The constrained nature of synthesizable chemical space poses a significant challenge for sampling molecules that are both synthetically accessible and possess desired properties. In this work, we present PrexSyn, an efficient and programmable model for molecular discovery within synthesizable chemical space. PrexSyn is based on a decoder-only transformer trained on a billion-scale datastream of synthesizable pathways paired with molecular properties, enabled by a real-time, high-throughput C++-based data generation engine. The large-scale training data allows PrexSyn to reconstruct the synthesizable chemical space nearly perfectly at a high inference speed and learn the association between properties and synthesizable molecules. Based on its learned property-pathway mappings, PrexSyn can generate synthesizable molecules that satisfy not only single-property conditions but also composite property queries joined by logical operators, thereby allowing users to ``program'' generation objectives. Moreover, by exploiting this property-based querying capability, PrexSyn can efficiently optimize molecules against black-box oracle functions via iterative query refinement, achieving higher sampling efficiency than even synthesis-agnostic baselines, making PrexSyn a powerful general-purpose molecular optimization tool. Overall, PrexSyn pushes the frontier of synthesizable molecular design by setting a new state of the art in synthesizable chemical space coverage, molecular sampling efficiency, and inference speed.

Accurate prediction of enzyme kinetic parameters is crucial for drug discovery, metabolic engineering, and synthetic biology applications. Current computational approaches face limitations in capturing complex enzyme-substrate interactions and often focus on single parameters while neglecting the joint prediction of catalytic turnover numbers (Kcat) and Michaelis-Menten constants (Km). We present EnzyCLIP, a novel dual-encoder framework that leverages contrastive learning and cross-attention mechanisms to predict enzyme kinetic parameters from protein sequences and substrate molecular structures. Our approach integrates ESM-2 protein language model embeddings with ChemBERTa chemical representations through a CLIP-inspired architecture enhanced with bidirectional cross-attention for dynamic enzyme-substrate interaction modeling. EnzyCLIP combines InfoNCE contrastive loss with Huber regression loss to learn aligned multimodal representations while predicting log10-transformed kinetic parameters. The model is trained on the CatPred-DB database containing 23,151 Kcat and 41,174 Km experimentally validated measurements, and achieved competitive performance with R2 scores of 0.593 for Kcat and 0.607 for Km prediction. XGBoost ensemble methods applied to the learned embeddings further improved Km prediction (R2 = 0.61) while maintaining robust Kcat performance.

Protein language models (PLMs) have transformed sequence-based protein analysis, yet most applications rely only on final-layer embeddings, which may overlook biologically meaningful information encoded in earlier layers. We systematically evaluate all 33 layers of ESM-2 for kinase functional prediction using both unsupervised clustering and supervised classification. We show that mid-to-late transformer layers (layers 20-33) outperform the final layer by 32 percent in unsupervised Adjusted Rand Index and improve homology-aware supervised accuracy to 75.7 percent. Domain-level extraction, calibrated probability estimates, and a reproducible benchmarking pipeline further strengthen reliability. Our results demonstrate that transformer depth contains functionally distinct biological signals and that principled layer selection significantly improves kinase function prediction.

Document chunking is a crucial component of Retrieval-Augmented Generation (RAG), as it directly affects the retrieval of relevant and precise context. Conventional fixed-length and recursive splitters often produce arbitrary, incoherent segments that fail to preserve semantic structure. Although semantic chunking has gained traction, its influence on generation quality remains underexplored. This paper introduces two efficient semantic chunking methods, Projected Similarity Chunking (PSC) and Metric Fusion Chunking (MFC), trained on PubMed data using three different embedding models. We further present an evaluation framework that measures the effect of chunking on both retrieval and generation by augmenting PubMedQA with full-text PubMed Central articles. Our results show substantial retrieval improvements ( 24x with PSC) in MRR and higher Hits@k on PubMedQA. We provide a comprehensive analysis, including statistical significance and response-time comparisons with common chunking libraries. Despite being trained on a single domain, PSC and MFC also generalize well, achieving strong out-of-domain generation performance across multiple datasets. Overall, our findings confirm that our semantic chunkers, especially PSC, consistently deliver superior performance.

Spatiotemporal forecasting often relies on computationally intensive models to capture complex dynamics. Knowledge distillation (KD) has emerged as a key technique for creating lightweight student models, with recent advances like frequency-aware KD successfully preserving spectral properties (i.e., high-frequency details and low-frequency trends). However, these methods are fundamentally constrained by operating on pixel-level signals, leaving them blind to the rich semantic and causal context behind the visual patterns. To overcome this limitation, we introduce S^2-KD, a novel framework that unifies Semantic priors with Spectral representations for distillation. Our approach begins by training a privileged, multimodal teacher model. This teacher leverages textual narratives from a Large Multimodal Model (LMM) to reason about the underlying causes of events, while its architecture simultaneously decouples spectral components in its latent space. The core of our framework is a new distillation objective that transfers this unified semantic-spectral knowledge into a lightweight, vision-only student. Consequently, the student learns to make predictions that are not only spectrally accurate but also semantically coherent, without requiring any textual input or architectural overhead at inference. Extensive experiments on benchmarks like WeatherBench and TaxiBJ+ show that S^2-KD significantly boosts the performance of simple student models, enabling them to outperform state-of-the-art methods, particularly in long-horizon and complex non-stationary scenarios.

