Directed evolution is a molecular biology technique that is transforming protein engineering by creating proteins with desirable properties and functions. However, it is experimentally impossible to perform the deep mutational scanning of the entire protein library due to the enormous mutational space, which scales as $20^N$ , where N is the number of amino acids. This has led to the rapid growth of AI-assisted directed evolution (AIDE) or AI-assisted protein engineering (AIPE) as an emerging research field. Aided with advanced natural language processing (NLP) techniques, including long short-term memory, autoencoder, and transformer, sequence-based embeddings have been dominant approaches in AIDE and AIPE. Persistent Laplacians, an emerging technique in topological data analysis (TDA), have made structure-based embeddings a superb option in AIDE and AIPE. We argue that a class of persistent topological Laplacians (PTLs), including persistent Laplacians, persistent path Laplacians, persistent sheaf Laplacians, persistent hypergraph Laplacians, persistent hyperdigraph Laplacians, and evolutionary de Rham-Hodge theory, can effectively overcome the limitations of the current TDA and offer a new generation of more powerful TDA approaches. In the general framework of topological deep learning, mathematics-assisted directed evolution (MADE) has a great potential for future protein engineering.

Monolingual word alignment is crucial to model semantic interactions between sentences. In particular, null alignment, a phenomenon in which words have no corresponding counterparts, is pervasive and critical in handling semantically divergent sentences. Identification of null alignment is useful on its own to reason about the semantic similarity of sentences by indicating there exists information inequality. To achieve unbalanced word alignment that values both alignment and null alignment, this study shows that the family of optimal transport (OT), i.e., balanced, partial, and unbalanced OT, are natural and powerful approaches even without tailor-made techniques. Our extensive experiments covering unsupervised and supervised settings indicate that our generic OT-based alignment methods are competitive against the state-of-the-arts specially designed for word alignment, remarkably on challenging datasets with high null alignment frequencies.

Few-shot question answering (QA) aims at precisely discovering answers to a set of questions from context passages while only a few training samples are available. Although existing studies have made some progress and can usually achieve proper results, they suffer from understanding deep semantics for reasoning out the questions. In this paper, we develop Gotta, a Generative prOmpT-based daTa Augmentation framework to mitigate the challenge above. Inspired by the human reasoning process, we propose to integrate the cloze task to enhance few-shot QA learning. Following the recent success of prompt-tuning, we present the cloze task in the same format as the main QA task, allowing the model to learn both tasks seamlessly together to fully take advantage of the power of prompt-tuning. Extensive experiments on widely used benchmarks demonstrate that Gotta consistently outperforms competitive baselines, validating the effectiveness of our proposed prompt-tuning-based cloze task, which not only fine-tunes language models but also learns to guide reasoning in QA tasks. Further analysis shows that the prompt-based loss incorporates the auxiliary task better than the multi-task loss, highlighting the strength of prompt-tuning on the few-shot QA task.

Cross-Lingual Semantic Parsing (CLSP) aims to translate queries in multiple natural languages (NLs) into meaning representations (MRs) such as SQL, lambda calculus, and logic forms. However, existing CLSP models are separately proposed and evaluated on datasets of limited tasks and applications, impeding a comprehensive and unified evaluation of CLSP on a diverse range of NLs and MRs. To this end, we present XSemPLR, a unified benchmark for cross-lingual semantic parsing featured with 22 natural languages and 8 meaning representations by examining and selecting 9 existing datasets to cover 5 tasks and 164 domains. We use XSemPLR to conduct a comprehensive benchmark study on a wide range of multilingual language models including encoder-based models (mBERT, XLM-R), encoder-decoder models (mBART, mT5), and decoder-based models (Codex, BLOOM). We design 6 experiment settings covering various lingual combinations (monolingual, multilingual, cross-lingual) and numbers of learning samples (full dataset, few-shot, and zero-shot). Our experiments show that encoder-decoder models (mT5) achieve the highest performance compared with other popular models, and multilingual training can further improve the average performance. Notably, multilingual large language models (e.g., BLOOM) are still inadequate to perform CLSP tasks. We also find that the performance gap between monolingual training and cross-lingual transfer learning is still significant for multilingual models, though it can be mitigated by cross-lingual few-shot training. Our dataset and code are available at https://github.com/psunlpgroup/XSemPLR.

The increasingly large size of modern pretrained language models not only makes them inherit more human-like biases from the training corpora, but also makes it computationally expensive to mitigate such biases. In this paper, we investigate recent parameter-efficient methods in combination with counterfactual data augmentation (CDA) for bias mitigation. We conduct extensive experiments with prefix tuning, prompt tuning, and adapter tuning on different language models and bias types to evaluate their debiasing performance and abilities to preserve the internal knowledge of a pre-trained model. We find that the parameter-efficient methods (i) are effective in mitigating gender bias, where adapter tuning is consistently the most effective one and prompt tuning is more suitable for GPT-2 than BERT, (ii) are less effective when it comes to racial and religious bias, which may be attributed to the limitations of CDA, and (iii) can perform similarly to or sometimes better than full fine-tuning with improved time and memory efficiency, as well as maintain the internal knowledge in BERT and GPT-2, evaluated via fact retrieval and downstream fine-tuning.

