Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

The dynamic expansion architecture is becoming popular in class incremental learning, mainly due to its advantages in alleviating catastrophic forgetting. However, task confusion is not well assessed within this framework, e.g., the discrepancy between classes of different tasks is not well learned (i.e., inter-task confusion, ITC), and certain priority is still given to the latest class batch (i.e., old-new confusion, ONC). We empirically validate the side effects of the two types of confusion. Meanwhile, a novel solution called Task Correlated Incremental Learning (TCIL) is proposed to encourage discriminative and fair feature utilization across tasks. TCIL performs a multi-level knowledge distillation to propagate knowledge learned from old tasks to the new one. It establishes information flow paths at both feature and logit levels, enabling the learning to be aware of old classes. Besides, attention mechanism and classifier re-scoring are applied to generate more fair classification scores. We conduct extensive experiments on CIFAR100 and ImageNet100 datasets. The results demonstrate that TCIL consistently achieves state-of-the-art accuracy. It mitigates both ITC and ONC, while showing advantages in battle with catastrophic forgetting even no rehearsal memory is reserved.

Semi-supervised learning based methods are current SOTA solutions to the noisy-label learning problem, which rely on learning an unsupervised label cleaner first to divide the training samples into a labeled set for clean data and an unlabeled set for noise data. Typically, the cleaner is obtained via fitting a mixture model to the distribution of per-sample training losses. However, the modeling procedure is \emph{class agnostic} and assumes the loss distributions of clean and noise samples are the same across different classes. Unfortunately, in practice, such an assumption does not always hold due to the varying learning difficulty of different classes, thus leading to sub-optimal label noise partition criteria. In this work, we reveal this long-ignored problem and propose a simple yet effective solution, named \textbf{C}lass \textbf{P}rototype-based label noise \textbf{C}leaner (\textbf{CPC}). Unlike previous works treating all the classes equally, CPC fully considers loss distribution heterogeneity and applies class-aware modulation to partition the clean and noise data. CPC takes advantage of loss distribution modeling and intra-class consistency regularization in feature space simultaneously and thus can better distinguish clean and noise labels. We theoretically justify the effectiveness of our method by explaining it from the Expectation-Maximization (EM) framework. Extensive experiments are conducted on the noisy-label benchmarks CIFAR-10, CIFAR-100, Clothing1M and WebVision. The results show that CPC consistently brings about performance improvement across all benchmarks. Codes and pre-trained models will be released at \url{https://github.com/hjjpku/CPC.git}.

Multimodal machine translation (MMT) aims to improve translation quality by incorporating information from other modalities, such as vision. Previous MMT systems mainly focus on better access and use of visual information and tend to validate their methods on image-related datasets. These studies face two challenges. First, they can only utilize triple data (bilingual texts with images), which is scarce; second, current benchmarks are relatively restricted and do not correspond to realistic scenarios. Therefore, this paper correspondingly establishes new methods and new datasets for MMT. First, we propose a framework 2/3-Triplet with two new approaches to enhance MMT by utilizing large-scale non-triple data: monolingual image-text data and parallel text-only data. Second, we construct an English-Chinese {e}-commercial {m}ulti{m}odal {t}ranslation dataset (including training and testing), named EMMT, where its test set is carefully selected as some words are ambiguous and shall be translated mistakenly without the help of images. Experiments show that our method is more suitable for real-world scenarios and can significantly improve translation performance by using more non-triple data. In addition, our model also rivals various SOTA models in conventional multimodal translation benchmarks.

Language tasks involving character-level manipulations (e.g., spelling correction, many word games) are challenging for models based in subword tokenization. To address this, we adapt the interchange intervention training method of Geiger et al. (2021) to operate on type-level variables over characters. This allows us to encode robust, position-independent character-level information in the internal representations of subword-based models. We additionally introduce a suite of character-level tasks that systematically vary in their dependence on meaning and sequence-level context. While simple character-level tokenization approaches still perform best on purely form-based tasks like string reversal, our method is superior for more complex tasks that blend form, meaning, and context, such as spelling correction in context and word search games. Our approach also leads to subword-based models with human-intepretable internal representations of characters.

The quality of knowledge retrieval is crucial in knowledge-intensive conversations. Two common strategies to improve the retrieval quality are finetuning the retriever or generating a self-contained query, while they encounter heavy burdens on expensive computation and elaborate annotations. In this paper, we propose an unsupervised query enhanced approach for knowledge-intensive conversations, namely QKConv. There are three modules in QKConv: a query generator, an off-the-shelf knowledge selector, and a response generator. Without extra supervision, the end-to-end joint training of QKConv explores multiple candidate queries and utilizes corresponding selected knowledge to yield the target response. To evaluate the effectiveness of the proposed method, we conducted comprehensive experiments on conversational question-answering, task-oriented dialogue, and knowledge-grounded conversation. Experimental results demonstrate that QKConv achieves state-of-the-art performance compared to unsupervised methods and competitive performance compared to supervised methods.

Label smoothing is a regularization technique widely used in supervised learning to improve the generalization of models on various tasks, such as image classification and machine translation. However, the effectiveness of label smoothing in multi-hop question answering (MHQA) has yet to be well studied. In this paper, we systematically analyze the role of label smoothing on various modules of MHQA and propose F1 smoothing, a novel label smoothing technique specifically designed for machine reading comprehension (MRC) tasks. We evaluate our method on the HotpotQA dataset and demonstrate its superiority over several strong baselines, including models that utilize complex attention mechanisms. Our results suggest that label smoothing can be effective in MHQA, but the choice of smoothing strategy can significantly affect performance.

Determining causal effects of temporal multi-intervention assists decision-making. Restricted by time-varying bias, selection bias, and interactions of multiple interventions, the disentanglement and estimation of multiple treatment effects from individual temporal data is still rare. To tackle these challenges, we propose a comprehensive framework of temporal counterfactual forecasting from an individual multiple treatment perspective (TCFimt). TCFimt constructs adversarial tasks in a seq2seq framework to alleviate selection and time-varying bias and designs a contrastive learning-based block to decouple a mixed treatment effect into separated main treatment effects and causal interactions which further improves estimation accuracy. Through implementing experiments on two real-world datasets from distinct fields, the proposed method shows satisfactory performance in predicting future outcomes with specific treatments and in choosing optimal treatment type and timing than state-of-the-art methods.

Making safe and human-like decisions is an essential capability of autonomous driving systems and learning-based behavior planning is a promising pathway toward this objective. Distinguished from existing learning-based methods that directly output decisions, this work introduces a predictive behavior planning framework that learns to predict and evaluate from human driving data. Concretely, a behavior generation module first produces a diverse set of candidate behaviors in the form of trajectory proposals. Then the proposed conditional motion prediction network is employed to forecast other agents' future trajectories conditioned on each trajectory proposal. Given the candidate plans and associated prediction results, we learn a scoring module to evaluate the plans using maximum entropy inverse reinforcement learning (IRL). We conduct comprehensive experiments to validate the proposed framework on a large-scale real-world urban driving dataset. The results reveal that the conditional prediction model is able to forecast multiple possible future trajectories given a candidate behavior and the prediction results are reactive to different plans. Moreover, the IRL-based scoring module can properly evaluate the trajectory proposals and select close-to-human ones. The proposed framework outperforms other baseline methods in terms of similarity to human driving trajectories. Moreover, we find that the conditional prediction model can improve both prediction and planning performance compared to the non-conditional model, and learning the scoring module is critical to correctly evaluating the candidate plans to align with human drivers.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.