biotech data teams

Abstract: Kernels encode the inductive bias of a wide range of machine learning models, yet automated kernel design faces a fundamental dilemma. A fixed grammar of base kernels and operators guarantees validity but limits the search to structures expressible by those building blocks. Conversely, unrestricted programs remove this limitation but no longer guarantee validity. In our stress tests, 22-58% of LLM-generated kernels that pass numerical checks on random inputs fail when evaluated at different scales or dimensions. We propose Kernel Autoresearch (Kernaut), which treats kernel design as open-ended model discovery. Coding agents write kernels as programs, while construction contracts ensure that every accepted kernel is valid. A quality-diversity archive retains high-performing kernels with distinct behaviors, and novelty screening steers agents toward functionally new candidates. Our experiments demonstrate that the discovered kernels encode reusable inductive biases that generalize to unseen tasks. On held-out black-box optimization families, a discovered kernel outperforms a meta-learned deep kernel trained on the same episodes. Furthermore, kernels discovered from ten enzyme-kinetic rate laws achieve lower error than tuned ARD and deep kernel baselines on five unseen mechanisms. The discovered kernels are also interpretable programs that human researchers can refine: a human-refined version of one further reduces the held-out predictive error by 5.7% and optimization regret by 7.8%.

Abstract: Destructive single-cell measurements provide unpaired population snapshots rather than observations of the same cells across conditions. Local cell states and transition requests may also be insufficient to distinguish responses across source populations. We introduce TempoBridge, a common source-conditioned transport formulation for temporal, genetic, and chemical population transitions. Source cells initialize latent transport and provide a fixed empirical population summary. The velocity field receives this summary alongside the evolving cell state, flow time, and a structured transition descriptor. Minibatch optimal transport (OT) supplies couplings only for conditional flow-matching training paths; inference requires neither target expression nor OT computation. On held-out donors, TempoBridge achieves an Energy distance of 0.129 versus 0.144 for scGen. Genetic mean-expression $L_2$ error is 2.261 versus 3.156 for scGPT-scratch under Seen 2/2. On held-out compounds, condition-averaged drug-effect correlation is 0.598 versus 0.561 for the CellFlow adapter. Temporal ablations show higher mean distributional error after removing source context, replacing optimal transport with random pairing, or replacing flow matching with static residual regression. Together, these results demonstrate the predictive utility of a common source-conditioned transport formulation across held-out donors, gene combinations, and compounds.

Abstract: Self-evolving vision-language models (VLMs), a form of self-improvement in which a model generates its own training data from unlabeled images, are a promising route toward agents that expand their reasoning capability in an unsupervised manner, without relying on ever-larger annotation budgets. Existing methods pair a Questioner that proposes problems with a Solver that answers them, but reward both roles mainly by agreement among sampled answers. Agreement is a weak proxy for truth: it cannot tell whether a question is grounded in the image, whether the proposed reference answer is right, or whether a confident majority is wrong in the same way. We present Trinity, in which one VLM plays three roles, Questioner, Solver, and Verifier, and the Verifier is a self-verifier: an exponential moving average (EMA) of the policy itself, requiring neither labels nor an external judge. The Verifier screens every generated question for image grounding and answer correctness before it becomes supervision, scores Solver reasoning against the image, and adjudicates disputes between the reference answer and a strong Solver consensus, correcting the reference and penalizing the Questioner when the consensus is right. Trained on images alone, Trinity improves Qwen3-VL-8B on mathematical visual reasoning and on science benchmarks with biology content, for example, +8.6 points on the biology split of SciVQR and +12.8 on MathVerse, and its reward dynamics behave as a healthy self-play curriculum should. These results suggest that a self-evolving multimodal agent can strengthen its scientific reasoning from unlabeled scientific images alone, with the model itself serving as the verifier.

Abstract: Graph foundation models need a discrete token representation, but casting a graph as a generatable token sequence faces a structural obstacle: edges spanning beyond the serialization window cannot be emitted in one pass--so one-pass autoregressive generators systematically under-produce cycles--and a single global condition cannot tell candidate edges apart. GraphVQ removes both obstacles: node contexts--features plus a local edge mask under multi-order breadth-first serialization--are quantized into a shared codebook by a VQ-VAE with BCE-calibrated Bernoulli edge decoding, and a second-stage structure-aware decoder emits the global adjacency conditioned on token-derived pair features, whose necessity over any global-summary condition is formalized in a scoped impossibility result. The tokenizer reconstructs node features at 0.86--0.99 accuracy and decodes local edges at AUROC >= 0.89 (ECE <= 0.007). Under one same-split protocol on four datasets, pair conditioning improves orbit MMD 0.248 -> 0.174 on PROTEINS and 3.4x on a ring stress test, and vanishes on a random-label control--the signature of attribute--topology coupling--so the gain is claimed exactly where attributes carry edge-relevant signal. GraphVQ ranks first among learned generators on PROTEINS, ties for first on SYN-COMM, and improves orbit MMD 2.7--17x over one-stage generation on three datasets, with seed-level bootstrap intervals confirming the rankings are not seed noise; on MUTAG the unweighted edge target under-generates and is reported as such. These results locate the structural control of autoregressive graph generation in the granularity of the condition: pair-level token context turns a quantized vocabulary into a usable capacity axis for distribution-faithful graph generation and future token-level pretraining.

Abstract: Predicting cellular responses to perturbations supports the study of gene function, disease mechanisms, and therapeutic strategies. Despite advances in single-cell perturbation modeling, existing models typically optimize surrogate losses that do not directly reflect the biological criteria used for evaluation, so better data fitting need not yield better biological predictions. To address this mismatch, we introduce \textbf{CellRFT}, a reinforcement fine-tuning framework that uses biological evaluation as direct training feedback. CellRFT uses policy-gradient optimization to learn from non-differentiable evaluations of generated cell populations and integrates multiple biological rewards through hierarchical reward aggregation. Comprehensive experiments demonstrate CellRFT's applicability across different pretrained models and effectiveness in improving perturbation prediction, reveal that optimizing one biological criterion can help or hinder others, and show that complementary rewards can improve criteria beyond those directly optimized, offering a way to probe how biological metrics shape model behavior, with the potential to inform evaluation design. Code will be made available.