Drug discovery is a critical task in biomedical natural language processing (NLP), yet explainable drug discovery remains underexplored. Meanwhile, large language models (LLMs) have shown remarkable abilities in natural language understanding and generation. Leveraging LLMs for explainable drug discovery has the potential to improve downstream tasks and real-world applications. In this study, we utilize open-source drug knowledge graphs, clinical trial data, and PubMed publications to construct a comprehensive dataset for the explainable drug discovery task, named \textbf{expRxRec}. Furthermore, we introduce \textbf{KEDRec-LM}, an instruction-tuned LLM which distills knowledge from rich medical knowledge corpus for drug recommendation and rationale generation. To encourage further research in this area, we will publicly release\footnote{A copy is attached with this submission} both the dataset and KEDRec-LM.

Large language models (LLMs) excel in tasks that require complex linguistic abilities, such as reference disambiguation and metaphor recognition/generation. Although LLMs possess impressive capabilities, their internal mechanisms for processing and representing linguistic knowledge remain largely opaque. Previous work on linguistic mechanisms has been limited by coarse granularity, insufficient causal analysis, and a narrow focus. In this study, we present a systematic and comprehensive causal investigation using sparse auto-encoders (SAEs). We extract a wide range of linguistic features from six dimensions: phonetics, phonology, morphology, syntax, semantics, and pragmatics. We extract, evaluate, and intervene on these features by constructing minimal contrast datasets and counterfactual sentence datasets. We introduce two indices-Feature Representation Confidence (FRC) and Feature Intervention Confidence (FIC)-to measure the ability of linguistic features to capture and control linguistic phenomena. Our results reveal inherent representations of linguistic knowledge in LLMs and demonstrate the potential for controlling model outputs. This work provides strong evidence that LLMs possess genuine linguistic knowledge and lays the foundation for more interpretable and controllable language modeling in future research.

Recent advancements have demonstrated that the performance of large language models (LLMs) can be significantly enhanced by scaling computational resources at test time. A common strategy involves generating multiple Chain-of-Thought (CoT) trajectories and aggregating their outputs through various selection mechanisms. This raises a fundamental question: can models with lower complexity leverage their superior generation throughput to outperform similarly sized Transformers for a fixed computational budget? To address this question and overcome the lack of strong subquadratic reasoners, we distill pure and hybrid Mamba models from pretrained Transformers. Trained on only 8 billion tokens, our distilled models show strong performance and scaling on mathematical reasoning datasets while being much faster at inference for large batches and long sequences. Despite the zero-shot performance hit due to distillation, both pure and hybrid Mamba models can scale their coverage and accuracy performance past their Transformer teacher models under fixed time budgets, opening a new direction for scaling inference compute.

Clinical decision-making depends on expert reasoning, which is guided by standardized, evidence-based guidelines. However, translating these guidelines into automated clinical decision support systems risks inaccuracy and importantly, loss of nuance. We share an application architecture, the Large Language Expert (LLE), that combines the flexibility and power of Large Language Models (LLMs) with the interpretability, explainability, and reliability of Expert Systems. LLMs help address key challenges of Expert Systems, such as integrating and codifying knowledge, and data normalization. Conversely, an Expert System-like approach helps overcome challenges with LLMs, including hallucinations, atomic and inexpensive updates, and testability. To highlight the power of the Large Language Expert (LLE) system, we built an LLE to assist with the workup of patients newly diagnosed with cancer. Timely initiation of cancer treatment is critical for optimal patient outcomes. However, increasing complexity in diagnostic recommendations has made it difficult for primary care physicians to ensure their patients have completed the necessary workup before their first visit with an oncologist. As with many real-world clinical tasks, these workups require the analysis of unstructured health records and the application of nuanced clinical decision logic. In this study, we describe the design & evaluation of an LLE system built to rapidly identify and suggest the correct diagnostic workup. The system demonstrated a high degree of clinical-level accuracy (>95%) and effectively addressed gaps identified in real-world data from breast and colon cancer patients at a large academic center.

Many recent studies have found evidence for emergent reasoning capabilities in large language models, but debate persists concerning the robustness of these capabilities, and the extent to which they depend on structured reasoning mechanisms. To shed light on these issues, we perform a comprehensive study of the internal mechanisms that support abstract rule induction in an open-source language model (Llama3-70B). We identify an emergent symbolic architecture that implements abstract reasoning via a series of three computations. In early layers, symbol abstraction heads convert input tokens to abstract variables based on the relations between those tokens. In intermediate layers, symbolic induction heads perform sequence induction over these abstract variables. Finally, in later layers, retrieval heads predict the next token by retrieving the value associated with the predicted abstract variable. These results point toward a resolution of the longstanding debate between symbolic and neural network approaches, suggesting that emergent reasoning in neural networks depends on the emergence of symbolic mechanisms.

