Prompting Decision Transformers for Zero-Shot Reach-Avoid Policies

Offline goal-conditioned reinforcement learning methods have shown promise for reach-avoid tasks, where an agent must reach a target state while avoiding undesirable regions of the state space. Existing approaches typically encode avoid-region information into an augmented state space and cost function, which prevents flexible, dynamic specification of novel avoid-region information at evaluation time. They also rely heavily on well-designed reward and cost functions, limiting scalability to complex or poorly structured environments. We introduce RADT, a decision transformer model for offline, reward-free, goal-conditioned, avoid region-conditioned RL. RADT encodes goals and avoid regions directly as prompt tokens, allowing any number of avoid regions of arbitrary size to be specified at evaluation time. Using only suboptimal offline trajectories from a random policy, RADT learns reach-avoid behavior through a novel combination of goal and avoid-region hindsight relabeling. We benchmark RADT against 3 existing offline goal-conditioned RL models across 11 tasks, environments, and experimental settings. RADT generalizes in a zero-shot manner to out-of-distribution avoid region sizes and counts, outperforming baselines that require retraining. In one such zero-shot setting, RADT achieves 35.7% improvement in normalized cost over the best retrained baseline while maintaining high goal-reaching success. We apply RADT to cell reprogramming in biology, where it reduces visits to undesirable intermediate gene expression states during trajectories to desired target states, despite stochastic transitions and discrete, structured state dynamics.

Token Reduction Should Go Beyond Efficiency in Generative Models -- From Vision, Language to Multimodality

In Transformer architectures, tokens\textemdash discrete units derived from raw data\textemdash are formed by segmenting inputs into fixed-length chunks. Each token is then mapped to an embedding, enabling parallel attention computations while preserving the input's essential information. Due to the quadratic computational complexity of transformer self-attention mechanisms, token reduction has primarily been used as an efficiency strategy. This is especially true in single vision and language domains, where it helps balance computational costs, memory usage, and inference latency. Despite these advances, this paper argues that token reduction should transcend its traditional efficiency-oriented role in the era of large generative models. Instead, we position it as a fundamental principle in generative modeling, critically influencing both model architecture and broader applications. Specifically, we contend that across vision, language, and multimodal systems, token reduction can: (i) facilitate deeper multimodal integration and alignment, (ii) mitigate "overthinking" and hallucinations, (iii) maintain coherence over long inputs, and (iv) enhance training stability, etc. We reframe token reduction as more than an efficiency measure. By doing so, we outline promising future directions, including algorithm design, reinforcement learning-guided token reduction, token optimization for in-context learning, and broader ML and scientific domains. We highlight its potential to drive new model architectures and learning strategies that improve robustness, increase interpretability, and better align with the objectives of generative modeling.

PyTDC: A multimodal machine learning training, evaluation, and inference platform for biomedical foundation models

Existing biomedical benchmarks do not provide end-to-end infrastructure for training, evaluation, and inference of models that integrate multimodal biological data and a broad range of machine learning tasks in therapeutics. We present PyTDC, an open-source machine-learning platform providing streamlined training, evaluation, and inference software for multimodal biological AI models. PyTDC unifies distributed, heterogeneous, continuously updated data sources and model weights and standardizes benchmarking and inference endpoints. This paper discusses the components of PyTDC's architecture and, to our knowledge, the first-of-its-kind case study on the introduced single-cell drug-target nomination ML task. We find state-of-the-art methods in graph representation learning and domain-specific methods from graph theory perform poorly on this task. Though we find a context-aware geometric deep learning method that outperforms the evaluated SoTA and domain-specific baseline methods, the model is unable to generalize to unseen cell types or incorporate additional modalities, highlighting PyTDC's capacity to facilitate an exciting avenue of research developing multimodal, context-aware, foundation models for open problems in biomedical AI.

TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools

Precision therapeutics require multimodal adaptive models that generate personalized treatment recommendations. We introduce TxAgent, an AI agent that leverages multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics. It retrieves and synthesizes evidence from multiple biomedical sources, assesses interactions between drugs and patient conditions, and refines treatment recommendations through iterative reasoning. It selects tools based on task objectives and executes structured function calls to solve therapeutic tasks that require clinical reasoning and cross-source validation. The ToolUniverse consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. TxAgent outperforms leading LLMs, tool-use models, and reasoning agents across five new benchmarks: DrugPC, BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering 3,168 drug reasoning tasks and 456 personalized treatment scenarios. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning. TxAgent generalizes across drug name variants and descriptions. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.

Multimodal Medical Code Tokenizer

Foundation models trained on patient electronic health records (EHRs) require tokenizing medical data into sequences of discrete vocabulary items. Existing tokenizers treat medical codes from EHRs as isolated textual tokens. However, each medical code is defined by its textual description, its position in ontological hierarchies, and its relationships to other codes, such as disease co-occurrences and drug-treatment associations. Medical vocabularies contain more than 600,000 codes with critical information for clinical reasoning. We introduce MedTok, a multimodal medical code tokenizer that uses the text descriptions and relational context of codes. MedTok processes text using a language model encoder and encodes the relational structure with a graph encoder. It then quantizes both modalities into a unified token space, preserving modality-specific and cross-modality information. We integrate MedTok into five EHR models and evaluate it on operational and clinical tasks across in-patient and out-patient datasets, including outcome prediction, diagnosis classification, drug recommendation, and risk stratification. Swapping standard EHR tokenizers with MedTok improves AUPRC across all EHR models, by 4.10% on MIMIC-III, 4.78% on MIMIC-IV, and 11.30% on EHRShot, with the largest gains in drug recommendation. Beyond EHR modeling, we demonstrate using MedTok tokenizer with medical QA systems. Our results demonstrate the potential of MedTok as a unified tokenizer for medical codes, improving tokenization for medical foundation models.

