arXiv subjects

Richard Zhu

Publications and source records attributed to Richard Zhu.

10 recordsLinked to original sources

arXiv2026

Evolutionary Curriculum Learning Improves Biological Sequence Modeling

Variational autoencoders (VAEs) trained on multiple sequence alignments (MSAs) have emerged as powerful generative models for biological sequences, with applications ranging from disease variant prediction to functional RNA design. However, standard biological VAE training treats all sequences as exchangeable, ignoring the rich evolutionary structure that organizes homologous sequences from evolutionarily close to highly divergent. We propose Evolutionary Curriculum Learning (ECL), a training strategy that exploits this structure by progressively exposing the model to sequences of increasing evolutionary distance from sampled anchors, following a power-law expansion schedule. Applied to two architecturally distinct VAE models and two biological domains--protein variant effect prediction with EVE and RNA family sequence generation with RfamGen--ECL improves downstream task performance across five random seeds per configuration. Mean ClinVar classification AUROC rises from 0.981 to 0.989 for p53; for PTEN, ECL attains 1.000 in every seed whereas the baseline is unstable (mean 0.905, falling as low as 0.54). For RNA, ECL raises mean covariance-model bit scores on all three families tested and exceeds its seed-matched baseline in 12 of 15 training runs, though with only three families the effect cannot be established as significant at the family level. Ablation experiments show that progressively expanding the sampled sequences by evolutionary distance outperforms fixed-size neighborhood sampling in addition to uniform random sampling. Evolutionary distance is therefore a useful inductive bias for ordering the training curriculum in biological sequence modeling.

cs.AI↗

arXiv2026

An AI agent for treatment reasoning over a biomedical tool universe

Treatment reasoning underpins every therapeutic decision, integrating disease context, comorbidities, medications, contraindications, and evolving biomedical knowledge to select an appropriate therapy. It is inherently iterative: candidates are weighed against many constraints, revised as evidence emerges, and grounded in verifiable sources. Here we introduce ATHENA-R1, an AI agent for treatment reasoning across all FDA approved drugs since 1939, trained by reinforcement learning over a universe of 212 biomedical tools. At each step it identifies missing information, selects and runs relevant tools, and incorporates the evidence. To train it without human-annotated traces, we build a two-level self-learning framework: multi-agent systems construct the tools, tasks, and reasoning trajectories for supervised fine-tuning, then reinforcement learning with scientific feedback rewards reasoning quality (evidence gathering, grounded tool use, logical non-redundancy). Across five benchmarks of 3,168 drug reasoning tasks and 456 patient treatment cases, ATHENA-R1 outperforms language models and tool-use systems, reaching 94.7% accuracy on open-ended drug reasoning and 82.9% on treatment reasoning, 17.8 and 10.7 points above GPT-5. In blinded evaluations by experts from 28 rare disease organizations, it is preferred over reference models on all criteria, and physicians rated it favorably on complex hospitalized cardiovascular and infectious-disease cases. Adverse-event hypotheses it generated, tested in electronic health records from 5.4 million patients, reached adjusted odds ratios of 1.48-1.84, with no elevation among negative controls. Because it requires knowing what evidence to seek before concluding, treatment reasoning has long been hard for AI; we show it can be reframed as a learnable process of iterative evidence gathering that reinforcement learning can train AI to perform.

cs.AI↗

arXiv2025

AIA Forecaster: Technical Report

This technical report describes the AIA Forecaster, a Large Language Model (LLM)-based system for judgmental forecasting using unstructured data. The AIA Forecaster approach combines three core elements: agentic search over high-quality news sources, a supervisor agent that reconciles disparate forecasts for the same event, and a set of statistical calibration techniques to counter behavioral biases in large language models. On the ForecastBench benchmark (Karger et al., 2024), the AIA Forecaster achieves performance equal to human superforecasters, surpassing prior LLM baselines. In addition to reporting on ForecastBench, we also introduce a more challenging forecasting benchmark sourced from liquid prediction markets. While the AIA Forecaster underperforms market consensus on this benchmark, an ensemble combining AIA Forecaster with market consensus outperforms consensus alone, demonstrating that our forecaster provides additive information. Our work establishes a new state of the art in AI forecasting and provides practical, transferable recommendations for future research. To the best of our knowledge, this is the first work that verifiably achieves expert-level forecasting at scale.

cs.AI↗

arXiv2025

ToolUniverse: An open platform for democratizing AI scientists

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analyses into a common ecosystem. We present ToolUniverse, an open platform for building AI scientists from any language or reasoning model across open- and closed-weight models. ToolUniverse standardizes how AI scientists identify and call tools through an AI-tool interaction standard, in which every tool declares its purpose in natural language, a typed schema for its inputs and outputs, and a backend-agnostic invocation format, and applies that standard to more than 2,700 scientific tools and over 130 research skills spanning machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design. It automatically refines tool interfaces for correct use by AI scientists, generates new tools from natural language descriptions, iteratively optimizes tool specifications, and composes tools into agentic workflows. In case studies, ToolUniverse was used to create AI scientists that carried out end-to-end analyses in target assessment, chemical strategy, and clinical-trial safety. The open-source ToolUniverse is available at https://aiscientist.tools.

cs.AI↗

arXiv2025

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.

cs.AI↗

arXiv2024

LLMs are Superior Feedback Providers: Bootstrapping Reasoning for Lie Detection with Self-Generated Feedback

