Efficient Prediction of Peptide Self-assembly through Sequential and Graphical Encoding

In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has enabled the efficient collection of large peptide datasets, providing reliable training data for deep learning. However, the lack of systematic analysis of the peptide encoding, which is essential for AI-assisted peptide-related tasks, makes it an urgent problem to be solved for the improvement of prediction accuracy. To address this issue, we first collect a high-quality, colossal simulation dataset of peptide self-assembly containing over 62,000 samples generated by coarse-grained molecular dynamics (CGMD). Then, we systematically investigate the effect of peptide encoding of amino acids into sequences and molecular graphs using state-of-the-art sequential (i.e., RNN, LSTM, and Transformer) and structural deep learning models (i.e., GCN, GAT, and GraphSAGE), on the accuracy of peptide self-assembly prediction, an essential physiochemical process prior to any peptide-related applications. Extensive benchmarking studies have proven Transformer to be the most powerful sequence-encoding-based deep learning model, pushing the limit of peptide self-assembly prediction to decapeptides. In summary, this work provides a comprehensive benchmark analysis of peptide encoding with advanced deep learning models, serving as a guide for a wide range of peptide-related predictions such as isoelectric points, hydration free energy, etc.

Cross-Lingual Cross-Age Group Adaptation for Low-Resource Elderly Speech Emotion Recognition

Speech emotion recognition plays a crucial role in human-computer interactions. However, most speech emotion recognition research is biased toward English-speaking adults, which hinders its applicability to other demographic groups in different languages and age groups. In this work, we analyze the transferability of emotion recognition across three different languages--English, Mandarin Chinese, and Cantonese; and 2 different age groups--adults and the elderly. To conduct the experiment, we develop an English-Mandarin speech emotion benchmark for adults and the elderly, BiMotion, and a Cantonese speech emotion dataset, YueMotion. This study concludes that different language and age groups require specific speech features, thus making cross-lingual inference an unsuitable method. However, cross-group data augmentation is still beneficial to regularize the model, with linguistic distance being a significant influence on cross-lingual transferability. We release publicly release our code at https://github.com/HLTCHKUST/elderly_ser.

AdaptGear: Accelerating GNN Training via Adaptive Subgraph-Level Kernels on GPUs

Graph neural networks (GNNs) are powerful tools for exploring and learning from graph structures and features. As such, achieving high-performance execution for GNNs becomes crucially important. Prior works have proposed to explore the sparsity (i.e., low density) in the input graph to accelerate GNNs, which uses the full-graph-level or block-level sparsity format. We show that they fail to balance the sparsity benefit and kernel execution efficiency. In this paper, we propose a novel system, referred to as AdaptGear, that addresses the challenge of optimizing GNNs performance by leveraging kernels tailored to the density characteristics at the subgraph level. Meanwhile, we also propose a method that dynamically chooses the optimal set of kernels for a given input graph. Our evaluation shows that AdaptGear can achieve a significant performance improvement, up to $6.49 \times$ ($1.87 \times$ on average), over the state-of-the-art works on two mainstream NVIDIA GPUs across various datasets.

Shall We Pretrain Autoregressive Language Models with Retrieval? A Comprehensive Study

Large decoder-only language models (LMs) can be largely improved in terms of perplexity by retrieval (e.g., RETRO), but its impact on text generation quality and downstream task accuracy is unclear. Thus, it is still an open question: shall we pretrain large autoregressive LMs with retrieval? To answer it, we perform a comprehensive study on a scalable pre-trained retrieval-augmented LM (i.e., RETRO) compared with standard GPT and retrieval-augmented GPT incorporated at fine-tuning or inference stages. We first provide the recipe to reproduce RETRO up to 9.5B parameters while retrieving a text corpus with 330B tokens. Based on that, we have the following novel findings: i) RETRO outperforms GPT on text generation with much less degeneration (i.e., repetition), moderately higher factual accuracy, and slightly lower toxicity with a nontoxic retrieval database. ii) On the LM Evaluation Harness benchmark, RETRO largely outperforms GPT on knowledge-intensive tasks, but is on par with GPT on other tasks. Furthermore, we introduce a simple variant of the model, RETRO++, which largely improves open-domain QA results of original RETRO (e.g., EM score +8.6 on Natural Question) and significantly outperforms retrieval-augmented GPT across different model sizes. Our findings highlight the promising direction of pretraining autoregressive LMs with retrieval as future foundation models. We release our implementation at: https://github.com/NVIDIA/Megatron-LM#retro

Towards Reasonable Budget Allocation in Untargeted Graph Structure Attacks via Gradient Debias

It has become cognitive inertia to employ cross-entropy loss function in classification related tasks. In the untargeted attacks on graph structure, the gradients derived from the attack objective are the attacker's basis for evaluating a perturbation scheme. Previous methods use negative cross-entropy loss as the attack objective in attacking node-level classification models. However, the suitability of the cross-entropy function for constructing the untargeted attack objective has yet been discussed in previous works. This paper argues about the previous unreasonable attack objective from the perspective of budget allocation. We demonstrate theoretically and empirically that negative cross-entropy tends to produce more significant gradients from nodes with lower confidence in the labeled classes, even if the predicted classes of these nodes have been misled. To free up these inefficient attack budgets, we propose a simple attack model for untargeted attacks on graph structure based on a novel attack objective which generates unweighted gradients on graph structures that are not affected by the node confidence. By conducting experiments in gray-box poisoning attack scenarios, we demonstrate that a reasonable budget allocation can significantly improve the effectiveness of gradient-based edge perturbations without any extra hyper-parameter.

