Emotion Recognition in Conversations (ERC) facilitates a deeper understanding of the emotions conveyed by speakers in each utterance within a conversation. Recently, Graph Neural Networks (GNNs) have demonstrated their strengths in capturing data relationships, particularly in contextual information modeling and multimodal fusion. However, existing methods often struggle to fully capture the complex interactions between multiple modalities and conversational context, limiting their expressiveness. To overcome these limitations, we propose ConxGNN, a novel GNN-based framework designed to capture contextual information in conversations. ConxGNN features two key parallel modules: a multi-scale heterogeneous graph that captures the diverse effects of utterances on emotional changes, and a hypergraph that models the multivariate relationships among modalities and utterances. The outputs from these modules are integrated into a fusion layer, where a cross-modal attention mechanism is applied to produce a contextually enriched representation. Additionally, ConxGNN tackles the challenge of recognizing minority or semantically similar emotion classes by incorporating a re-weighting scheme into the loss functions. Experimental results on the IEMOCAP and MELD benchmark datasets demonstrate the effectiveness of our method, achieving state-of-the-art performance compared to previous baselines.

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Latent space optimization (LSO) is a powerful method for designing discrete, high-dimensional biological sequences that maximize expensive black-box functions, such as wet lab experiments. This is accomplished by learning a latent space from available data and using a surrogate model fΦ to guide optimization algorithms toward optimal outputs. However, existing methods struggle when labeled data is limited, as training fΦ with few labeled data points can lead to subpar outputs, offering no advantage over the training data itself. We address this challenge by introducing GROOT, a GRaph-based Latent SmOOThing for Biological Sequence Optimization. In particular, GROOT generates pseudo-labels for neighbors sampled around the training latent embeddings. These pseudo-labels are then refined and smoothed by Label Propagation. Additionally, we theoretically and empirically justify our approach, demonstrate GROOT's ability to extrapolate to regions beyond the training set while maintaining reliability within an upper bound of their expected distances from the training regions. We evaluate GROOT on various biological sequence design tasks, including protein optimization (GFP and AAV) and three tasks with exact oracles from Design-Bench. The results demonstrate that GROOT equalizes and surpasses existing methods without requiring access to black-box oracles or vast amounts of labeled data, highlighting its practicality and effectiveness. We release our code at https://github.com/Fsoft-AIC/GROOT.

Directed evolution, a strategy for protein engineering, optimizes protein properties (i.e., fitness) by a rigorous and resource-intensive process of screening or selecting among a vast range of mutations. By conducting an in-silico screening of sequence properties, machine learning-guided directed evolution (MLDE) can expedite the optimization process and alleviate the experimental workload. In this work, we propose a general MLDE framework in which we apply recent advancements of deep learning in protein representation learning and protein property prediction to accelerate the searching and optimization processes. In particular, we introduce an optimization pipeline that utilizes the large language models (LLMs) to pinpoint the mutation hotspots in the sequence and then suggest replacements to improve the overall fitness. Our experiments have shown the superior efficiency and efficacy of our proposed framework in the conditional protein generation, in comparison with the other state-of-the-art baseline algorithms. We expect this work will shed a new light on not only protein engineering but also on solving the combinatorial problems using the data-driven methods.