Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

This paper introduces CodeQUEST, a novel framework leveraging Large Language Models (LLMs) to iteratively evaluate and enhance code quality across multiple dimensions, including readability, maintainability, efficiency, and security. The framework is divided into two main components: an Evaluator that assesses code quality across ten dimensions, providing both quantitative scores and qualitative summaries, and an Optimizer that iteratively improves the code based on the Evaluator's feedback. Our study demonstrates that CodeQUEST can effectively and robustly evaluate code quality, with its assessments aligning closely with established code quality metrics. Through a series of experiments using a curated dataset of Python and JavaScript examples, CodeQUEST demonstrated significant improvements in code quality, achieving a mean relative percentage improvement of 52.6%. The framework's evaluations were validated against a set of proxy metrics comprising of Pylint Score, Radon Maintainability Index, and Bandit output logs, showing a meaningful correlation. This highlights the potential of LLMs in automating code quality evaluation and improvement processes, presenting a significant advancement toward enhancing software development practices. The code implementation of the framework is available at: https://github.com/jpmorganchase/CodeQuest.

The growing volume of digitized historical texts requires effective semantic search using text embeddings. However, pre-trained multilingual models, typically evaluated on contemporary texts, face challenges with historical digitized content due to OCR noise and outdated spellings. We explore the use of multilingual embeddings for cross-lingual semantic search on historical Luxembourgish, a low-resource language. We collect historical Luxembourgish news articles spanning various time periods and use GPT-4o to segment and translate them into closely related languages, creating 20,000 parallel training sentences per language pair. We further create a historical bitext mining evaluation set and find that these models struggle to perform cross-lingual search on historical Luxembourgish. To address this, we propose a simple adaptation method using in-domain training data, achieving up to 98\% accuracy in cross-lingual evaluations. We release our adapted models and historical Luxembourgish-German/French bitexts to support further research.

Sarcasm is a linguistic phenomenon that intends to ridicule a target (e.g., entity, event, or person) in an inherent way. Multimodal Sarcasm Explanation (MuSE) aims at revealing the intended irony in a sarcastic post using a natural language explanation. Though important, existing systems overlooked the significance of the target of sarcasm in generating explanations. In this paper, we propose a Target-aUgmented shaRed fusion-Based sarcasm explanatiOn model, aka. TURBO. We design a novel shared-fusion mechanism to leverage the inter-modality relationships between an image and its caption. TURBO assumes the target of the sarcasm and guides the multimodal shared fusion mechanism in learning intricacies of the intended irony for explanations. We evaluate our proposed TURBO model on the MORE+ dataset. Comparison against multiple baselines and state-of-the-art models signifies the performance improvement of TURBO by an average margin of $+3.3\%$. Moreover, we explore LLMs in zero and one-shot settings for our task and observe that LLM-generated explanation, though remarkable, often fails to capture the critical nuances of the sarcasm. Furthermore, we supplement our study with extensive human evaluation on TURBO's generated explanations and find them out to be comparatively better than other systems.

Large language models (LLMs) have achieved impressive success, but their high memory requirements present challenges for long-context token generation. The memory complexity of long-context LLMs is primarily due to the need to store Key-Value (KV) embeddings in their KV cache. We present BalanceKV, a KV cache compression method based on geometric sampling process stemming from Banaszczyk's vector balancing theory, which introduces dependencies informed by the geometry of keys and value tokens, and improves precision. BalanceKV offers both theoretically proven and empirically validated performance improvements over existing methods.

Recent theoretical work by [Kalai and Vempala 2024] proves that a particular notion of hallucination rate in LLMs must be lower bounded by the training data monofact rate (related to the classical Good-Turing missing mass estimator) minus model miscalibration. Through systematic experiments with n-gram models and in-context learning with LLMs, we empirically investigate and validate this theory by examining how different underlying data distributions affect the monofact rate and a model's tendency to hallucinate. We then vary model miscalibration through controlled upweighting of training samples while holding monofact rates constant, allowing us to isolate miscalibration's reduction effect on hallucination. These findings suggest that both the distribution of fact frequencies in training data and the calibration-hallucination trade-off are inherent to probabilistic language generation. Our results also suggest that current practices of aggressive deduplication in training data may need to be reconsidered, as selective duplication could serve as a principled mechanism for reducing hallucination.