We study timestamped question answering over educational lecture videos under a single-GPU latency/memory budget. Given a natural-language query, the system retrieves relevant timestamped segments and synthesizes a grounded answer. We present CourseTimeQA (52.3 h, 902 queries across six courses) and a lightweight, latency-constrained cross-modal retriever (CrossFusion-RAG) that combines frozen encoders, a learned 512->768 vision projection, shallow query-agnostic cross-attention over ASR and frames with a temporal-consistency regularizer, and a small cross-attentive reranker. On CourseTimeQA, CrossFusion-RAG improves nDCG@10 by 0.10 and MRR by 0.08 over a strong BLIP-2 retriever while achieving approximately 1.55 s median end-to-end latency on a single A100. Closest comparators (zero-shot CLIP multi-frame pooling; CLIP + cross-encoder reranker + MMR; learned late-fusion gating; text-only hybrid with cross-encoder reranking and its MMR variant; caption-augmented text retrieval; non-learned temporal smoothing) are evaluated under matched hardware and indexing. We report robustness across ASR noise (WER quartiles), diagnostics for temporal localization, and full training/tuning details to support reproducible comparison.

We introduce MedCondDiff, a diffusion-based framework for multi-organ medical image segmentation that is efficient and anatomically grounded. The model conditions the denoising process on semantic priors extracted by a Pyramid Vision Transformer (PVT) backbone, yielding a semantically guided and lightweight diffusion architecture. This design improves robustness while reducing both inference time and VRAM usage compared to conventional diffusion models. Experiments on multi-organ, multi-modality datasets demonstrate that MedCondDiff delivers competitive performance across anatomical regions and imaging modalities, underscoring the potential of semantically guided diffusion models as an effective class of architectures for medical imaging tasks.

Large language models (LLMs) are increasingly deployed as conversational tutors in STEM education, yet most systems still rely on a single LLM with a static retrieval-augmented generation (RAG) pipeline over course materials. This design struggles in complex domains such as digital signal processing (DSP), where tutors must maintain coherent long-term student models, manage heterogeneous knowledge bases, and adapt teaching strategies over extended interactions. We argue that retrieval, memory, and control should be treated as a coupled cognitive evolution process. We instantiate this view in CogEvo-Edu, a hierarchical educational multi-agent system comprising a Cognitive Perception Layer (CPL), a Knowledge Evolution Layer (KEL), and a Meta-Control Layer (MCL). CPL maintains dual memories and performs confidence-weighted consolidation to build structured, self-correcting student profiles under limited context. KEL assigns each knowledge chunk a spatiotemporal value that drives activation, semantic compression, and forgetting. MCL formulates tutoring as hierarchical sequential decision making, orchestrating specialized agents and jointly adapting CPL/KEL hyperparameters via a dual inner--outer loop. To evaluate CogEvo-Edu, we construct DSP-EduBench, a vertical benchmark for DSP tutoring with heterogeneous resources, simulated student profiles, and long-horizon interaction scripts. Using a three-model LLM-as-a-Judge ensemble, CogEvo-Edu raises the overall score from 5.32 to 9.23 and improves all six indicators over static RAG, simple memory, and a single-agent variant, demonstrating the value of jointly evolving student profiles, knowledge bases, and teaching policies.

Temporal reasoning over evolving semi-structured tables poses a challenge to current QA systems. We propose a SQL-based approach that involves (1) generating a 3NF schema from Wikipedia infoboxes, (2) generating SQL queries, and (3) query execution. Our central finding challenges model scaling assumptions: the quality of schema design has a greater impact on QA precision than model capacity. We establish three evidence-based principles: normalization that preserves context, semantic naming that reduces ambiguity, and consistent temporal anchoring. Our best configuration (Gemini 2.5 Flash schema + Gemini-2.0-Flash queries) achieves 80.39 EM, a 16.8\% improvement over the baseline (68.89 EM).

Bug reports are often unstructured and verbose, making it challenging for developers to efficiently comprehend software issues. Existing summarization approaches typically rely on surface-level textual cues, resulting in incomplete or redundant summaries, and they frequently ignore associated code snippets, which are essential for accurate defect diagnosis. To address these limitations, we propose a progressive code-integration framework for LLM-based abstractive bug report summarization. Our approach incrementally incorporates long code snippets alongside textual content, overcoming standard LLM context window constraints and producing semantically rich summaries. Evaluated on four benchmark datasets using eight LLMs, our pipeline outperforms extractive baselines by 7.5%-58.2% and achieves performance comparable to state-of-the-art abstractive methods, highlighting the benefits of jointly leveraging textual and code information for enhanced bug comprehension.