Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity Recognition (NER). Recent research in biomedical language processing has offered a number of biomedical LMs pre-trained using different methods and techniques that advance results on many BioNLP tasks, including NER. However, there is still a lack of a comprehensive comparison of pre-training approaches that would work more optimally in the biomedical domain. This paper aims to investigate different pre-training methods, such as pre-training the biomedical LM from scratch and pre-training it in a continued fashion. We compare existing methods with our proposed pre-training method of initializing weights for new tokens by distilling existing weights from the BERT model inside the context where the tokens were found. The method helps to speed up the pre-training stage and improve performance on NER. In addition, we compare how masking rate, corruption strategy, and masking strategies impact the performance of the biomedical LM. Finally, using the insights from our experiments, we introduce a new biomedical LM (BIOptimus), which is pre-trained using Curriculum Learning (CL) and contextualized weight distillation method. Our model sets new states of the art on several biomedical Named Entity Recognition (NER) tasks. We release our code and all pre-trained models

With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting position-specific scoring matrices (PSSMs) of such search engines represent a crucial input to many machine learning (ML) models in the field of bioinformatics and computational biology. A protein sequence is a collection of contiguous tokens or characters called amino acids (AAs). The analogy to natural language allowed us to exploit the recent advancements in the field of Natural Language Processing (NLP) and therefore transfer NLP state-of-the-art algorithms to bioinformatics. This research presents an Embedding Language Model (ELMo), converting a protein sequence to a numerical vector representation. While the original ELMo trained a 2-layer bidirectional Long Short-Term Memory (LSTMs) network following a two-path architecture, one for the forward and the second for the backward pass, by merging the idea of PSSMs with the concept of transfer-learning, this work introduces a novel bidirectional language model (bi-LM) with four times less free parameters and using rather a single path for both passes. The model was trained not only on predicting the next AA but also on the probability distribution of the next AA derived from similar, yet different sequences as summarized in a PSSM, simultaneously for multi-task learning, hence learning evolutionary information of protein sequences as well. The network architecture and the pre-trained model are made available as open source under the permissive MIT license on GitHub at https://github.com/issararab/PEvoLM.

Continual learning refers to the capability of a machine learning model to learn and adapt to new information, without compromising its performance on previously learned tasks. Although several studies have investigated continual learning methods for information retrieval tasks, a well-defined task formulation is still lacking, and it is unclear how typical learning strategies perform in this context. To address this challenge, a systematic task formulation of continual neural information retrieval is presented, along with a multiple-topic dataset that simulates continuous information retrieval. A comprehensive continual neural information retrieval framework consisting of typical retrieval models and continual learning strategies is then proposed. Empirical evaluations illustrate that the proposed framework can successfully prevent catastrophic forgetting in neural information retrieval and enhance performance on previously learned tasks. The results indicate that embedding-based retrieval models experience a decline in their continual learning performance as the topic shift distance and dataset volume of new tasks increase. In contrast, pretraining-based models do not show any such correlation. Adopting suitable learning strategies can mitigate the effects of topic shift and data augmentation.

Graph Neural Network (GNN) has demonstrated extraordinary performance in classifying graph properties. However, due to the selection bias of training and testing data (e.g., training on small graphs and testing on large graphs, or training on dense graphs and testing on sparse graphs), distribution deviation is widespread. More importantly, we often observe \emph{hybrid structure distribution shift} of both scale and density, despite of one-sided biased data partition. The spurious correlations over hybrid distribution deviation degrade the performance of previous GNN methods and show large instability among different datasets. To alleviate this problem, we propose \texttt{OOD-GMixup} to jointly manipulate the training distribution with \emph{controllable data augmentation} in metric space. Specifically, we first extract the graph rationales to eliminate the spurious correlations due to irrelevant information. Secondly, we generate virtual samples with perturbation on graph rationale representation domain to obtain potential OOD training samples. Finally, we propose OOD calibration to measure the distribution deviation of virtual samples by leveraging Extreme Value Theory, and further actively control the training distribution by emphasizing the impact of virtual OOD samples. Extensive studies on several real-world datasets on graph classification demonstrate the superiority of our proposed method over state-of-the-art baselines.

Detoxification for LLMs is challenging since it requires models to avoid generating harmful content while maintaining the generation capability. To ensure the safety of generations, previous detoxification methods detoxify the models by changing the data distributions or constraining the generations from different aspects in a single-step manner. However, these approaches will dramatically affect the generation quality of LLMs, e.g., discourse coherence and semantic consistency, since language models tend to generate along the toxic prompt while detoxification methods work in the opposite direction. To handle such a conflict, we decompose the detoxification process into different sub-steps, where the detoxification is concentrated in the input stage and the subsequent continual generation is based on the non-toxic prompt. Besides, we also calibrate the strong reasoning ability of LLMs by designing a Detox-Chain to connect the above sub-steps in an orderly manner, which allows LLMs to detoxify the text step-by-step. Automatic and human evaluation on two benchmarks reveals that by training with Detox-Chain, six LLMs scaling from 1B to 33B can obtain significant detoxification and generation improvement. Our code and data are available at https://github.com/CODINNLG/Detox-CoT. Warning: examples in the paper may contain uncensored offensive content.