Whole slide pathology image classification presents challenges due to gigapixel image sizes and limited annotation labels, hindering model generalization. This paper introduces a prompt learning method to adapt large vision-language models for few-shot pathology classification. We first extend the Prov-GigaPath vision foundation model, pre-trained on 1.3 billion pathology image tiles, into a vision-language model by adding adaptors and aligning it with medical text encoders via contrastive learning on 923K image-text pairs. The model is then used to extract visual features and text embeddings from few-shot annotations and fine-tunes with learnable prompt embeddings. Unlike prior methods that combine prompts with frozen features using prefix embeddings or self-attention, we propose multi-granular attention that compares interactions between learnable prompts with individual image patches and groups of them. This approach improves the model's ability to capture both fine-grained details and broader context, enhancing its recognition of complex patterns across sub-regions. To further improve accuracy, we leverage (unbalanced) optimal transport-based visual-text distance to secure model robustness by mitigating perturbations that might occur during the data augmentation process. Empirical experiments on lung, kidney, and breast pathology modalities validate the effectiveness of our approach; thereby, we surpass several of the latest competitors and consistently improve performance across diverse architectures, including CLIP, PLIP, and Prov-GigaPath integrated PLIP. We release our implementations and pre-trained models at this MGPATH.

The application of Large Language Models (LLMs) in analog integrated circuit design could pioneer a new era of AI applications in domains traditionally dominated by human expertise. Analog semiconductor chips are the core building blocks in sensing and communication systems. Contrary to digital chip development, where computer-aided design automation has been widely adopted for a few decades, analog design, often perceived more as a craftsmanship than a well-established engineering procedure, relies heavily on the designer's experience and intuition to navigate in the trade space of efficiency, noise, linearity, and speed to meet certain specifications. This domain's depth, requiring a blend of acumen and creativity, underscores the high barriers to entry and the extensive training required to master its intricacies, which exacerbated the critical labor shortfall of the semiconductor industry in this decade [Ravi, 2023]. The advent of AI-assisted design automation in analog circuit design holds considerable promise to tackle the aforementioned challenge. It offers the potential to significantly streamline design cycles, enabling engineers to focus more on strategic, high-level design considerations and the exploration of novel ideas and applications.

Named Entity Recognition (NER) is a fundamental problem in natural language processing (NLP). However, the task of extracting longer entity spans (e.g., awards) from extended texts (e.g., homepages) is barely explored. Current NER methods predominantly fall into two categories: span-based methods and generation-based methods. Span-based methods require the enumeration of all possible token-pair spans, followed by classification on each span, resulting in substantial redundant computations and excessive GPU memory usage. In contrast, generation-based methods involve prompting or fine-tuning large language models (LLMs) to adapt to downstream NER tasks. However, these methods struggle with the accurate generation of longer spans and often incur significant time costs for effective fine-tuning. To address these challenges, this paper introduces a lightweight span-based NER method called SeNER, which incorporates a bidirectional arrow attention mechanism coupled with LogN-Scaling on the [CLS] token to embed long texts effectively, and comprises a novel bidirectional sliding-window plus-shaped attention (BiSPA) mechanism to reduce redundant candidate token-pair spans significantly and model interactions between token-pair spans simultaneously. Extensive experiments demonstrate that our method achieves state-of-the-art extraction accuracy on three long NER datasets and is capable of extracting entities from long texts in a GPU-memory-friendly manner. Code: https://github.com/THUDM/scholar-profiling/tree/main/sener

Large Language Models (LLMs) have achieved impressive results across numerous domains, yet they experience notable deficiencies in legal question-answering tasks. LLMs often generate generalized responses that lack the logical specificity required for expert legal advice and are prone to hallucination, providing answers that appear correct but are unreliable. Retrieval-Augmented Generation (RAG) techniques offer partial solutions to address this challenge, but existing approaches typically focus only on semantic similarity, neglecting the logical structure essential to legal reasoning. In this paper, we propose the Logical-Semantic Integration Model (LSIM), a novel supervised framework that bridges semantic and logical coherence. LSIM comprises three components: reinforcement learning predicts a structured fact-rule chain for each question, a trainable Deep Structured Semantic Model (DSSM) retrieves the most relevant candidate questions by integrating semantic and logical features, and in-context learning generates the final answer using the retrieved content. Our experiments on a real-world legal QA dataset-validated through both automated metrics and human evaluation-demonstrate that LSIM significantly enhances accuracy and reliability compared to existing methods.