对RAS和RAF蛋白的行为与细胞膜中局部脂质环境之间关系之间的关系的了解对了解癌症形成的基础机制至关重要。在这项工作中，我们采用深度学习（DL）来学习这种关系，通过预测基于脂质膜的RAS和RAS-RAF蛋白复合物的蛋白质定位状态，该状态基于蛋白质结构域周围的脂质密度（CG），相对于脂质膜。分子动力学（MD）模拟。我们的DL模型可以预测六个蛋白质状态，总体准确性超过80％。这项工作的发现为蛋白质如何调节脂质环境提供了新的见解，这反过来又可以帮助设计新型疗法以调节与癌症发展相关的机制中的这种相互作用。

捕获复杂的生物学现象通常需要多尺度建模，在使用有限的昂贵和高保真模型的有限组件开发粗糙和廉价的模型的情况下。在这里，我们在癌症生物学的背景下考虑了这样的多尺度框架，并解决了评估使用分子动力学模型的一维统计数据开发的连续模型的描述能力的挑战。使用深度学习，我们开发了一个高度预测性的分类模型，该模型可以从连续模型中识别复杂和新兴行为。两次模拟证明了超过99.9％的精度，我们的方法证实了蛋白质特异性的“脂质指纹”的存在，即脂质的空间重排以响应感兴趣的蛋白质。通过此演示，我们的模型还提供了对连续模型的外部验证，肯定了这种多尺度建模的价值，并可以通过进一步分析这些指纹来促进新的见解。

Landing an unmanned aerial vehicle unmanned aerial vehicle (UAV) on top of an unmanned surface vehicle (USV) in harsh open waters is a challenging problem, owing to forces that can damage the UAV due to a severe roll and/or pitch angle of the USV during touchdown. To tackle this, we propose a novel model predictive control (MPC) approach enabling a UAV to land autonomously on a USV in these harsh conditions. The MPC employs a novel objective function and an online decomposition of the oscillatory motion of the vessel to predict, attempt, and accomplish the landing during near-zero tilt of the landing platform. The nonlinear prediction of the motion of the vessel is performed using visual data from an onboard camera. Therefore, the system does not require any communication with the USV or a control station. The proposed method was analyzed in numerous robotics simulations in harsh and extreme conditions and further validated in various real-world scenarios.

Real-world datasets exhibit imbalances of varying types and degrees. Several techniques based on re-weighting and margin adjustment of loss are often used to enhance the performance of neural networks, particularly on minority classes. In this work, we analyze the class-imbalanced learning problem by examining the loss landscape of neural networks trained with re-weighting and margin-based techniques. Specifically, we examine the spectral density of Hessian of class-wise loss, through which we observe that the network weights converge to a saddle point in the loss landscapes of minority classes. Following this observation, we also find that optimization methods designed to escape from saddle points can be effectively used to improve generalization on minority classes. We further theoretically and empirically demonstrate that Sharpness-Aware Minimization (SAM), a recent technique that encourages convergence to a flat minima, can be effectively used to escape saddle points for minority classes. Using SAM results in a 6.2\% increase in accuracy on the minority classes over the state-of-the-art Vector Scaling Loss, leading to an overall average increase of 4\% across imbalanced datasets. The code is available at: https://github.com/val-iisc/Saddle-LongTail.

Parkinson's disease is marked by altered and increased firing characteristics of pathological oscillations in the brain. In other words, it causes abnormal synchronous oscillations and suppression during neurological processing. In order to examine and regulate the synchronization and pathological oscillations in motor circuits, deep brain stimulators (DBS) are used. Although machine learning methods have been applied for the investigation of suppression, these models require large amounts of training data and computational power, both of which pose challenges to resource-constrained DBS. This research proposes a novel reinforcement learning (RL) framework for suppressing the synchronization in neuronal activity during episodes of neurological disorders with less power consumption. The proposed RL algorithm comprises an ensemble of a temporal representation of stimuli and a twin-delayed deep deterministic (TD3) policy gradient algorithm. We quantify the stability of the proposed framework to noise and reduced synchrony using RL for three pathological signaling regimes: regular, chaotic, and bursting, and further eliminate the undesirable oscillations. Furthermore, metrics such as evaluation rewards, energy supplied to the ensemble, and the mean point of convergence were used and compared to other RL algorithms, specifically the Advantage actor critic (A2C), the Actor critic with Kronecker-featured trust region (ACKTR), and the Proximal policy optimization (PPO).