This paper investigates the prospect of developing human-interpretable, explainable artificial intelligence (AI) systems based on active inference and the free energy principle. We first provide a brief overview of active inference, and in particular, of how it applies to the modeling of decision-making, introspection, as well as the generation of overt and covert actions. We then discuss how active inference can be leveraged to design explainable AI systems, namely, by allowing us to model core features of ``introspective'' processes and by generating useful, human-interpretable models of the processes involved in decision-making. We propose an architecture for explainable AI systems using active inference. This architecture foregrounds the role of an explicit hierarchical generative model, the operation of which enables the AI system to track and explain the factors that contribute to its own decisions, and whose structure is designed to be interpretable and auditable by human users. We outline how this architecture can integrate diverse sources of information to make informed decisions in an auditable manner, mimicking or reproducing aspects of human-like consciousness and introspection. Finally, we discuss the implications of our findings for future research in AI, and the potential ethical considerations of developing AI systems with (the appearance of) introspective capabilities.

An important problem in time-series analysis is modeling systems with time-varying dynamics. Probabilistic models with joint continuous and discrete latent states offer interpretable, efficient, and experimentally useful descriptions of such data. Commonly used models include autoregressive hidden Markov models (ARHMMs) and switching linear dynamical systems (SLDSs), each with its own advantages and disadvantages. ARHMMs permit exact inference and easy parameter estimation, but are parameter intensive when modeling long dependencies, and hence are prone to overfitting. In contrast, SLDSs can capture long-range dependencies in a parameter efficient way through Markovian latent dynamics, but present an intractable likelihood and a challenging parameter estimation task. In this paper, we propose switching autoregressive low-rank tensor (SALT) models, which retain the advantages of both approaches while ameliorating the weaknesses. SALT parameterizes the tensor of an ARHMM with a low-rank factorization to control the number of parameters and allow longer range dependencies without overfitting. We prove theoretical and discuss practical connections between SALT, linear dynamical systems, and SLDSs. We empirically demonstrate quantitative advantages of SALT models on a range of simulated and real prediction tasks, including behavioral and neural datasets. Furthermore, the learned low-rank tensor provides novel insights into temporal dependencies within each discrete state.

We present bgGLUE(Bulgarian General Language Understanding Evaluation), a benchmark for evaluating language models on Natural Language Understanding (NLU) tasks in Bulgarian. Our benchmark includes NLU tasks targeting a variety of NLP problems (e.g., natural language inference, fact-checking, named entity recognition, sentiment analysis, question answering, etc.) and machine learning tasks (sequence labeling, document-level classification, and regression). We run the first systematic evaluation of pre-trained language models for Bulgarian, comparing and contrasting results across the nine tasks in the benchmark. The evaluation results show strong performance on sequence labeling tasks, but there is a lot of room for improvement for tasks that require more complex reasoning. We make bgGLUE publicly available together with the fine-tuning and the evaluation code, as well as a public leaderboard at https://bgglue.github.io/, and we hope that it will enable further advancements in developing NLU models for Bulgarian.

The black-box nature of complex Neural Network (NN)-based models has hindered their widespread adoption in security domains due to the lack of logical explanations and actionable follow-ups for their predictions. To enhance the transparency and accountability of Graph Neural Network (GNN) security models used in system provenance analysis, we propose PROVEXPLAINER, a framework for projecting abstract GNN decision boundaries onto interpretable feature spaces. We first replicate the decision-making process of GNNbased security models using simpler and explainable models such as Decision Trees (DTs). To maximize the accuracy and fidelity of the surrogate models, we propose novel graph structural features founded on classical graph theory and enhanced by extensive data study with security domain knowledge. Our graph structural features are closely tied to problem-space actions in the system provenance domain, which allows the detection results to be explained in descriptive, human language. PROVEXPLAINER allowed simple DT models to achieve 95% fidelity to the GNN on program classification tasks with general graph structural features, and 99% fidelity on malware detection tasks with a task-specific feature package tailored for direct interpretation. The explanations for malware classification are demonstrated with case studies of five real-world malware samples across three malware families.

Transformers have been shown to work well for the task of English euphemism disambiguation, in which a potentially euphemistic term (PET) is classified as euphemistic or non-euphemistic in a particular context. In this study, we expand on the task in two ways. First, we annotate PETs for vagueness, a linguistic property associated with euphemisms, and find that transformers are generally better at classifying vague PETs, suggesting linguistic differences in the data that impact performance. Second, we present novel euphemism corpora in three different languages: Yoruba, Spanish, and Mandarin Chinese. We perform euphemism disambiguation experiments in each language using multilingual transformer models mBERT and XLM-RoBERTa, establishing preliminary results from which to launch future work.