The increasing adoption of natural language processing (NLP) models across industries has led to practitioners' need for machine learning systems to handle these models efficiently, from training to serving them in production. However, training, deploying, and updating multiple models can be complex, costly, and time-consuming, mainly when using transformer-based pre-trained language models. Multi-Task Learning (MTL) has emerged as a promising approach to improve efficiency and performance through joint training, rather than training separate models. Motivated by this, we first provide an overview of transformer-based MTL approaches in NLP. Then, we discuss the challenges and opportunities of using MTL approaches throughout typical ML lifecycle phases, specifically focusing on the challenges related to data engineering, model development, deployment, and monitoring phases. This survey focuses on transformer-based MTL architectures and, to the best of our knowledge, is novel in that it systematically analyses how transformer-based MTL in NLP fits into ML lifecycle phases. Furthermore, we motivate research on the connection between MTL and continual learning (CL), as this area remains unexplored. We believe it would be practical to have a model that can handle both MTL and CL, as this would make it easier to periodically re-train the model, update it due to distribution shifts, and add new capabilities to meet real-world requirements.

As the complexity and computational demands of deep learning models rise, the need for effective optimization methods for neural network designs becomes paramount. This work introduces an innovative search mechanism for automatically selecting the best bit-width and layer-width for individual neural network layers. This leads to a marked enhancement in deep neural network efficiency. The search domain is strategically reduced by leveraging Hessian-based pruning, ensuring the removal of non-crucial parameters. Subsequently, we detail the development of surrogate models for favorable and unfavorable outcomes by employing a cluster-based tree-structured Parzen estimator. This strategy allows for a streamlined exploration of architectural possibilities and swift pinpointing of top-performing designs. Through rigorous testing on well-known datasets, our method proves its distinct advantage over existing methods. Compared to leading compression strategies, our approach records an impressive 20% decrease in model size without compromising accuracy. Additionally, our method boasts a 12x reduction in search time relative to the best search-focused strategies currently available. As a result, our proposed method represents a leap forward in neural network design optimization, paving the way for quick model design and implementation in settings with limited resources, thereby propelling the potential of scalable deep learning solutions.

Current developments in large language models (LLMs) have enabled impressive zero-shot capabilities across various natural language tasks. An interesting application of these systems is in the automated assessment of natural language generation (NLG), a highly challenging area with great practical benefit. In this paper, we explore two options for exploiting the emergent abilities of LLMs for zero-shot NLG assessment: absolute score prediction, and comparative assessment which uses relative comparisons between pairs of candidates. Though comparative assessment has not been extensively studied in NLG assessment, we note that humans often find it more intuitive to compare two options rather than scoring each one independently. This work examines comparative assessment from multiple perspectives: performance compared to absolute grading; positional biases in the prompt; and efficient ranking in terms of the number of comparisons. We illustrate that LLM comparative assessment is a simple, general and effective approach for NLG assessment. For moderate-sized open-source LLMs, such as FlanT5 and Llama2-chat, comparative assessment is superior to prompt scoring, and in many cases can achieve performance competitive with state-of-the-art methods. Additionally, we demonstrate that LLMs often exhibit strong positional biases when making pairwise comparisons, and we propose debiasing methods that can further improve performance.

Isolated Sign Language Recognition (SLR) has mostly been applied on datasets containing signs executed slowly and clearly by a limited group of signers. In real-world scenarios, however, we are met with challenging visual conditions, coarticulated signing, small datasets, and the need for signer independent models. To tackle this difficult problem, we require a robust feature extractor to process the sign language videos. One could expect human pose estimators to be ideal candidates. However, due to a domain mismatch with their training sets and challenging poses in sign language, they lack robustness on sign language data and image-based models often still outperform keypoint-based models. Furthermore, whereas the common practice of transfer learning with image-based models yields even higher accuracy, keypoint-based models are typically trained from scratch on every SLR dataset. These factors limit their usefulness for SLR. From the existing literature, it is also not clear which, if any, pose estimator performs best for SLR. We compare the three most popular pose estimators for SLR: OpenPose, MMPose and MediaPipe. We show that through keypoint normalization, missing keypoint imputation, and learning a pose embedding, we can obtain significantly better results and enable transfer learning. We show that keypoint-based embeddings contain cross-lingual features: they can transfer between sign languages and achieve competitive performance even when fine-tuning only the classifier layer of an SLR model on a target sign language. We furthermore achieve better performance using fine-tuned transferred embeddings than models trained only on the target sign language. The embeddings can also be learned in a multilingual fashion. The application of these embeddings could prove particularly useful for low resource sign languages in the future.

In this paper, we investigate the in-context learning ability of retrieval-augmented encoder-decoder language models. We first conduct a comprehensive analysis of the state-of-the-art ATLAS model and identify its limitations in in-context learning, primarily due to a mismatch between pretraining and testing, as well as a restricted context length. To address these issues, we propose RAVEN, a model that combines retrieval-augmented masked language modeling and prefix language modeling. We further introduce Fusion-in-Context Learning to enhance the few-shot performance by enabling the model to leverage more in-context examples without requiring additional training or model modifications. Through extensive experiments, we demonstrate that RAVEN significantly outperforms ATLAS and achieves results comparable to the most advanced language models in certain scenarios, despite having substantially fewer parameters. Our work underscores the potential of retrieval-augmented encoder-decoder language models for in-context learning and encourages further research in this direction.