Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Temporal Dissociation of Neocortical and Hippocampal Contributions to Mental Time Travel Using Intracranial Recordings in Humans

In mental time travel (MTT) one is “traveling” back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100–300 ms, and hippocampal electrodes, activated at ~400–600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self

Data Driven Equation Discovery Reveals Non-linear Reinforcement Learning in Humans

Computational models of reinforcement learning (RL), have significantly contributed to our understanding of human behavior and decision-making. Traditional RL models, however, often adopt a linear approach to updating reward expectations, potentially oversimplifying the nuanced relationship between human behavior and rewards. To address these challenges and explore new models of reinforcement learning, we utilized a novel method of model discovery using equation discovery algorithms. This method, currently used mainly in physics and biology, attempts to capture data by proposing a differential equation from an array of suggested linear and nonlinear functions. Using this novel method, we were able to identify a new model of RL which we termed, the Quadratic Q-Weighted model. The model suggests that reward prediction errors obey nonlinear dynamics and exhibit negativity biases, resulting in an underweighting of reward when expectations are low, and an overweighting of the absence of reward when expectations are high. We tested the generalizability of our model by comparing it to classical models used in 9 published studies. Our model surpassed traditional models in predictive accuracy across eight out of these nine published datasets, demonstrating not only its generalizability but also its potential to offer new insights into the complexities of human learning. This work showcases the integration of a novel behavioral task with advanced computational methodologies as a potent strategy for uncovering the intricate patterns of human cognition, marking a significant step forward in the development of computational models that are both interpretable and broadly applicable

Dynamic computational phenotyping of human cognition

Computational phenotyping has emerged as a powerful tool for characterizing individual variability across a variety of cognitive domains. An individual's computational phenotype is defined as a set of mechanistically interpretable parameters obtained from fitting computational models to behavioral data. However, the interpretation of these parameters hinges critically on their psychometric properties, which are rarely studied. In order to identify the sources governing the temporal variability of the computational phenotype, we carried out a 12-week longitudinal study using a battery of seven tasks that measure aspects of human learning, memory, perception, and decision making. To examine the influence of state-like effects, each week participants provided reports tracking their mood, habits and daily activities. We developed a dynamic computational phenotyping framework, which allowed us to tease apart the time-varying effects of practice and internal states such as affective valence and arousal. Our results show that many phenotype dimensions covary with practice and affective factors, indicating that what appears to be unreliability may reflect previously unmeasured structure. These results support a fundamentally dynamic understanding of cognitive variability within an individual

Temporal Dissociation of Neocortical and Hippocampal Contributions to Mental Time Travel Using Intracranial Recordings in Humans

In mental time travel (MTT) one is "traveling" back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100-300 ms, and hippocampal electrodes, activated at ~400-600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self

Image8.TIF

<p>In mental time travel (MTT) one is “traveling” back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100–300 ms, and hippocampal electrodes, activated at ~400–600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self.</p

Table1.DOCX

<p>In mental time travel (MTT) one is “traveling” back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100–300 ms, and hippocampal electrodes, activated at ~400–600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self.</p

Image2.TIF

<p>In mental time travel (MTT) one is “traveling” back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100–300 ms, and hippocampal electrodes, activated at ~400–600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self.</p

Table2.DOCX

<p>In mental time travel (MTT) one is “traveling” back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100–300 ms, and hippocampal electrodes, activated at ~400–600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self.</p

Image4.TIF

<p>In mental time travel (MTT) one is “traveling” back-and-forth in time, remembering, and imagining events. Despite intensive research regarding memory processes in the hippocampus, it was only recently shown that the hippocampus plays an essential role in encoding the temporal order of events remembered, and therefore plays an important role in MTT. Does it also encode the temporal relations of these events to the remembering self? We asked patients undergoing pre-surgical evaluation with depth electrodes penetrating the temporal lobes bilaterally toward the hippocampus to project themselves in time to a past, future, or present time-point, and then make judgments regarding various events. Classification analysis of intracranial evoked potentials revealed clear temporal dissociation in the left hemisphere between lateral-temporal electrodes, activated at ~100–300 ms, and hippocampal electrodes, activated at ~400–600 ms. This dissociation may suggest a division of labor in the temporal lobe during self-projection in time, hinting toward the different roles of the lateral-temporal cortex and the hippocampus in MTT and the temporal organization of the related events with respect to the experiencing self.</p