A high-resolution anatomical atlas of the transcriptome in the mouse embryo.

Ascertaining when and where genes are expressed is of crucial importance to understanding or predicting the physiological role of genes and proteins and how they interact to form the complex networks that underlie organ development and function. It is, therefore, crucial to determine on a genome-wide level, the spatio-temporal gene expression profiles at cellular resolution. This information is provided by colorimetric RNA in situ hybridization that can elucidate expression of genes in their native context and does so at cellular resolution. We generated what is to our knowledge the first genome-wide transcriptome atlas by RNA in situ hybridization of an entire mammalian organism, the developing mouse at embryonic day 14.5. This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org), consists of a searchable database of annotated images that can be interactively viewed. We generated anatomy-based expression profiles for over 18,000 coding genes and over 400 microRNAs. We identified 1,002 tissue-specific genes that are a source of novel tissue-specific markers for 37 different anatomical structures. The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organization for the hypothalamus, and insight on the Wnt network involved in renal epithelial differentiation during kidney development. The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease.

The political preferences of LLMs.

I report here a comprehensive analysis about the political preferences embedded in Large Language Models (LLMs). Namely, I administer 11 political orientation tests, designed to identify the political preferences of the test taker, to 24 state-of-the-art conversational LLMs, both closed and open source. When probed with questions/statements with political connotations, most conversational LLMs tend to generate responses that are diagnosed by most political test instruments as manifesting preferences for left-of-center viewpoints. This does not appear to be the case for five additional base (i.e. foundation) models upon which LLMs optimized for conversation with humans are built. However, the weak performance of the base models at coherently answering the tests' questions makes this subset of results inconclusive. Finally, I demonstrate that LLMs can be steered towards specific locations in the political spectrum through Supervised Fine-Tuning (SFT) with only modest amounts of politically aligned data, suggesting SFT's potential to embed political orientation in LLMs. With LLMs beginning to partially displace traditional information sources like search engines and Wikipedia, the societal implications of political biases embedded in LLMs are substantial.

Longitudinal analysis of sentiment and emotion in news media headlines using automated labelling with Transformer language models.

This work describes a chronological (2000-2019) analysis of sentiment and emotion in 23 million headlines from 47 news media outlets popular in the United States. We use Transformer language models fine-tuned for detection of sentiment (positive, negative) and Ekman's six basic emotions (anger, disgust, fear, joy, sadness, surprise) plus neutral to automatically label the headlines. Results show an increase of sentiment negativity in headlines across written news media since the year 2000. Headlines from right-leaning news media have been, on average, consistently more negative than headlines from left-leaning outlets over the entire studied time period. The chronological analysis of headlines emotionality shows a growing proportion of headlines denoting anger, fear, disgust and sadness and a decrease in the prevalence of emotionally neutral headlines across the studied outlets over the 2000-2019 interval. The prevalence of headlines denoting anger appears to be higher, on average, in right-leaning news outlets than in left-leaning news media.

Wide range screening of algorithmic bias in word embedding models using large sentiment lexicons reveals underreported bias types.

Concerns about gender bias in word embedding models have captured substantial attention in the algorithmic bias research literature. Other bias types however have received lesser amounts of scrutiny. This work describes a large-scale analysis of sentiment associations in popular word embedding models along the lines of gender and ethnicity but also along the less frequently studied dimensions of socioeconomic status, age, physical appearance, sexual orientation, religious sentiment and political leanings. Consistent with previous scholarly literature, this work has found systemic bias against given names popular among African-Americans in most embedding models examined. Gender bias in embedding models however appears to be multifaceted and often reversed in polarity to what has been regularly reported. Interestingly, using the common operationalization of the term bias in the fairness literature, novel types of so far unreported bias types in word embedding models have also been identified. Specifically, the popular embedding models analyzed here display negative biases against middle and working-class socioeconomic status, male children, senior citizens, plain physical appearance and intellectual phenomena such as Islamic religious faith, non-religiosity and conservative political orientation. Reasons for the paradoxical underreporting of these bias types in the relevant literature are probably manifold but widely held blind spots when searching for algorithmic bias and a lack of widespread technical jargon to unambiguously describe a variety of algorithmic associations could conceivably be playing a role. The causal origins for the multiplicity of loaded associations attached to distinct demographic groups within embedding models are often unclear but the heterogeneity of said associations and their potential multifactorial roots raises doubts about the validity of grouping them all under the umbrella term bias. Richer and more fine-grained terminology as well as a more comprehensive exploration of the bias landscape could help the fairness epistemic community to characterize and neutralize algorithmic discrimination more efficiently.

Improving Video Based Heart Rate Monitoring.

Non-contact measurements of cardiac pulse can provide robust measurement of heart rate (HR) without the annoyance of attaching electrodes to the body. In this paper we explore a novel and reliable method to carry out video-based HR estimation and propose various performance improvement over existing approaches. The investigated method uses Independent Component Analysis (ICA) to detect the underlying HR signal from a mixed source signal present in the RGB channels of the image. The original ICA algorithm was implemented and several modifications were explored in order to determine which one could be optimal for accurate HR estimation. Using statistical analysis, we compared the cardiac pulse rate estimation from the different methods under comparison on the extracted videos to a commercially available oximeter. We found that some of these methods are quite effective and efficient in terms of improving accuracy and latency of the system. We have made the code of our algorithms openly available to the scientific community so that other researchers can explore how to integrate video-based HR monitoring in novel health technology applications. We conclude by noting that recent advances in video-based HR monitoring permit computers to be aware of a user's psychophysiological status in real time.

Improving the performance of an EEG-based motor imagery brain computer interface using task evoked changes in pupil diameter.

For individuals with high degrees of motor disability or locked-in syndrome, it is impractical or impossible to use mechanical switches to interact with electronic devices. Brain computer interfaces (BCIs) can use motor imagery to detect interaction intention from users but lack the accuracy of mechanical switches. Hence, there exists a strong need to improve the accuracy of EEG-based motor imagery BCIs attempting to implement an on/off switch. Here, we investigate how monitoring the pupil diameter of a person as a psycho-physiological parameter in addition to traditional EEG channels can improve the classification accuracy of a switch-like BCI. We have recently noticed in our lab (work not yet published) how motor imagery is associated with increases in pupil diameter when compared to a control rest condition. The pupil diameter parameter is easily accessible through video oculography since most gaze tracking systems report pupil diameter invariant to head position. We performed a user study with 30 participants using a typical EEG based motor imagery BCI. We used common spatial patterns to separate motor imagery, signaling movement intention, from a rest control condition. By monitoring the pupil diameter of the user and using this parameter as an additional feature, we show that the performance of the classifier trying to discriminate motor imagery from a control condition improves over the traditional approach using just EEG derived features. Given the limitations of EEG to construct highly robust and reliable BCIs, we postulate that multi-modal approaches, such as the one presented here that monitor several psycho-physiological parameters, can be a successful strategy in making BCIs more accurate and less vulnerable to constraints such as requirements for long training sessions or high signal to noise ratio of electrode channels.