Controllable Sequence Editing for Counterfactual Generation

Sequence models generate counterfactuals by modifying parts of a sequence based on a given condition, enabling reasoning about "what if" scenarios. While these models excel at conditional generation, they lack fine-grained control over when and where edits occur. Existing approaches either focus on univariate sequences or assume that interventions affect the entire sequence globally. However, many applications require precise, localized modifications, where interventions take effect only after a specified time and impact only a subset of co-occurring variables. We introduce CLEF, a controllable sequence editing model for counterfactual reasoning about both immediate and delayed effects. CLEF learns temporal concepts that encode how and when interventions should influence a sequence. With these concepts, CLEF selectively edits relevant time steps while preserving unaffected portions of the sequence. We evaluate CLEF on cellular and patient trajectory datasets, where gene regulation affects only certain genes at specific time steps, or medical interventions alter only a subset of lab measurements. CLEF improves immediate sequence editing by up to 36.01% in MAE compared to baselines. Unlike prior methods, CLEF enables one-step generation of counterfactual sequences at any future time step, outperforming baselines by up to 65.71% in MAE. A case study on patients with type 1 diabetes mellitus shows that CLEF identifies clinical interventions that shift patient trajectories toward healthier outcomes.

A Causality-aware Paradigm for Evaluating Creativity of Multimodal Large Language Models

Recently, numerous benchmarks have been developed to evaluate the logical reasoning abilities of large language models (LLMs). However, assessing the equally important creative capabilities of LLMs is challenging due to the subjective, diverse, and data-scarce nature of creativity, especially in multimodal scenarios. In this paper, we consider the comprehensive pipeline for evaluating the creativity of multimodal LLMs, with a focus on suitable evaluation platforms and methodologies. First, we find the Oogiri game, a creativity-driven task requiring humor, associative thinking, and the ability to produce unexpected responses to text, images, or both. This game aligns well with the input-output structure of modern multimodal LLMs and benefits from a rich repository of high-quality, human-annotated creative responses, making it an ideal platform for studying LLM creativity. Next, beyond using the Oogiri game for standard evaluations like ranking and selection, we propose LoTbench, an interactive, causality-aware evaluation framework, to further address some intrinsic risks in standard evaluations, such as information leakage and limited interpretability. The proposed LoTbench not only quantifies LLM creativity more effectively but also visualizes the underlying creative thought processes. Our results show that while most LLMs exhibit constrained creativity, the performance gap between LLMs and humans is not insurmountable. Furthermore, we observe a strong correlation between results from the multimodal cognition benchmark MMMU and LoTbench, but only a weak connection with traditional creativity metrics. This suggests that LoTbench better aligns with human cognitive theories, highlighting cognition as a critical foundation in the early stages of creativity and enabling the bridging of diverse concepts. https://lotbench.github.io

Multi Scale Graph Neural Network for Alzheimer's Disease

Alzheimer's disease (AD) is a complex, progressive neurodegenerative disorder characterized by extracellular A\b{eta} plaques, neurofibrillary tau tangles, glial activation, and neuronal degeneration, involving multiple cell types and pathways. Current models often overlook the cellular context of these pathways. To address this, we developed a multiscale graph neural network (GNN) model, ALZ PINNACLE, using brain omics data from donors spanning the entire aging to AD spectrum. ALZ PINNACLE is based on the PINNACLE GNN framework, which learns context-aware protein, cell type, and tissue representations within a unified latent space. ALZ PINNACLE was trained on 14,951 proteins, 206,850 protein interactions, 7 cell types, and 48 cell subtypes or states. After pretraining, we investigated the learned embedding of APOE, the largest genetic risk factor for AD, across different cell types. Notably, APOE embeddings showed high similarity in microglial, neuronal, and CD8 cells, suggesting a similar role of APOE in these cell types. Fine tuning the model on AD risk genes revealed cell type contexts predictive of the role of APOE in AD. Our results suggest that ALZ PINNACLE may provide a valuable framework for uncovering novel insights into AD neurobiology.

FoldMark: Protecting Protein Generative Models with Watermarking

Protein structure is key to understanding protein function and is essential for progress in bioengineering, drug discovery, and molecular biology. Recently, with the incorporation of generative AI, the power and accuracy of computational protein structure prediction/design have been improved significantly. However, ethical concerns such as copyright protection and harmful content generation (biosecurity) pose challenges to the wide implementation of protein generative models. Here, we investigate whether it is possible to embed watermarks into protein generative models and their outputs for copyright authentication and the tracking of generated structures. As a proof of concept, we propose a two-stage method FoldMark as a generalized watermarking strategy for protein generative models. FoldMark first pretrain watermark encoder and decoder, which can minorly adjust protein structures to embed user-specific information and faithfully recover the information from the encoded structure. In the second step, protein generative models are fine-tuned with watermark Low-Rank Adaptation (LoRA) modules to preserve generation quality while learning to generate watermarked structures with high recovery rates. Extensive experiments are conducted on open-source protein structure prediction models (e.g., ESMFold and MultiFlow) and de novo structure design models (e.g., FrameDiff and FoldFlow) and we demonstrate that our method is effective across all these generative models. Meanwhile, our watermarking framework only exerts a negligible impact on the original protein structure quality and is robust under potential post-processing and adaptive attacks.

Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.