biotech data engineers

Abstract: Federated optimization over heterogeneous multimodal data enables distributed institutions to collaboratively optimize a shared model using medical images, genomic profiles, clinical records, and physiological signals without centralizing raw data. However, protecting modality-specific data throughout the optimization lifecycle remains insufficiently explored, particularly when heterogeneous modalities require separate encryption keys and selective local access. This paper proposes a secure multimodal federated optimization framework that separates local data protection from federated-update protection. A trusted key-management authority securely provisions one client key through Hybrid Public Key Encryption (HPKE), from which each client locally derives modality-specific symmetric keys using the domain-separated HMAC-based Extract-and-Expand Key Derivation Function (HKDF). Heterogeneous modalities are mapped into a unified DNA-domain representation and processed through a DNA-origami-inspired structural transformation before authenticated encryption with AES-GCM. During local optimization, only the required modalities are decrypted within an authorized client environment. Individual model updates are independently protected through secure aggregation, allowing the coordinator to observe only aggregated updates rather than each client's contribution. Together, these components establish a structured approach to modality-specific protection and secure collaborative optimization, integrating hierarchical key management, authenticated local encryption, and aggregation-level update protection within a unified framework.

Abstract: Deploying a language model under different computing and latency budgets calls for compact models with different quality-cost trade-offs. Towards this end, elastic spectral state space models provide ordered and temporally decomposed channels that can be truncated, but they are associated with linear time-invariant filters that cannot selectively preserve relevant past information or forget irrelevant information as the context evolves. To address this, we introduce the Elastic Selective Spectral Hybrid (ESSH), which realizes each Hankel spectral channel as an independent recurrent unit using fitted damped rotation modes. It also features an input-dependent decay and write/read gates that make temporal retention and state update input-dependent while preserving channel-wise truncation and a structured recurrence for efficient execution. ESSH combines these selective spectral mixers with sliding-window attention and jointly trains multiple capacities by reducing spectral-channel count and feed-forward width at different rates through a two-rate capacity map with full-model distillation. The resulting models support chunked parallel training and fused recurrent decoding while avoiding computation for discarded channels. At full capacity, ESSH achieves language-modeling quality comparable to similarly sized independently trained models, while smaller exports exhibit a smooth quality-cost trade-off. We validate the effectiveness of the proposed framework using language understanding, retrieval, cross-domain text, and DNA experiments, by assessing quality retention and the trade-off against independently trained and elastic baselines. At the 1.53B model configuration, fused batch-one decoding takes 1.37 ms per token on a B300, providing a 2.14-2.80x speedup over the tested Mamba-2 and Mamba-3 implementations and 3.03x over Transformer++ at matched parameter counts.

Abstract: Bringing multiscale geometric analysis directly to irregular point clouds remains difficult: quantities such as local dimension, anisotropy, density variation, and geometric transitions are typically estimated through explicit neighborhood, manifold, or graph constructions, or left for neural networks to infer from coordinates. We introduce Heat Field Signatures (HFS), which lift a point cloud to a multiscale family of smooth ambient heat fields, providing a direct interface from discrete samples to geometric analysis. From this field, HFS computes closed-form global and local signatures directly from pairwise distances, capturing heat concentration, intrinsic dimension, anisotropy, and scale transitions. We further introduce the Heat Dimension Spectrum (HDS), a compact summary of multiscale geometric composition. HFS can be used as a closed-form descriptor, a lightweight learned representation, or a geometric feature channel for neural point-cloud models. Across synthetic and real-world benchmarks spanning subcellular, neuronal, tree, and protein data, HFS outperforms strong point-cloud and multiparameter-persistence baselines while substantially reducing end-to-end cost. On SCOP protein-fold classification, HFS improves over the strongest deep baseline by nearly $24$ percentage points using coordinates alone, while standalone HFS representations are exactly rotation-invariant by construction. More broadly, HFS turns a classical heat field into a practical interface for multiscale geometric analysis in modern point-cloud learning.