Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem solving. However, the potential and efficacy of these models in bioinformatics remain incompletely explored. In this work, we study the performance LLMs on a wide spectrum of crucial bioinformatics tasks. These tasks include the identification of potential coding regions, extraction of named entities for genes and proteins, detection of antimicrobial and anti-cancer peptides, molecular optimization, and resolution of educational bioinformatics problems. Our findings indicate that, given appropriate prompts, LLMs like GPT variants can successfully handle most of these tasks. In addition, we provide a thorough analysis of their limitations in the context of complicated bioinformatics tasks. In conclusion, we believe that this work can provide new perspectives and motivate future research in the field of LLMs applications, AI for Science and bioinformatics.

This paper studies the problem of traffic flow forecasting, which aims to predict future traffic conditions on the basis of road networks and traffic conditions in the past. The problem is typically solved by modeling complex spatio-temporal correlations in traffic data using spatio-temporal graph neural networks (GNNs). However, the performance of these methods is still far from satisfactory since GNNs usually have limited representation capacity when it comes to complex traffic networks. Graphs, by nature, fall short in capturing non-pairwise relations. Even worse, existing methods follow the paradigm of message passing that aggregates neighborhood information linearly, which fails to capture complicated spatio-temporal high-order interactions. To tackle these issues, in this paper, we propose a novel model named Dynamic Hypergraph Structure Learning (DyHSL) for traffic flow prediction. To learn non-pairwise relationships, our DyHSL extracts hypergraph structural information to model dynamics in the traffic networks, and updates each node representation by aggregating messages from its associated hyperedges. Additionally, to capture high-order spatio-temporal relations in the road network, we introduce an interactive graph convolution block, which further models the neighborhood interaction for each node. Finally, we integrate these two views into a holistic multi-scale correlation extraction module, which conducts temporal pooling with different scales to model different temporal patterns. Extensive experiments on four popular traffic benchmark datasets demonstrate the effectiveness of our proposed DyHSL compared with a broad range of competing baselines.

Although graph neural networks (GNNs) have achieved impressive achievements in graph classification, they often need abundant task-specific labels, which could be extensively costly to acquire. A credible solution is to explore additional labeled graphs to enhance unsupervised learning on the target domain. However, how to apply GNNs to domain adaptation remains unsolved owing to the insufficient exploration of graph topology and the significant domain discrepancy. In this paper, we propose Coupled Contrastive Graph Representation Learning (CoCo), which extracts the topological information from coupled learning branches and reduces the domain discrepancy with coupled contrastive learning. CoCo contains a graph convolutional network branch and a hierarchical graph kernel network branch, which explore graph topology in implicit and explicit manners. Besides, we incorporate coupled branches into a holistic multi-view contrastive learning framework, which not only incorporates graph representations learned from complementary views for enhanced understanding, but also encourages the similarity between cross-domain example pairs with the same semantics for domain alignment. Extensive experiments on popular datasets show that our CoCo outperforms these competing baselines in different settings generally.

In this paper, we investigate the challenge of spatio-temporal video prediction, which involves generating future videos based on historical data streams. Existing approaches typically utilize external information such as semantic maps to enhance video prediction, which often neglect the inherent physical knowledge embedded within videos. Furthermore, their high computational demands could impede their applications for high-resolution videos. To address these constraints, we introduce a novel approach called Physics-assisted Spatio-temporal Network (PastNet) for generating high-quality video prediction. The core of our PastNet lies in incorporating a spectral convolution operator in the Fourier domain, which efficiently introduces inductive biases from the underlying physical laws. Additionally, we employ a memory bank with the estimated intrinsic dimensionality to discretize local features during the processing of complex spatio-temporal signals, thereby reducing computational costs and facilitating efficient high-resolution video prediction. Extensive experiments on various widely-used Figure 1: Performance comparison of different video prediction datasets demonstrate the effectiveness and efficiency of the proposed methods on MovingMNIST. Our PastNet outperforms PastNet compared with a range of state-of-the-art methods, previous models in terms of training time and image quality.

This paper studies semi-supervised graph classification, a crucial task with a wide range of applications in social network analysis and bioinformatics. Recent works typically adopt graph neural networks to learn graph-level representations for classification, failing to explicitly leverage features derived from graph topology (e.g., paths). Moreover, when labeled data is scarce, these methods are far from satisfactory due to their insufficient topology exploration of unlabeled data. We address the challenge by proposing a novel semi-supervised framework called Twin Graph Neural Network (TGNN). To explore graph structural information from complementary views, our TGNN has a message passing module and a graph kernel module. To fully utilize unlabeled data, for each module, we calculate the similarity of each unlabeled graph to other labeled graphs in the memory bank and our consistency loss encourages consistency between two similarity distributions in different embedding spaces. The two twin modules collaborate with each other by exchanging instance similarity knowledge to fully explore the structure information of both labeled and unlabeled data. We evaluate our TGNN on various public datasets and show that it achieves strong performance.

