Bryan Cheng

Bryan Cheng, Austin Jin

Proteolysis-targeting chimeras (PROTACs) can selectively degrade disease-causing proteins, yet predicting which targets are amenable to degradation remains a critical bottleneck: existing computational methods require the complete PROTAC molecular structure, information unavailable before synthesis. We present DegradoMap, a graph neural network that predicts PROTAC-mediated degradability from protein structure and E3 ligase identity alone -- the minimal information available at the target selection stage. The model encodes biophysical priors through lysine-weighted graph pooling with per-protein normalization, models protein-E3 compatibility via cross-attention, and integrates cellular context from the Cancer Dependency Map. On the PROTAC-8K benchmark (3,101 samples, 155 targets, 10 E3 ligases), DegradoMap achieves 0.646+-0.124 AUROC on target-unseen evaluation (best seed: 0.7449) and 0.811 AUROC on CRBN->VHL E3-unseen transfer, outperforming GNN and machine learning baselines. The model additionally recommends optimal E3 ligases with 74% Hit@3 accuracy. Two findings carry broader implications: E(3)-equivariant architectures underperform the simpler invariant design for this scalar prediction task, and ESM-2 embeddings improve peak performance only with careful regularization -- naive integration fails. DegradoMap provides pre-synthesis computational guidance for degradability assessment; its well-calibrated confidence scores (ECE = 0.029, target-unseen) enable practitioners to prioritize high-confidence predictions for experimental follow-up. However, the high seed variance (std = 0.124) and limited E3 coverage require ensembling for reliable deployment.

Bryan Cheng, Austin Jin, Joshua Chang

Splice-mediated drug resistance occurs in up to 40% of patients on targeted kinase inhibitors, yet state-of-the-art druggability tools operate on single structures and cannot compare across isoforms. We introduce SpliceBind, a graph neural network framework for isoform-aware druggability prediction. Beyond improving prediction accuracy (AUROC 0.703 vs. P2Rank 0.634, p = 0.026), we address a more fundamental question: when do structural methods succeed, and when must they fail? Systematic analysis of six clinically validated variants spanning five mechanism classes reveals a two-tier resistance taxonomy. Domain deletions (AR-V7, Delta = -18.39) and pocket disruptions produce structurally detectable changes, while allosteric mechanisms (BRAF-p61) remain fundamentally invisible to any pocket-centric approach -- a boundary no algorithmic improvement can cross. Notably, learned embeddings capture affinity-based resistance missed by geometry alone (ALK-L1196M: Delta_SB = -0.228 vs. Delta_P2Rank = -0.95), partially bridging the structural-biochemical gap. On 229 kinase pockets spanning 25 families, SpliceBind achieves AUROC 0.703 (p = 0.026 vs. P2Rank) with robust generalization to held-out families (AUROC 0.761). This taxonomy transforms clinical workflows: upon discovering a splice variant, clinicians can immediately determine whether computational triage suffices or biochemical validation is required -- reducing time from variant discovery to therapeutic decision.

Bryan Cheng, Austin Jin, Jasper Zhang

Sign language recognition suffers from catastrophic scaling failure: models achieving high accuracy on small vocabularies collapse at realistic sizes. Existing architectures treat signs as atomic visual patterns, learning flat representations that cannot exploit the compositional structure of sign languages-systematically organized from discrete phonological parameters (handshape, location, movement, orientation) reused across the vocabulary. We introduce PHONSSM, enforcing phonological decomposition through anatomically-grounded graph attention, explicit factorization into orthogonal subspaces, and prototypical classification enabling few-shot transfer. Using skeleton data alone on the largest ASL dataset ever assembled (5,565 signs), PHONSSM achieves 72.1% on WLASL2000 (+18.4pp over skeleton SOTA), surpassing most RGB methods without video input. Gains are most dramatic in the few-shot regime (+225% relative), and the model transfers zero-shot to ASL Citizen, exceeding supervised RGB baselines. The vocabulary scaling bottleneck is fundamentally a representation learning problem, solvable through compositional inductive biases mirroring linguistic structure.

