Additive Models (NAM) and variations thereof in both regression and classification of time series tasks, achieving a predictive performance that is comparable to the top non-interpretable methods for time series, LSTM and XGBoost.

Machine learning models are known to memorize private data to reduce their training loss, which can be inadvertently exploited by privacy attacks such as model inversion and membership inference. To protect against these attacks, differential privacy (DP) has become the de facto standard for privacy-preserving machine learning, particularly those popular training algorithms using stochastic gradient descent, such as DPSGD. Nonetheless, DPSGD still suffers from severe utility loss due to its slow convergence. This is partially caused by the random sampling, which brings bias and variance to the gradient, and partially by the Gaussian noise, which leads to fluctuation of gradient updates. Our key idea to address these issues is to apply selective updates to the model training, while discarding those useless or even harmful updates. Motivated by this, this paper proposes DPSUR, a Differentially Private training framework based on Selective Updates and Release, where the gradient from each iteration is evaluated based on a validation test, and only those updates leading to convergence are applied to the model. As such, DPSUR ensures the training in the right direction and thus can achieve faster convergence than DPSGD. The main challenges lie in two aspects -- privacy concerns arising from gradient evaluation, and gradient selection strategy for model update. To address the challenges, DPSUR introduces a clipping strategy for update randomization and a threshold mechanism for gradient selection. Experiments conducted on MNIST, FMNIST, CIFAR-10, and IMDB datasets show that DPSUR significantly outperforms previous works in terms of convergence speed and model utility.