Transformer-based methods have recently achieved great advancement on 2D image-based vision tasks. For 3D video-based tasks such as action recognition, however, directly applying spatiotemporal transformers on video data will bring heavy computation and memory burdens due to the largely increased number of patches and the quadratic complexity of self-attention computation. How to efficiently and effectively model the 3D self-attention of video data has been a great challenge for transformers. In this paper, we propose a Temporal Patch Shift (TPS) method for efficient 3D self-attention modeling in transformers for video-based action recognition. TPS shifts part of patches with a specific mosaic pattern in the temporal dimension, thus converting a vanilla spatial self-attention operation to a spatiotemporal one with little additional cost. As a result, we can compute 3D self-attention using nearly the same computation and memory cost as 2D self-attention. TPS is a plug-and-play module and can be inserted into existing 2D transformer models to enhance spatiotemporal feature learning. The proposed method achieves competitive performance with state-of-the-arts on Something-something V1 & V2, Diving-48, and Kinetics400 while being much more efficient on computation and memory cost. The source code of TPS can be found at https://github.com/MartinXM/TPS.

Knowledge Distillation (KD) is a popular technique to transfer knowledge from a teacher model or ensemble to a student model. Its success is generally attributed to the privileged information on similarities/consistency between the class distributions or intermediate feature representations of the teacher model and the student model. However, directly pushing the student model to mimic the probabilities/features of the teacher model to a large extent limits the student model in learning undiscovered knowledge/features. In this paper, we propose a novel inheritance and exploration knowledge distillation framework (IE-KD), in which a student model is split into two parts - inheritance and exploration. The inheritance part is learned with a similarity loss to transfer the existing learned knowledge from the teacher model to the student model, while the exploration part is encouraged to learn representations different from the inherited ones with a dis-similarity loss. Our IE-KD framework is generic and can be easily combined with existing distillation or mutual learning methods for training deep neural networks. Extensive experiments demonstrate that these two parts can jointly push the student model to learn more diversified and effective representations, and our IE-KD can be a general technique to improve the student network to achieve SOTA performance. Furthermore, by applying our IE-KD to the training of two networks, the performance of both can be improved w.r.t. deep mutual learning. The code and models of IE-KD will be make publicly available at https://github.com/yellowtownhz/IE-KD.

We propose a causal framework to explain the catastrophic forgetting in Class-Incremental Learning (CIL) and then derive a novel distillation method that is orthogonal to the existing anti-forgetting techniques, such as data replay and feature/label distillation. We first 1) place CIL into the framework, 2) answer why the forgetting happens: the causal effect of the old data is lost in new training, and then 3) explain how the existing techniques mitigate it: they bring the causal effect back. Based on the framework, we find that although the feature/label distillation is storage-efficient, its causal effect is not coherent with the end-to-end feature learning merit, which is however preserved by data replay. To this end, we propose to distill the Colliding Effect between the old and the new data, which is fundamentally equivalent to the causal effect of data replay, but without any cost of replay storage. Thanks to the causal effect analysis, we can further capture the Incremental Momentum Effect of the data stream, removing which can help to retain the old effect overwhelmed by the new data effect, and thus alleviate the forgetting of the old class in testing. Extensive experiments on three CIL benchmarks: CIFAR-100, ImageNet-Sub&Full, show that the proposed causal effect distillation can improve various state-of-the-art CIL methods by a large margin (0.72%--9.06%).

We present a novel counterfactual framework for both Zero-Shot Learning (ZSL) and Open-Set Recognition (OSR), whose common challenge is generalizing to the unseen-classes by only training on the seen-classes. Our idea stems from the observation that the generated samples for unseen-classes are often out of the true distribution, which causes severe recognition rate imbalance between the seen-class (high) and unseen-class (low). We show that the key reason is that the generation is not Counterfactual Faithful, and thus we propose a faithful one, whose generation is from the sample-specific counterfactual question: What would the sample look like, if we set its class attribute to a certain class, while keeping its sample attribute unchanged? Thanks to the faithfulness, we can apply the Consistency Rule to perform unseen/seen binary classification, by asking: Would its counterfactual still look like itself? If ``yes'', the sample is from a certain class, and ``no'' otherwise. Through extensive experiments on ZSL and OSR, we demonstrate that our framework effectively mitigates the seen/unseen imbalance and hence significantly improves the overall performance. Note that this framework is orthogonal to existing methods, thus, it can serve as a new baseline to evaluate how ZSL/OSR models generalize. Codes are available at https://github.com/yue-zhongqi/gcm-cf.

Skeleton-based human action recognition has attracted much attention with the prevalence of accessible depth sensors. Recently, graph convolutional networks (GCNs) have been widely used for this task due to their powerful capability to model graph data. The topology of the adjacency graph is a key factor for modeling the correlations of the input skeletons. Thus, previous methods mainly focus on the design/learning of the graph topology. But once the topology is learned, only a single-scale feature and one transformation exist in each layer of the networks. Many insights, such as multi-scale information and multiple sets of transformations, that have been proven to be very effective in convolutional neural networks (CNNs), have not been investigated in GCNs. The reason is that, due to the gap between graph-structured skeleton data and conventional image/video data, it is very challenging to embed these insights into GCNs. To overcome this gap, we reinvent the split-transform-merge strategy in GCNs for skeleton sequence processing. Specifically, we design a simple and highly modularized graph convolutional network architecture for skeleton-based action recognition. Our network is constructed by repeating a building block that aggregates multi-granularity information from both the spatial and temporal paths. Extensive experiments demonstrate that our network outperforms state-of-the-art methods by a significant margin with only 1/5 of the parameters and 1/10 of the FLOPs.