Jasper Zhang, Bryan Cheng

Multi-task learning shows strikingly inconsistent results -- sometimes joint training helps substantially, sometimes it actively harms performance -- yet the field lacks a principled framework for predicting these outcomes. We identify a fundamental but unstated assumption underlying gradient-based task analysis: tasks must share training instances for gradient conflicts to reveal genuine relationships. When tasks are measured on the same inputs, gradient alignment reflects shared mechanistic structure; when measured on disjoint inputs, any apparent signal conflates task relationships with distributional shift. We discover this sample overlap requirement exhibits a sharp phase transition: below 30% overlap, gradient-task correlations are statistically indistinguishable from noise; above 40%, they reliably recover known biological structure. Comprehensive validation across multiple datasets achieves strong correlations and recovers biological pathway organization. Standard benchmarks systematically violate this requirement -- MoleculeNet operates at <5% overlap, TDC at 8-14% -- far below the threshold where gradient analysis becomes meaningful. This provides the first principled explanation for seven years of inconsistent MTL results.

Bryan Cheng, Jasper Zhang

We present the first systematic study of when target context helps molecular property prediction, evaluating context conditioning across 10 diverse protein families, 4 fusion architectures, data regimes spanning 67-9,409 training compounds, and both temporal and random evaluation splits. Using NestDrug, a FiLM-based architecture that conditions molecular representations on target identity, we characterize both success and failure modes with three principal findings. First, fusion architecture dominates: FiLM outperforms concatenation by 24.2 percentage points and additive conditioning by 8.6 pp; how you incorporate context matters more than whether you include it. Second, context enables otherwise impossible predictions: on data-scarce CYP3A4 (67 training compounds), multi-task transfer achieves 0.686 AUC where per-target Random Forest collapses to 0.238. Third, context can systematically hurt: distribution mismatch causes 10.2 pp degradation on BACE1; few-shot adaptation consistently underperforms zero-shot. Beyond methodology, we expose fundamental flaws in standard benchmarking: 1-nearest-neighbor Tanimoto achieves 0.991 AUC on DUD-E without any learning, and 50% of actives leak from training data, rendering absolute performance metrics meaningless. Our temporal split evaluation (train up to 2020, test 2021-2024) achieves stable 0.843 AUC with no degradation, providing the first rigorous evidence that context-conditional molecular representations generalize to future chemical space.

Bryan Cheng, Jasper Zhang

Understanding how large language models encode task identity from few-shot demonstrations is a central open problem in mechanistic interpretability. Prior work uses linear probing to localize task representations, reporting high classification accuracy at specific layers. We reveal a striking dissociation: probing accuracy completely fails to predict causal importance. Single-position activation intervention achieves 0% task transfer across all 28 layers of Llama-3.2-3B-despite 100% probing accuracy at those same positions. This null result is itself a key finding, demonstrating that task encoding is fundamentally distributed. Multi-position intervention-replacing activations at all demonstration output tokens simultaneously-achieves up to 96% transfer (N=50, 95% CI: [87%, 99%]) at layer 8, pinpointing for the first time the causal locus of ICL task identity. We establish the generality of these findings across four models spanning three architecture families (LLaMA, Qwen, Gemma), discovering a universal intervention window at ~30% network depth. Causal tracing uncovers an asymmetric architecture: the query position is strictly necessary (53-100% disruption) while no individual demonstration position is necessary (0% disruption)-resolving a key ambiguity in prior accounts. Crucially, transfer depends on internal representation compatibility, not surface similarity (r=-0.05 vs r=0.31), ruling out trivial explanations. These results establish the distributed template hypothesis: ICL task identity is encoded as output format templates distributed across demonstration tokens, fundamentally reshaping our understanding of how in-context learning operates.