M. Zitnik
Famous AuthorPublications
MatrAIx: Simulating the World with 8.3 Billion Persona Agents
Human evaluation of AI systems and digital products is costly, slow, and difficult to scale. Offline evaluations are more scalable but often abstract away human diversity and interactive behavior. We therefore introduce MatrAIx, a population-scale simulated-user evaluation infrastructure for testing AI systems and digital products with heterogeneous users. MatrAIx has three core components: First, Persona 8B contains 8.3 billion persona records represented by 1,290 categorical dimensions. Records are either sampled from a dependency graph that preserves correlated attributes or derived from human-authored profiles. We release a quality-filtered coreset of approximately 1 million personas, comprising 599,847 human-grounded and 400,000 synthetic records. Second, the MatrAIx Playground provides four environments in which diverse users evaluate and interact with digital products: Survey, AI Chatbot, Web, and App. Third, MatrAIx provides 1,010 application tasks spanning more than 25 domains, including Commerce, Software, Finance, and Healthcare. We conducted 18,189 evaluation trials across eight representative tasks. Persona agents were powered by three LLMs: Claude Opus 4.8, GPT 5.5, and Claude Haiku 4.5. The resulting feedback captures how decisions and preferences vary across persona backgrounds, including hesitation after a price increase, willingness to continue after an AI assistant fails, and latency tolerance. We conducted two main validation studies: First, a 400-trial controlled study evaluated persona adherence across ten behavioral attributes and all four environments. The declared behavior was expressed or correctly suppressed in 366 trials (91.5%). Second, human and LLM judges evaluated the extraction quality of human-grounded personas. Overall, MatrAIx provides an end-to-end infrastructure for evaluating AI systems and digital products with diverse simulated human users.
AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation
Scientific research proceeds through iterative cycles of hypothesis generation, experiment design, execution, and revision. AI agents can automate parts of this process, but existing approaches typically follow a single research trajectory or coordinate through a central planner with fixed objectives. As a result, they struggle to sustain parallel exploration, adapt as experimental evidence changes, or preserve knowledge of failed directions over long-running experiments. We introduce AutoScientists, a decentralized team of AI agents for long-running computational scientific experimentation. Agents interpret a shared experimental state, self-organize into teams around promising hypotheses, critique proposals before using experimental compute, and share successes and failures to reduce redundant exploration. Under matched experimental budgets, AutoScientists improves over prior AI agents across biomedical machine learning, language-model training optimization, and protein fitness prediction. On BioML-Bench, spanning biomedical imaging, protein engineering, single-cell omics, and drug discovery, AutoScientists achieves a mean leaderboard percentile of 74.4% across 24 tasks, improving over the strongest AI agent by +8.33%. On GPT training optimization, AutoScientists reaches a target validation bits-per-byte 1.9x faster than Autoresearch and continues discovering improvements from a starting champion where the single-agent approach finds none (7 vs. 0 accepted improvements). On ProteinGym fitness prediction, AutoScientists discovers a method for ACE2-Spike binding that improves over the current state-of-the-art model by +12.5% in Spearman correlation. Applied without modification across all 217 ProteinGym assays, the same method improves over the prior state of the art by +6.5% (Spearman correlation).
OptimusKG: Unifying biomedical knowledge in a modern multimodal graph
Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.
Evaluating Relational Reasoning in LLMs with REL
Relational reasoning is the ability to infer relations that jointly bind multiple entities, attributes, or variables. This ability is central to scientific reasoning, but existing evaluations of relational reasoning in large language models often focus on structured inputs such as tables, graphs, or synthetic tasks, and do not isolate the difficulty introduced by higher-arity relational binding. We study this problem through the lens of Relational Complexity (RC), which we define as the minimum number of independent entities or operands that must be simultaneously bound to apply a relation. RC provides a principled way to vary reasoning difficulty while controlling for confounders such as input size, vocabulary, and representational choices. Building on RC, we introduce REL, a generative benchmark framework spanning algebra, chemistry, and biology that varies RC within each domain. Across frontier LLMs, performance degrades consistently and monotonically as RC increases, even when the total number of entities is held fixed. This failure mode persists with increased test-time compute and in-context learning, suggesting a limitation tied to the arity of the required relational binding rather than to insufficient inference steps or lack of exposure to examples. Our results identify a regime of higher-arity reasoning in which current models struggle, and motivate re-examining benchmarks through the lens of relational complexity.
Beyond Affinity: A Benchmark of 1D, 2D, and 3D Methods Reveals Critical Trade-offs in Structure-Based Drug Design
Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models within a single algorithmic category, cross-algorithm comparisons remain scarce. In this paper, to fill the gap, we establish a benchmark to evaluate the performance of fifteen models across these different algorithmic foundations by assessing the pharmaceutical properties of the generated molecules and their docking affinities and poses with specified target proteins. We highlight the unique advantages of each algorithmic approach and offer recommendations for the design of future SBDD models. We emphasize that 1D/2D ligand-centric drug design methods can be used in SBDD by treating the docking function as a black-box oracle, which is typically neglected. Our evaluation reveals distinct patterns across model categories. 3D structure-based models excel in binding affinities but show inconsistencies in chemical validity and pose quality. 1D models demonstrate reliable performance in standard molecular metrics but rarely achieve optimal binding affinities. 2D models offer balanced performance, maintaining high chemical validity while achieving moderate binding scores. Through detailed analysis across multiple protein targets, we identify key improvement areas for each model category, providing insights for researchers to combine strengths of different approaches while addressing their limitations. All the code that are used for benchmarking is available in https://github.com/zkysfls/2025-sbdd-benchmark