Problem statement: Standardisation of AI fairness rules and benchmarks is challenging because AI fairness and other ethical requirements depend on multiple factors such as context, use case, type of the AI system, and so on. In this paper, we elaborate that the AI system is prone to biases at every stage of its lifecycle, from inception to its usage, and that all stages require due attention for mitigating AI bias. We need a standardised approach to handle AI fairness at every stage. Gap analysis: While AI fairness is a hot research topic, a holistic strategy for AI fairness is generally missing. Most researchers focus only on a few facets of AI model-building. Peer review shows excessive focus on biases in the datasets, fairness metrics, and algorithmic bias. In the process, other aspects affecting AI fairness get ignored. The solution proposed: We propose a comprehensive approach in the form of a novel seven-layer model, inspired by the Open System Interconnection (OSI) model, to standardise AI fairness handling. Despite the differences in the various aspects, most AI systems have similar model-building stages. The proposed model splits the AI system lifecycle into seven abstraction layers, each corresponding to a well-defined AI model-building or usage stage. We also provide checklists for each layer and deliberate on potential sources of bias in each layer and their mitigation methodologies. This work will facilitate layer-wise standardisation of AI fairness rules and benchmarking parameters.

We introduce a language generation task grounded in a popular video game environment. KNUDGE (KNowledge Constrained User-NPC Dialogue GEneration) involves generating dialogue trees conditioned on an ontology captured in natural language passages providing quest and entity specifications. KNUDGE is constructed from side quest dialogues drawn directly from game data of Obsidian Entertainment's The Outer Worlds, leading to real-world complexities in generation: (1) dialogues are branching trees as opposed to linear chains of utterances; (2) utterances must remain faithful to the game lore--character personas, backstories, and entity relationships; and (3) a dialogue must accurately reveal new quest-related details to the human player. We report results for supervised and in-context learning techniques, finding there is significant room for future work on creating realistic game-quality dialogues.

Recent work has shown that large language models are capable of generating natural language reasoning steps or Chains-of-Thoughts (CoT) to answer a multi-step question when prompted to do so. This is insufficient, however, when the necessary knowledge is not available or up-to-date within a model's parameters. A straightforward approach to address this is to retrieve text from an external knowledge source using the question as a query and prepend it as context to the model's input. This, however, is also insufficient for multi-step QA where \textit{what to retrieve} depends on \textit{what has already been derived}. To address this issue we propose IRCoT, a new approach that interleaves retrieval with CoT for multi-step QA, guiding the retrieval with CoT and in turn using retrieved results to improve CoT. Our experiments with GPT3 show substantial improvements in retrieval (up to 22 points) and downstream QA (up to 16 points) over the baselines on four datasets: HotpotQA, 2WikiMultihopQA, MuSiQue, and IIRC. Notably, our method also works well for much smaller models such as T5-Flan-large (0.7B) without any additional training.

Code generation models have achieved impressive performance. However, they tend to be brittle as slight edits to a prompt could lead to very different generations; these robustness properties, critical for user experience when deployed in real-life applications, are not well understood. Most existing works on robustness in text or code tasks have focused on classification, while robustness in generation tasks is an uncharted area and to date there is no comprehensive benchmark for robustness in code generation. In this paper, we propose ReCode, a comprehensive robustness evaluation benchmark for code generation models. We customize over 30 transformations specifically for code on docstrings, function and variable names, code syntax, and code format. They are carefully designed to be natural in real-life coding practice, preserve the original semantic meaning, and thus provide multifaceted assessments of a model's robustness performance. With human annotators, we verified that over 90% of the perturbed prompts do not alter the semantic meaning of the original prompt. In addition, we define robustness metrics for code generation models considering the worst-case behavior under each type of perturbation, taking advantage of the fact that executing the generated code can serve as objective evaluation. We demonstrate ReCode on SOTA models using HumanEval, MBPP, as well as function completion tasks derived from them. Interesting observations include: better robustness for CodeGen over InCoder and GPT-J; models are most sensitive to syntax perturbations; more challenging robustness evaluation on MBPP over HumanEval.

While pre-trained language models (LM) for code have achieved great success in code completion, they generate code conditioned only on the contents within the file, i.e., in-file context, but ignore the rich semantics in other files within the same project, i.e., cross-file context, a critical source of information that is especially useful in modern modular software development. Such overlooking constrains code language models' capacity in code completion, leading to unexpected behaviors such as generating hallucinated class member functions or function calls with unexpected arguments. In this work, we develop a cross-file context finder tool, CCFINDER, that effectively locates and retrieves the most relevant cross-file context. We propose CoCoMIC, a framework that incorporates cross-file context to learn the in-file and cross-file context jointly on top of pretrained code LMs. CoCoMIC successfully improves the existing code LM with a 19.30% relative increase in exact match and a 15.41% relative increase in identifier matching for code completion when the cross-file context is provided.