Shreya Saxena

Muneeswaran I, Shreya Saxena, Siva Prasad et al.

Large Language Models (LLMs) are widely used in critical fields such as healthcare, education, and finance due to their remarkable proficiency in various language-related tasks. However, LLMs are prone to generating factually incorrect responses or "hallucinations," which can lead to a loss of credibility and trust among users. To address this issue, we propose a multi-stage framework that generates the rationale first, verifies and refines incorrect ones, and uses them as supporting references to generate the answer. The generated rationale enhances the transparency of the answer and our framework provides insights into how the model arrived at this answer, by using this rationale and the references to the context. In this paper, we demonstrate its effectiveness in improving the quality of responses to drug-related inquiries in the life sciences industry. Our framework improves traditional Retrieval Augmented Generation (RAG) by enabling OpenAI GPT-3.5-turbo to be 14-25% more faithful and 16-22% more accurate on two datasets. Furthermore, fine-tuning samples based on our framework improves the accuracy of smaller open-access LLMs by 33-42% and competes with RAG on commercial models.

Shreya Saxena, Raj Sangani, Siva Prasad et al.

Recent advances in the healthcare industry have led to an abundance of unstructured data, making it challenging to perform tasks such as efficient and accurate information retrieval at scale. Our work offers an all-in-one scalable solution for extracting and exploring complex information from large-scale research documents, which would otherwise be tedious. First, we briefly explain our knowledge synthesis process to extract helpful information from unstructured text data of research documents. Then, on top of the knowledge extracted from the documents, we perform complex information retrieval using three major components- Paragraph Retrieval, Triplet Retrieval from Knowledge Graphs, and Complex Question Answering (QA). These components combine lexical and semantic-based methods to retrieve paragraphs and triplets and perform faceted refinement for filtering these search results. The complexity of biomedical queries and documents necessitates using a QA system capable of handling queries more complex than factoid queries, which we evaluate qualitatively on the COVID-19 Open Research Dataset (CORD-19) to demonstrate the effectiveness and value-add.

Shreya Saxena, Siva Prasad, Zishan Ahmad et al.

Code translation is a crucial process in software development and migration projects, enabling interoperability between different programming languages and enhancing software adaptability and thus longevity. Traditional automated translation methods rely heavily on handcrafted transformation rules, which often lack flexibility and scalability. Meanwhile, advanced language models present promising alternatives but are often limited by proprietary, API-based implementations that raise concerns over data security and reliance. In this paper, we present Auto-Train for Code Translation (ACT), an innovative framework that aims to improve code translation capabilities by enabling in-house finetuning of open-source Large Language Models (LLMs). ACT's automated pipeline significantly boosts the performance of these models, narrowing the gap between open-source accessibility and the high performance of closed-source solutions. Central to ACT is its synthetic data generation module, which builds extensive, high-quality datasets from initial code samples, incorporating unit tests to ensure functional accuracy and diversity. ACT's evaluation framework incorporates execution-level checks, offering a comprehensive assessment of translation quality. A key feature in ACT is its controller module, which manages the entire pipeline by dynamically adjusting hyperparameters, orchestrating iterative data generation, and finetuning based on real-time evaluations. This enables ACT to intelligently optimize when to continue training, generate additional targeted training data, or stop the process. Our results demonstrate that ACT consistently enhances the effectiveness of open-source models, offering businesses and developers a secure and reliable alternative. Additionally, applying our data generation pipeline to industry-scale migration projects has led to a notable increase in developer acceleration.

Josue Ortega Caro, Yongxu Zhang, Hannah M Batchelor et al.

Many biological systems evolve through continuous local dynamics while switching between latent regimes defined by learning, stimulus context, internal state, or developmental stage. These processes are often observed only as unpaired longitudinal snapshots: the same cells, neurons, or animals are not tracked as matched trajectories, even though population states are sampled across successive stages. This creates two coupled challenges. First, trajectories must respect curved low-dimensional manifolds embedded in high-dimensional biological measurements. Second, the model must identify when the transport mechanism itself changes. We introduce FLUX (FLow matching for Unpaired longitudinal data with miXture-of-experts), a geometry-aware longitudinal flow-matching framework for joint transport modeling and unsupervised regime discovery. FLUX learns a data-dependent metric from pooled labeled and unlabeled observations, uses that metric to construct geometry-aware conditional paths between adjacent marginals, and decomposes the resulting velocity field into sparse expert vector fields selected by a Straight-Through Gumbel-Softmax router. Across manifold controls, a regime-switching Lorenz system, widefield cortical calcium imaging during associative learning, and embryoid body single-cell differentiation, FLUX reconstructs longitudinal transport while recovering interpretable regime structure. Ablations show that mixture-of-experts routing alone is insufficient: FLUX without geometric learning can fit local transport but fails or weakens regime discovery when regimes are encoded in local dynamics. These results suggest that geometry-aware velocity decomposition provides a general strategy for discovering latent biological state transitions from unpaired longitudinal snapshots.

