BZPEERReading, trust and collaboration for research
Menu

Discover

GraphFollow connections around a paper, topic or saved view.

Workspaces

HomePick up where your research flow left off.InboxHandle requests, replies and notifications from one place.CollectionsCurate reading lists, evidence sets and shareable dossiers.ResearchSee your private provenance graph, trail and imports.CollaborationMove from discovery into focused discussion rooms.PublishDraft, preview and publish full-text research articles.

Network

ExpertsFind specialists worth following or asking for help.CommunitiesJoin research circles organized around shared work.PartnersSee external organizations active around the same topics.

Opportunities

ListingsBrowse roles, calls and collaborations with clearer fit signals.

Account

Log inReturn to your reading and collaboration workspace.Create accountStart saving work, following people and joining teams.
Log inCreate account

Researcher profile

Ziyu Xu

Ziyu Xu contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine Learningmath.STStatistics TheoryArtificial IntelligenceBiomoleculesData Structures and AlgorithmsMethodologyq-bio.MNQuantitative Methods

Trust snapshot

Quick read

Trust 19 - UnverifiedVerification L1Unclaimed author
5works
0followers
9topics
4close collaborators

Actions

Decide how to stay connected

Follow researcher0

Identity and collaboration

How to connect with this researcher

Claiming links this public author record to a researcher profile and unlocks direct collaboration workflows.

Log in to claim

Direct collaboration

Open a focused conversation when the fit is right

Claim this author entity first to unlock direct invitations.

Research graph

See the researcher in context

Open full explorer

Inspect adjacent work, topics, institutions and collaborators without jumping out to a separate graph page.

Building this graph slice

BZPEER is loading the nearby papers, people, topics and institutions for this page.

Published work

5 published item(s)

preprint2026arXiv

Bringing Closure to False Discovery Rate Control: A General Principle for Multiple Testing

We present a novel necessary and sufficient principle for multiple testing methods controlling an expected loss. This principle asserts that every such multiple testing method is a special case of a general closed testing procedure based on e-values. It generalizes the Closure Principle, known to underlie all methods controlling familywise error and tail probabilities of false discovery proportions, to a large class of error rates -- in particular to the false discovery rate (FDR). By writing existing methods as special cases of this procedure, we can achieve uniform improvements, as we demonstrate for the e-Benjamini-Hochberg and the Benjamini-Yekutieli procedures, and the self-consistent method of Su (2018). We also show that methods derived using our novel e-Closure Principle generally control their error rate not just for one rejected set, but simultaneously over many, allowing post hoc flexibility for the researcher. Moreover, we show that because all multiple testing methods for all error metrics are derived from the same procedure, researchers may even choose the error metric post hoc. Under certain conditions, this flexibility even extends to post hoc choice of the nominal error rate.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design

When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for drug action. In this work, we formalize \emph{Transcriptome-based Drug Design (TBDD)} as a generative inverse problem: designing drug molecules conditioned on desired transcriptomic state transitions. We analyze the inherently ill-posed nature of this task, which is further complicated by the profound domain gap between biology and chemistry and by the sparsity of transcriptomic signals. To address these challenges, we propose \textbf{\themodel{}} (A \textbf{C}ell\textbf{U}lar \textbf{R}esponse \textbf{E}ngine), a multi-resolution transcriptome-guided diffusion framework. \themodel{} features a specialized \textbf{Transcriptome Perturbation Functional Feature Extractor (TFE)} that (1) distills function-oriented perturbation embeddings from pre/post states, (2) aligns these signatures to dual chemical views to bridge the cross-modal gap, and (3) performs heterogeneity-aware aggregation to extract robust state-specific signals from noisy transcriptomic data. Extensive evaluations on both standard benchmarks and rigorous out-of-distribution protocols demonstrate that \themodel{} consistently outperforms strong baselines in structural quality and functional consistency. Furthermore, we validate its practical utility via a zero-shot gene-inhibitor design task, highlighting the potential of phenotype-driven generative discovery.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Memory Bounds for the Experts Problem

Online learning with expert advice is a fundamental problem of sequential prediction. In this problem, the algorithm has access to a set of $n$ "experts" who make predictions on each day. The goal on each day is to process these predictions, and make a prediction with the minimum cost. After making a prediction, the algorithm sees the actual outcome on that day, updates its state, and then moves on to the next day. An algorithm is judged by how well it does compared to the best expert in the set. The classical algorithm for this problem is the multiplicative weights algorithm. However, every application, to our knowledge, relies on storing weights for every expert, and uses $Ω(n)$ memory. There is little work on understanding the memory required to solve the online learning with expert advice problem, or run standard sequential prediction algorithms, in natural streaming models, which is especially important when the number of experts, as well as the number of days on which the experts make predictions, is large. We initiate the study of the learning with expert advice problem in the streaming setting, and show lower and upper bounds. Our lower bound for i.i.d., random order, and adversarial order streams uses a reduction to a custom-built problem using a novel masking technique, to show a smooth trade-off for regret versus memory. Our upper bounds show novel ways to run standard sequential prediction algorithms in rounds on small "pools" of experts, thus reducing the necessary memory. For random-order streams, we show that our upper bound is tight up to low order terms. We hope that these results and techniques will have broad applications in online learning, and can inspire algorithms based on standard sequential prediction techniques, like multiplicative weights, for a wide range of other problems in the memory-constrained setting.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Class-Weighted Classification: Trade-offs and Robust Approaches

We address imbalanced classification, the problem in which a label may have low marginal probability relative to other labels, by weighting losses according to the correct class. First, we examine the convergence rates of the expected excess weighted risk of plug-in classifiers where the weighting for the plug-in classifier and the risk may be different. This leads to irreducible errors that do not converge to the weighted Bayes risk, which motivates our consideration of robust risks. We define a robust risk that minimizes risk over a set of weightings and show excess risk bounds for this problem. Finally, we show that particular choices of the weighting set leads to a special instance of conditional value at risk (CVaR) from stochastic programming, which we call label conditional value at risk (LCVaR). Additionally, we generalize this weighting to derive a new robust risk problem that we call label heterogeneous conditional value at risk (LHCVaR). Finally, we empirically demonstrate the efficacy of LCVaR and LHCVaR on improving class conditional risks.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Multiclass Classification via Class-Weighted Nearest Neighbors

We study statistical properties of the k-nearest neighbors algorithm for multiclass classification, with a focus on settings where the number of classes may be large and/or classes may be highly imbalanced. In particular, we consider a variant of the k-nearest neighbor classifier with non-uniform class-weightings, for which we derive upper and minimax lower bounds on accuracy, class-weighted risk, and uniform error. Additionally, we show that uniform error bounds lead to bounds on the difference between empirical confusion matrix quantities and their population counterparts across a set of weights. As a result, we may adjust the class weights to optimize classification metrics such as F1 score or Matthew's Correlation Coefficient that are commonly used in practice, particularly in settings with imbalanced classes. We additionally provide a simple example to instantiate our bounds and numerical experiments.

0 citations0 reviewsNo code linkedOpen access