Generative protein language models are a natural way to design new proteins with desired functions.

Richard Holmes, our greatest living biographer, is back with an enthralling chronicle of the poet. Enter your email to receive alerts for this author. You can manage your newsletter subscriptions at any time. You're already subscribed to the aa_Laura_Miller newsletter. You can manage your newsletter subscriptions at any time.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families.

While large language models (LLMs) are driving the rapid advancement of artificial intelligence, effectively and reliably training these large models remains one of the field's most significant challenges. To address this challenge, we propose POET, a novel reParameterized training algorithm that uses Orthogonal Equivalence Transformation to optimize neurons. Specifically, POET reparameterizes each neuron with two learnable orthogonal matrices and a fixed random weight matrix. Because of its provable preservation of spectral properties of weight matrices, POET can stably optimize the objective function with improved generalization. We further develop efficient approximations that make POET flexible and scalable for training large-scale neural networks. Extensive experiments validate the effectiveness and scalability of POET in training LLMs.

Generative protein language models are a natural way to design new proteins with desired functions.

Direct Alignment Algorithms (DAAs), such as Direct Preference Optimization (DPO) and Simple Preference Optimization (SimPO), have emerged as efficient alternatives to Reinforcement Learning from Human Feedback (RLHF) algorithms for aligning large language models (LLMs) with human preferences. However, DAAs suffer from a fundamental limitation we identify as the "reward-generation gap" -- a misalignment between optimization objectives during training and actual generation performance during inference. In this paper, we find a contributor to the reward-generation gap is the mismatch between the inherent importance of prefix tokens during the LLM generation process and how this importance is reflected in the implicit reward functions of DAAs. To bridge the gap, we adopt a token-level MDP perspective of DAAs to analyze its limitations and introduce a simple yet effective approach called Prefix-Oriented Equal-length Training (POET), which truncates both preferred and dispreferred responses to match the shorter one's length. Training with \mname, where both responses in each sample are truncated to equal length, resulting in diverse truncated lengths across samples, the optimization of DAAs objective is implicitly constrained to converge across all timesteps of token-level MDP, thus paying more attention to prefix tokens than the standard DAAs. We conduct experiments with DPO and SimPO, two representative DAAs, demonstrating that POET improves over their standard implementations, achieving up to 15.6 points in AlpacaEval 2 and overall improvements across downstream tasks. Our results highlight the importance of addressing the misalignment between reward optimization and generation performance in DAAs.

This study formalizes a computational model to simulate classical Persian poets' dynamics of influence through constructing a multi-dimensional similarity network. Using a rigorously curated dataset based on Ganjoor's corpus, we draw upon semantic, lexical, stylistic, thematic, and metrical features to demarcate each poet's corpus. Each is contained within weighted similarity matrices, which are then appended to generate an aggregate graph showing poet-to-poet influence. Further network investigation is carried out to identify key poets, style hubs, and bridging poets by calculating degree, closeness, betweenness, eigenvector, and Katz centrality measures. Further, for typological insight, we use the Louvain community detection algorithm to demarcate clusters of poets sharing both style and theme coherence, which correspond closely to acknowledged schools of literature like Sabk-e Hindi, Sabk-e Khorasani, and the Bazgasht-e Adabi phenomenon. Our findings provide a new data-driven view of Persian literature distinguished between canonical significance and interextual influence, thus highlighting relatively lesser-known figures who hold great structural significance. Combining computational linguistics with literary study, this paper produces an interpretable and scalable model for poetic tradition, enabling retrospective reflection as well as forward-looking research within digital humanities.

There are not one but two dimensions of bias that can be revealed through the study of large AI models: not only bias in training data or the products of an AI, but also bias in society, such as disparity in employment or health outcomes between different demographic groups. Often training data and AI output is biased for or against certain demographics (i.e. older white people are overrepresented in image datasets), but sometimes large AI models accurately illustrate biases in the real world (i.e. young black men being disproportionately viewed as threatening). These social disparities often appear in image generation AI outputs in the form of 'marked' features, where some feature of an individual or setting is a social marker of disparity, and prompts both humans and AI systems to treat subjects that are marked in this way as exceptional and requiring special treatment. Generative AI has proven to be very sensitive to such marked features, to the extent of over-emphasising them and thus often exacerbating social biases. I briefly discuss how we can use complex prompts to image generation AI to investigate either dimension of bias, emphasising how we can probe the large language models underlying image generation AI through, for example, automated sentiment analysis of the text prompts used to generate images.

According to the recently introduced theory of artistic support tools, creativity support tools exert normative influences over artistic production, instantiating a normative ground that shapes both the process and product of artistic expression. We argue that the normative ground of most existing automated writing tools is misaligned with writerly values and identify a potential alternative frame-material writing support-for experimental poetry tools that flexibly support the finding, processing, transforming, and shaping of text(s). Based on this frame, we introduce Phraselette, an artistic material writing support interface that helps experimental poets search for words and phrases. To provide material writing support, Phraselette is designed to counter the dominant mode of automated writing tools, while offering language model affordances in line with writerly values. We further report on an extended expert evaluation involving 10 published poets that indicates support for both our framing of material writing support and for Phraselette itself.

First-order logic (FOL) reasoning, which involves sequential deduction, is pivotal for intelligent systems and serves as a valuable task for evaluating reasoning capabilities, particularly in chain-of-thought (CoT) contexts. Existing benchmarks often rely on extensive human annotation or handcrafted templates, making it difficult to achieve the necessary complexity, scalability, and diversity for robust evaluation. To address these limitations, we propose a novel framework called ProverGen that synergizes the generative strengths of Large Language Models (LLMs) with the rigor and precision of symbolic provers, enabling the creation of a scalable, diverse, and high-quality FOL reasoning dataset, ProverQA. ProverQA is also distinguished by its inclusion of accessible and logically coherent intermediate reasoning steps for each problem. Our evaluation shows that state-of-the-art LLMs struggle to solve ProverQA problems, even with CoT prompting, highlighting the dataset's challenging nature. We also finetune Llama3.1-8B-Instruct on a separate training set generated by our framework. The finetuned model demonstrates consistent improvements on both in-distribution and out-of-distribution test sets, suggesting the value of our proposed data generation framework. Code available at: https://github.com/opendatalab/ProverGen