Il Memming Park, Ayesha Vermani, Gonzalo G. de Polavieja et al.

Large-scale neuroscience is generating rich datasets across animals, brain areas and behavioral contexts, yet our modeling efforts remains fragmented across isolated experiments. We argue that understanding behavior requires integrative neurocybernetic models: understandable dynamical models that capture the closed-loop coupling of brain, body and environment, treat the brain as a controller pursuing latent objectives, represent structured variation across scales, and scale to heterogeneous datasets. Such models shift the goal from predicting neural recordings in isolation to inferring the organizing principles that govern neural and behavioral dynamics. We outline a practical route toward this goal by combining nonlinear state-space models and meta-dynamical extensions with scalable inference, knowledge distillation, mixed open- and closed-loop training, and connectomics-informed architectures. By pooling complementary constraints from recordings, behavior, perturbations and anatomy, integrative neurocybernetic models can provide statistical amplification, few-shot generalization, and mechanistic insight into shared dynamical structure, individual variation, and the control objectives that govern behavior. This agenda offers a model-centric path from fragmented data to a mechanistic science of how brains produce behavior.

Lulu Gong, Shreya Saxena

Mixtures of linear dynamical systems (MoLDS) provide a path to model time-series data that exhibit diverse temporal dynamics across trajectories. However, its application remains challenging in complex and noisy settings, limiting its effectiveness for neural data analysis. Tensor-based moment methods can provide global identifiability guarantees for MoLDS, but their performance degrades under noise and complexity. Commonly used expectation-maximization (EM) methods offer flexibility in fitting latent models but are highly sensitive to initialization and prone to poor local minima. Here, we propose a tensor-based method that provides identifiability guarantees for learning MoLDS, which is followed by EM updates to combine the strengths of both approaches. The novelty in our approach lies in the construction of moment tensors using the input-output data to recover globally consistent estimates of mixture weights and system parameters. These estimates can then be refined through a Kalman EM algorithm, with closed-form updates for all LDS parameters. We validate our framework on synthetic benchmarks and real-world datasets. On synthetic data, the proposed Tensor-EM method achieves more reliable recovery and improved robustness compared to either pure tensor or randomly initialized EM methods. We then analyze neural recordings from the primate somatosensory cortex while a non-human primate performs reaches in different directions. Our method successfully models and clusters different conditions as separate subsystems, consistent with supervised single-LDS fits for each condition. Finally, we apply this approach to another neural dataset where monkeys perform a sequential reaching task. These results demonstrate that MoLDS provides an effective framework for modeling complex neural data, and that Tensor-EM is a reliable approach to MoLDS learning for these applications.

Muhammad Noman Almani, John Lazzari, Jeff Walker et al.

We review how sensorimotor control is dictated by interacting neural populations, optimal feedback mechanisms, and the biomechanics of bodies. First, we outline the distributed anatomical loops that shuttle sensorimotor signals between cortex, subcortical regions, and spinal cord. We then summarize evidence that neural population activity occupies low-dimensional, dynamically evolving manifolds during planning and execution of movements. Next, we summarize literature explaining motor behavior through the lens of optimal control theory, which clarifies the role of internal models and feedback during motor control. Finally, recent studies on embodied sensorimotor control address gaps within each framework by aiming to elucidate neural population activity through the explicit control of musculoskeletal dynamics. We close by discussing open problems and opportunities: multi-tasking and cognitively rich behavior, multi-regional circuit models, and the level of anatomical detail needed in body and network models. Together, this review and recent advances point towards reaching an integrative account of the neural control of movement.

Daniel Hernandez, Antonio Khalil Moretti, Ziqiang Wei et al.

Latent variable models have been widely applied for the analysis of time series resulting from experimental neuroscience techniques. In these datasets, observations are relatively smooth and possibly nonlinear. We present Variational Inference for Nonlinear Dynamics (VIND), a variational inference framework that is able to uncover nonlinear, smooth latent dynamics from sequential data. The framework is a direct extension of PfLDS; including a structured approximate posterior describing spatially-dependent linear dynamics, as well as an algorithm that relies on the fixed-point iteration method to achieve convergence. We apply VIND to electrophysiology, single-cell voltage and widefield imaging datasets with state-of-the-art results in reconstruction error. In single-cell voltage data, VIND finds a 5D latent space, with variables akin to those of Hodgkin-Huxley-like models. VIND's learned dynamics are further quantified by predicting future neural activity. VIND excels in this task, in some cases substantially outperforming current methods.