The emergence of long-context large language models (LLMs) offers a promising alternative to traditional retrieval-augmented generation (RAG) for processing extensive documents. However, the computational overhead of long-context inference, particularly in managing key-value (KV) caches, presents significant efficiency challenges. While Speculative Decoding (SD) traditionally accelerates inference using smaller draft models, its effectiveness diminishes substantially in long-context scenarios due to memory-bound KV cache operations. We present Retrieval-Augmented Speculative Decoding (RAPID), which leverages RAG for both accelerating and enhancing generation quality in long-context inference. RAPID introduces the RAG drafter-a draft LLM operating on shortened retrieval contexts-to speculate on the generation of long-context target LLMs. Our approach enables a new paradigm where same-scale or even larger LLMs can serve as RAG drafters while maintaining computational efficiency. To fully leverage the potentially superior capabilities from stronger RAG drafters, we develop an inference-time knowledge transfer dynamic that enriches the target distribution by RAG. Extensive experiments on the LLaMA-3.1 and Qwen2.5 backbones demonstrate that RAPID effectively integrates the strengths of both approaches, achieving significant performance improvements (e.g., from 39.33 to 42.83 on InfiniteBench for LLaMA-3.1-8B) with more than 2x speedups. Our analyses reveal that RAPID achieves robust acceleration beyond 32K context length and demonstrates superior generation quality in real-world applications.

The representation disparity between visual generation and understanding imposes a critical gap in integrating these capabilities into a single framework. To bridge this gap, we introduce UniTok, a discrete visual tokenizer that encodes fine-grained details for generation while also capturing high-level semantics for understanding. Despite recent studies have shown that these objectives could induce loss conflicts in training, we reveal that the underlying bottleneck stems from limited representational capacity of discrete tokens. We address this by introducing multi-codebook quantization, which divides vector quantization with several independent sub-codebooks to expand the latent feature space, while avoiding training instability caused by overlarge codebooks. Our method significantly raises the upper limit of unified discrete tokenizers to match or even surpass domain-specific continuous tokenizers. For instance, UniTok achieves a remarkable rFID of 0.38 (versus 0.87 for SD-VAE) and a zero-shot accuracy of 78.6% (versus 76.2% for CLIP) on ImageNet. Our code is available at https://github.com/FoundationVision/UniTok.

Composing language models (LMs) into multi-step language programs and automatically optimizing their modular prompts is now a mainstream paradigm for building AI systems, but the tradeoffs in this space have only scarcely been studied before. We introduce LangProBe, the first large-scale benchmark for evaluating the architectures and optimization strategies for language programs, with over 2000 combinations of tasks, architectures, optimizers, and choices of LMs. Using LangProBe, we are the first to study the impact of program architectures and optimizers (and their compositions together and with different models) on tradeoffs of quality and cost. We find that optimized language programs offer strong cost--quality Pareto improvement over raw calls to models, but simultaneously demonstrate that human judgment (or empirical decisions) about which compositions to pursue is still necessary for best performance. We will open source the code and evaluation data for LangProBe.

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

Fake news poses global risks by influencing elections and spreading misinformation, making detection critical. Existing NLP and supervised Machine Learning methods perform well under cross-validation but struggle to generalise across datasets, even within the same domain. This issue stems from coarsely labelled training data, where articles are labelled based on their publisher, introducing biases that token-based models like TF-IDF and BERT are sensitive to. While Large Language Models (LLMs) offer promise, their application in fake news detection remains limited. This study demonstrates that meaningful features can still be extracted from coarsely labelled data to improve real-world robustness. Stylistic features-lexical, syntactic, and semantic-are explored due to their reduced sensitivity to dataset biases. Additionally, novel social-monetisation features are introduced, capturing economic incentives behind fake news, such as advertisements, external links, and social media elements. The study trains on the coarsely labelled NELA 2020-21 dataset and evaluates using the manually labelled Facebook URLs dataset, a gold standard for generalisability. Results highlight the limitations of token-based models trained on biased data and contribute to the scarce evidence on LLMs like LLaMa in this field. Findings indicate that stylistic and social-monetisation features offer more generalisable predictions than token-based methods and LLMs. Statistical and permutation feature importance analyses further reveal their potential to enhance performance and mitigate dataset biases, providing a path forward for improving fake news detection.