Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification, often fail to capture complex concepts not explicitly stated in the text. To overcome this limitation, we introduce MA-COIR, a framework that reformulates concept recognition as an indexing-recognition task. By assigning semantic search indexes (ssIDs) to concepts, MA-COIR resolves ambiguities in ontology entries and enhances recognition efficiency. Using a pretrained BART-based model fine-tuned on small datasets, our approach reduces computational requirements to facilitate adoption by domain experts. Furthermore, we incorporate large language models (LLMs)-generated queries and synthetic data to improve recognition in low-resource settings. Experimental results on three scenarios (CDR, HPO, and HOIP) highlight the effectiveness of MA-COIR in recognizing both explicit and implicit concepts without the need for mention-level annotations during inference, advancing ontology-driven concept recognition in biomedical domain applications. Our code and constructed data are available at https://github.com/sl-633/macoir-master.

Estimating causal networks from biological data is a critical step in systems biology. When evaluating the inferred network, assessing the networks based on their intervention effects is particularly important for downstream probabilistic reasoning and the identification of potential drug targets. In the context of gene regulatory network inference, biological databases are often used as reference sources. These databases typically describe relationships in a qualitative rather than quantitative manner. However, few evaluation metrics have been developed that take this qualitative nature into account. To address this, we developed a metric, the sign-augmented Structural Intervention Distance (sSID), and a weighted sSID that incorporates the net effects of the intervention. Through simulations and analyses of real transcriptomic datasets, we found that our proposed metrics could identify a different algorithm as optimal compared to conventional metrics, and the network selected by sSID had a superior performance in the classification task of clinical covariates using transcriptomic data. This suggests that sSID can distinguish networks that are structurally correct but functionally incorrect, highlighting its potential as a more biologically meaningful and practical evaluation metric.

This paper introduces a novel mobile sensing application - life journaling - designed to generate semantic descriptions of users' daily lives. We present AutoLife, an automatic life journaling system based on commercial smartphones. AutoLife only inputs low-cost sensor data (without photos or audio) from smartphones and can automatically generate comprehensive life journals for users. To achieve this, we first derive time, motion, and location contexts from multimodal sensor data, and harness the zero-shot capabilities of Large Language Models (LLMs), enriched with commonsense knowledge about human lives, to interpret diverse contexts and generate life journals. To manage the task complexity and long sensing duration, a multilayer framework is proposed, which decomposes tasks and seamlessly integrates LLMs with other techniques for life journaling. This study establishes a real-life dataset as a benchmark and extensive experiment results demonstrate that AutoLife produces accurate and reliable life journals.

Latent linear dynamical systems with generalised-linear observation models arise in a variety of applications, for instance when modelling the spiking activity of populations of neurons. Here, we show how spectral learning methods (usually called subspace identification in this context) for linear systems with linear-Gaussian observations can be extended to estimate the parameters of a generalised-linear dynamical system model despite a non-linear and non-Gaussian observation process. We use this approach to obtain estimates of parameters for a dynamical model of neural population data, where the observed spike-counts are Poisson-distributed with log-rates determined by the latent dynamical process, possibly driven by external inputs. We show that the extended subspace identification algorithm is consistent and accurately recovers the correct parameters on large simulated data sets with a single calculation, avoiding the costly iterative computation of approximate expectation-maximisation (EM). Even on smaller data sets, it provides an effective initialisation for EM, avoiding local optima and speeding convergence. These benefits are shown to extend to real neural data.

We propose a new approach to value function approximation which combines linear temporal difference reinforcement learning with subspace identification. In practical applications, reinforcement learning (RL) is complicated by the fact that state is either high-dimensional or partially observable. Therefore, RL methods are designed to work with features of state rather than state itself, and the success or failure of learning is often determined by the suitability of the selected features. By comparison, subspace identification (SSID) methods are designed to select a feature set which preserves as much information as possible about state. In this paper we connect the two approaches, looking at the problem of reinforcement learning with a large set of features, each of which may only be marginally useful for value function approximation.

Unsupervised domain adaptation (UDA) has attracted considerable attention, which transfers knowledge from a label-rich source domain to a related but unlabeled target domain. Reducing inter-domain differences has always been a crucial factor to improve performance in UDA, especially for tasks where there is a large gap between source and target domains. To this end, we propose a novel style-aware feature fusion method (SAFF) to bridge the large domain gap and transfer knowledge while alleviating the loss of class-discriminative information. Inspired by the human transitive inference and learning ability, a novel style-aware self-intermediate domain (SSID) is investigated to link two seemingly unrelated concepts through a series of intermediate auxiliary synthesized concepts. Specifically, we propose a novel learning strategy of SSID, which selects samples from both source and target domains as anchors, and then randomly fuses the object and style features of these anchors to generate labeled and style-rich intermediate auxiliary features for knowledge transfer. Moreover, we design an external memory bank to store and update specified labeled features to obtain stable class features and class-wise style features. Based on the proposed memory bank, the intra- and inter-domain loss functions are designed to improve the class recognition ability and feature compatibility, respectively. Meanwhile, we simulate the rich latent feature space of SSID by infinite sampling and the convergence of the loss function by mathematical theory. Finally, we conduct comprehensive experiments on commonly used domain adaptive benchmarks to evaluate the proposed SAFF, and the experimental results show that the proposed SAFF can be easily combined with different backbone networks and obtain better performance as a plug-in-plug-out module.

We propose a new approach to value function approximation which combines linear temporal difference reinforcement learning with subspace identification. In practical applications, reinforcement learning (RL) is complicated by the fact that state is either high-dimensional or partially observable. Therefore, RL methods are designed to work with features of state rather than state itself, and the success or failure of learning is often determined by the suitability of the selected features. By comparison, subspace identification (SSID) methods are designed to select a feature set which preserves as much information as possible about state. In this paper we connect the two approaches, looking at the problem of reinforcement learning with a large set of features, each of which may only be marginally useful for value function approximation.

Low dimensional representations of words allow accurate NLP models to be trained on limited annotated data. While most representations ignore words' local context, a natural way to induce context-dependent representations is to perform inference in a probabilistic latent-variable sequence model. Given the recent success of continuous vector space word representations, we provide such an inference procedure for continuous states, where words' representations are given by the posterior mean of a linear dynamical system. Here, efficient inference can be performed using Kalman filtering. Our learning algorithm is extremely scalable, operating on simple cooccurrence counts for both parameter initialization using the method of moments and subsequent iterations of EM. In our experiments, we employ our inferred word embeddings as features in standard tagging tasks, obtaining significant accuracy improvements. Finally, the Kalman filter updates can be seen as a linear recurrent neural network. We demonstrate that using the parameters of our model to initialize a non-linear recurrent neural network language model reduces its training time by a day and yields lower perplexity.

Latent linear dynamical systems with generalised-linear observation models arise in a variety of applications, for example when modelling the spiking activity of populations of neurons. Here, we show how spectral learning methods for linear systems with Gaussian observations (usually called subspace identification in this context) can be extended to estimate the parameters of dynamical system models observed through non-Gaussian noise models. We use this approach to obtain estimates of parameters for a dynamical model of neural population data, where the observed spike-counts are Poisson-distributed with log-rates determined by the latent dynamical process, possibly driven by external inputs. We show that the extended system identification algorithm is consistent and accurately recovers the correct parameters on large simulated data sets with much smaller computational cost than approximate expectation-maximisation (EM) due to the non-iterative nature of subspace identification. Even on smaller data sets, it provides an effective initialization for EM, leading to more robust performance and faster convergence. These benefits are shown to extend to real neural data.