Re-ViLM: Retrieval-Augmented Visual Language Model for Zero and Few-Shot Image Captioning

Augmenting pretrained language models (LMs) with a vision encoder (e.g., Flamingo) has obtained state-of-the-art results in image-to-text generation. However, these models store all the knowledge within their parameters, thus often requiring enormous model parameters to model the abundant visual concepts and very rich textual descriptions. Additionally, they are inefficient in incorporating new data, requiring a computational-expensive fine-tuning process. In this work, we introduce a Retrieval-augmented Visual Language Model, Re-ViLM, built upon the Flamingo, that supports retrieving the relevant knowledge from the external database for zero and in-context few-shot image-to-text generations. By storing certain knowledge explicitly in the external database, our approach reduces the number of model parameters and can easily accommodate new data during evaluation by simply updating the database. We also construct an interleaved image and text data that facilitates in-context few-shot learning capabilities. We demonstrate that Re-ViLM significantly boosts performance for image-to-text generation tasks, especially for zero-shot and few-shot generation in out-of-domain settings with 4 times less parameters compared with baseline methods.

Improving (Dis)agreement Detection with Inductive Social Relation Information From Comment-Reply Interactions

(Dis)agreement detection aims to identify the authors' attitudes or positions (\textit{{agree, disagree, neutral}}) towards a specific text. It is limited for existing methods merely using textual information for identifying (dis)agreements, especially for cross-domain settings. Social relation information can play an assistant role in the (dis)agreement task besides textual information. We propose a novel method to extract such relation information from (dis)agreement data into an inductive social relation graph, merely using the comment-reply pairs without any additional platform-specific information. The inductive social relation globally considers the historical discussion and the relation between authors. Textual information based on a pre-trained language model and social relation information encoded by pre-trained RGCN are jointly considered for (dis)agreement detection. Experimental results show that our model achieves state-of-the-art performance for both the in-domain and cross-domain tasks on the benchmark -- DEBAGREEMENT. We find social relations can boost the performance of the (dis)agreement detection model, especially for the long-token comment-reply pairs, demonstrating the effectiveness of the social relation graph. We also explore the effect of the knowledge graph embedding methods, the information fusing method, and the time interval in constructing the social relation graph, which shows the effectiveness of our model.

RHO ($ρ$): Reducing Hallucination in Open-domain Dialogues with Knowledge Grounding

Dialogue systems can leverage large pre-trained language models and knowledge to generate fluent and informative responses. However, these models are still prone to produce hallucinated responses not supported by the input source, which greatly hinders their application. The heterogeneity between external knowledge and dialogue context challenges representation learning and source integration, and further contributes to unfaithfulness. To handle this challenge and generate more faithful responses, this paper presents RHO ($\rho$) utilizing the representations of linked entities and relation predicates from a knowledge graph (KG). We propose (1) local knowledge grounding to combine textual embeddings with the corresponding KG embeddings; and (2) global knowledge grounding to equip RHO with multi-hop reasoning abilities via the attention mechanism. In addition, we devise a response re-ranking technique based on walks over KG sub-graphs for better conversational reasoning. Experimental results on OpenDialKG show that our approach significantly outperforms state-of-the-art methods on both automatic and human evaluation by a large margin, especially in hallucination reduction (17.54% in FeQA).

Cross-Domain Local Characteristic Enhanced Deepfake Video Detection

As ultra-realistic face forgery techniques emerge, deepfake detection has attracted increasing attention due to security concerns. Many detectors cannot achieve accurate results when detecting unseen manipulations despite excellent performance on known forgeries. In this paper, we are motivated by the observation that the discrepancies between real and fake videos are extremely subtle and localized, and inconsistencies or irregularities can exist in some critical facial regions across various information domains. To this end, we propose a novel pipeline, Cross-Domain Local Forensics (XDLF), for more general deepfake video detection. In the proposed pipeline, a specialized framework is presented to simultaneously exploit local forgery patterns from space, frequency, and time domains, thus learning cross-domain features to detect forgeries. Moreover, the framework leverages four high-level forgery-sensitive local regions of a human face to guide the model to enhance subtle artifacts and localize potential anomalies. Extensive experiments on several benchmark datasets demonstrate the impressive performance of our method, and we achieve superiority over several state-of-the-art methods on cross-dataset generalization. We also examined the factors that contribute to its performance through ablations, which suggests that exploiting cross-domain local characteristics is a noteworthy direction for developing more general deepfake detectors.

Plausible May Not Be Faithful: Probing Object Hallucination in Vision-Language Pre-training

Large-scale vision-language pre-trained (VLP) models are prone to hallucinate non-existent visual objects when generating text based on visual information. In this paper, we exhaustively probe the object hallucination problem from three aspects. First, we examine various state-of-the-art VLP models, showing that models achieving better scores on standard metrics(e.g., BLEU-4, CIDEr) could hallucinate objects more frequently. Second, we investigate how different types of visual features in VLP influence hallucination, including region-based, grid-based, and patch-based. Surprisingly, we find that patch-based features perform the best and smaller patch resolution yields a non-trivial reduction in object hallucination. Third, we decouple various VLP objectives and demonstrate their effectiveness in alleviating object hallucination. Based on that, we propose a new pre-training loss, object masked language modeling, to further reduce object hallucination. We evaluate models on both COCO (in-domain) and NoCaps (out-of-domain) datasets with our improved CHAIR metric. Furthermore, we investigate the effects of various text decoding strategies and image augmentation methods on object hallucination.