Large Language Models (LLMs) excel at generating human-like dialogues and comprehending text. However, understanding the subtleties of complex exchanges in language remains a challenge. We propose a bootstrapping framework that leverages self-generated feedback to enhance LLM reasoning capabilities for lie detection. The framework consists of three stages: suggestion, feedback collection, and modification. In the suggestion stage, a cost-effective language model generates initial predictions based on game state and dialogue. The feedback-collection stage involves a language model providing feedback on these predictions. In the modification stage, a more advanced language model refines the initial predictions using the auto-generated feedback. We investigate the application of the proposed framework for detecting betrayal and deception in Diplomacy games, and compare it with feedback from professional human players. The LLM-generated feedback exhibits superior quality and significantly enhances the performance of the model. Our approach achieves a 39% improvement over the zero-shot baseline in lying-F1 without the need for any training data, rivaling state-of-the-art supervised learning results.

cs.CL↗

arXiv2024

CharXiv: Charting Gaps in Realistic Chart Understanding in Multimodal LLMs

Chart understanding plays a pivotal role when applying Multimodal Large Language Models (MLLMs) to real-world tasks such as analyzing scientific papers or financial reports. However, existing datasets often focus on oversimplified and homogeneous charts with template-based questions, leading to an over-optimistic measure of progress. We demonstrate that although open-source models can appear to outperform strong proprietary models on these benchmarks, a simple stress test with slightly different charts or questions can deteriorate performance by up to 34.5%. In this work, we propose CharXiv, a comprehensive evaluation suite involving 2,323 natural, challenging, and diverse charts from arXiv papers. CharXiv includes two types of questions: 1) descriptive questions about examining basic chart elements and 2) reasoning questions that require synthesizing information across complex visual elements in the chart. To ensure quality, all charts and questions are handpicked, curated, and verified by human experts. Our results reveal a substantial, previously underestimated gap between the reasoning skills of the strongest proprietary model (i.e., GPT-4o), which achieves 47.1% accuracy, and the strongest open-source model (i.e., InternVL Chat V1.5), which achieves 29.2%. All models lag far behind human performance of 80.5%, underscoring weaknesses in the chart understanding capabilities of existing MLLMs. We hope CharXiv facilitates future research on MLLM chart understanding by providing a more realistic and faithful measure of progress. Project page and leaderboard: https://charxiv.github.io/

cs.CL↗

arXiv2024

Fast Exact Retrieval for Nearest-neighbor Lookup (FERN)

Exact nearest neighbor search is a computationally intensive process, and even its simpler sibling -- vector retrieval -- can be computationally complex. This is exacerbated when retrieving vectors which have high-dimension $d$ relative to the number of vectors, $N$, in the database. Exact nearest neighbor retrieval has been generally acknowledged to be a $O(Nd)$ problem with no sub-linear solutions. Attention has instead shifted towards Approximate Nearest-Neighbor (ANN) retrieval techniques, many of which have sub-linear or even logarithmic time complexities. However, if our intuition from binary search problems (e.g. $d=1$ vector retrieval) carries, there ought to be a way to retrieve an organized representation of vectors without brute-forcing our way to a solution. For low dimension (e.g. $d=2$ or $d=3$ cases), \texttt{kd-trees} provide a $O(d\log N)$ algorithm for retrieval. Unfortunately the algorithm deteriorates rapidly to a $O(dN)$ solution at high dimensions (e.g. $k=128$), in practice. We propose a novel algorithm for logarithmic Fast Exact Retrieval for Nearest-neighbor lookup (FERN), inspired by \texttt{kd-trees}. The algorithm achieves $O(d\log N)$ look-up with 100\% recall on 10 million $d=128$ uniformly randomly generated vectors.\footnote{Code available at https://github.com/RichardZhu123/ferns}

cs.CL↗

arXiv2024

Comparing Importance Sampling Based Methods for Mitigating the Effect of Class Imbalance

Most state-of-the-art computer vision models heavily depend on data. However, many datasets exhibit extreme class imbalance which has been shown to negatively impact model performance. Among the training-time and data-generation solutions that have been explored, one subset that leverages existing data is importance sampling. A good deal of this work focuses primarily on the CIFAR-10 and CIFAR-100 datasets which fail to be representative of the scale, composition, and complexity of current state-of-the-art datasets. In this work, we explore and compare three techniques that derive from importance sampling: loss reweighting, undersampling, and oversampling. Specifically, we compare the effect of these techniques on the performance of two encoders on an impactful satellite imagery dataset, Planet's Amazon Rainforest dataset, in preparation for another work. Furthermore, we perform supplemental experimentation on a scene classification dataset, ADE20K, to test on a contrasting domain and clarify our results. Across both types of encoders, we find that up-weighting the loss for and undersampling has a negigible effect on the performance on underrepresented classes. Additionally, our results suggest oversampling generally improves performance for the same underrepresented classes. Interestingly, our findings also indicate that there may exist some redundancy in data in the Planet dataset. Our work aims to provide a foundation for further work on the Planet dataset and similar domain-specific datasets. We open-source our code at https://github.com/RichardZhu123/514-class-imbalance for future work on other satellite imagery datasets as well.

cs.CV↗

arXiv2015

Optimal Seed Solver: Optimizing Seed Selection in Read Mapping

Motivation: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while the total frequency of all selected seeds determines the speed of the mapper. Modern seed-and-extend mappers usually select seeds with either an equal and fixed-length scheme or with an inflexible placement scheme, both of which limit the potential of the mapper to select less frequent seeds to speed up the mapping process. Therefore, it is crucial to develop a new algorithm that can adjust both the individual seed length and the seed placement, as well as derive less frequent seeds. Results: We present the Optimal Seed Solver (OSS), a dynamic programming algorithm that discovers the least frequently-occurring set of x seeds in an L-bp read in $O(x \times L)$ operations on average and in $O(x \times L^{2})$ operations in the worst case. We compared OSS against four state-of-the-art seed selection schemes and observed that OSS provides a 3-fold reduction of average seed frequency over the best previous seed selection optimizations.

cs.CE↗